'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘knitr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following significant warnings:
  parse-spec.c:131:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  parse-spec.c:132:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/tibblify.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘badger’ ‘ggplot2’ ‘lubridate’ ‘scales’ ‘xgboost’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘fpc’ in Rd xrefs
Note: found 4546 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘tidyselect’ in Rd xrefs
Undeclared packages ‘fastDummies’, ‘widyr’, ‘pacman’, ‘sjmisc’ in Rd xrefs
Undeclared packages ‘tidyfst’, ‘tidyr’, ‘fastDummies’ in Rd xrefs
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'gate_interactive_chr_int.Rd':
  ‘gate_list’

Documented arguments not in \usage in Rd file 'gate_programmatic.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'gate_programmatic_chr_int.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
Note: found 182 marked UTF-8 strings
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'deprecated-se.Rd':
  ‘expand_cols’

Documented arguments not in \usage in Rd file 'tidyr_legacy.Rd':
  ‘nm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'vars_select.Rd':
  ‘args’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘SingleR’
Undeclared package ‘crosstalk’ in Rd xrefs
Undeclared package ‘datawizard’ in Rd xrefs
Note: found 113 marked UTF-8 strings
Note: found 34206 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   4.5Mb
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 4581 marked UTF-8 strings
Package suggested but not available for checking: ‘rrelaxiv’
installed size is 85.5Mb
  sub-directories of 1Mb or more:
    libs     2.2Mb
    tiledb  80.9Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'timeperiodsR-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'timeSeq_1.0.4-package.Rd':
  ‘timeSeq_1.0.4-package’
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 2750 marked UTF-8 strings
Undeclared package ‘pkgdown’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.4Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘sp’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    examples   1.1Mb
    include    3.7Mb
GNU make is a SystemRequirements.
Note: found 134043 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Invalid package aliases in Rd file 'tm.plugin.alceste-package.Rd':
  ‘tm.plugin.europresse-package’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
Undeclared packages ‘tm.plugin.dc’, ‘readtext’, ‘graph’, ‘tau’, ‘tokenizers’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvtnorm/libs/tmvtnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'TNRS_core.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data-tables   1.5Mb
    doc           2.0Mb
    help          1.2Mb
Note: found 160 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
Package suggested but not available for checking: ‘corpus.JSS.papers’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    R         5.6Mb
    help      1.7Mb
    include   1.8Mb
    libs     26.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
Namespace in Imports field not imported from: ‘hdi’
  All declared Imports should be used.
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
Specified C++11: please drop specification unless essential
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'createLink.Rd':
  ‘hits’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘moveVis’
Undeclared package ‘rlang’ in Rd xrefs
Unknown package ‘moveVis’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc    2.7Mb
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
Argument items with no description in Rd file 'abrams.Rd':
  ‘prior’ ‘change’
Argument items with no description in Rd file 'absoluteIncreaseALL.Rd':
  ‘storedev’ ‘\dots’
Argument items with no description in Rd file 'boundaryLineALL.Rd':
  ‘\dots’
Argument items with no description in Rd file 'growthAveragingALL.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plotFirstYears.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plotRelease.Rd':
  ‘\dots’
Argument items with no description in Rd file 'splechtnaALL.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxidata’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'seqimplic.Rd':
  ‘ylim’
Note: found 827 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in Rd file 'transport-internal.Rd':
  ‘gif.generate’ ‘plot_pgrid_wpp’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘fwelnet’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR', 'Capr'
Documented arguments not in \usage in Rd file 'clean_data.Rd':
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Undeclared package ‘dplR’ in Rd xrefs
Documented arguments not in \usage in Rd file 'correct_continuous.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'tc_correlation.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'tc_efunc.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'tc_mfunc.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'tc_response.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'truncate_input.Rd':
  ‘moving’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Package suggested but not available for checking: ‘TreeDistData’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘ISLR’ in Rd xrefs
Auto-generated content requiring editing in Rd file 'treemisc-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.2Mb
    doc       1.3Mb
    extdata  14.8Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   9.5Mb
GNU make is a SystemRequirements.
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Undeclared package ‘akima’ in Rd xrefs
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘Using_TropFishR_ELEFAN_functions.Rmd’ using rmarkdown

Quitting from lines 220-236 [unnamed-chunk-10] (Using_TropFishR_ELEFAN_functions.Rmd)
Error: processing vignette 'Using_TropFishR_ELEFAN_functions.Rmd' failed with diagnostics:
no rows to aggregate
--- failed re-building ‘Using_TropFishR_ELEFAN_functions.Rmd’

--- re-building ‘lfqData.Rmd’ using rmarkdown
--- finished re-building ‘lfqData.Rmd’

--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 147-161 [Figure 4] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
no rows to aggregate
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘Using_TropFishR_ELEFAN_functions.Rmd’ ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
Undeclared packages ‘fpc’, ‘clValid’, ‘clv’ in Rd xrefs
Documented arguments not in \usage in Rd file 'dvinecopula_objective.Rd':
  ‘udata’

Documented arguments not in \usage in Rd file 'wobjective.Rd':
  ‘vt’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Objects in \usage without \alias in Rd file 'nlar.struct.Rd':
  ‘getNUsed’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
File ‘tseriesTARMA/libs/tseriesTARMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'tsibble-vctrs.Rd':
  ‘vec_ptype2.tbl_ts’ ‘vec_cast.tbl_ts’ ‘vec_cast.yearmonth’
  ‘vec_ptype2.yearmonth’ ‘vec_cast.yearquarter’
  ‘vec_ptype2.yearquarter’ ‘vec_cast.yearweek’ ‘vec_ptype2.yearweek’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'tsoutliers-package.Rd':
  ‘tsouliers-package’
Undeclared package ‘tseries’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘gimms’ in Rd xrefs
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Invalid package aliases in Rd file 'TTAinterface-package.Rd':
  ‘TTAinterface-package’
Undeclared packages ‘ggplot2’, ‘crosstalk’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Undeclared packages ‘multcomp’, ‘agricolae’ in Rd xrefs
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Undeclared package ‘randomForest’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘rlang’ in Rd xrefs
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘twang’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 34 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc     6.6Mb
    ubinc   2.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.0Mb
    libs   5.4Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
Note: found 2 marked UTF-8 strings
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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    dummydata   1.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
Namespaces in Imports field not imported from:
  ‘foreign’ ‘psychTools’ ‘pwr’ ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'HC.Rd':
  ‘X’ ‘K’
Argument items with no description in Rd file 'KA.Rd':
  ‘X’ ‘K’ ‘distancemetric’
Argument items with no description in Rd file 'SOMs.Rd':
  ‘X’ ‘K’ ‘topo’ ‘rlen’ ‘alpha’ ‘n.hood’
Argument items with no description in Rd file 'binarise.Rd':
  ‘U’ ‘K’ ‘technique’ ‘parameter’
Argument items with no description in Rd file 'closestToSquareFactors.Rd':
  ‘n’
Argument items with no description in Rd file 'clustDist.Rd':
  ‘U1’ ‘U2’ ‘X’ ‘criterion’
Argument items with no description in Rd file 'clustVec2partMat.Rd':
  ‘C’
Argument items with no description in Rd file 'clusterDataset.Rd':
  ‘X’ ‘K’ ‘D’ ‘methods’
Argument items with no description in Rd file 'factors.Rd':
  ‘n’ ‘primeonly’
Argument items with no description in Rd file 'fixnans.Rd':
  ‘X’ ‘type’
Argument items with no description in Rd file 'fuzzystretch.Rd':
  ‘X’ ‘x0’
Argument items with no description in Rd file 'generateCoPaM.Rd':
  ‘U’ ‘relabel_technique’ ‘w’ ‘X’ ‘distCriterion’ ‘K’ ‘GDM’
Argument items with no description in Rd file 'isValidBPM.Rd':
  ‘U’
Argument items with no description in Rd file 'isempty.Rd':
  ‘X’
Argument items with no description in Rd file 'isnullorempty.Rd':
  ‘X’
Argument items with no description in Rd file 'kmeansKA.Rd':
  ‘X’ ‘K’ ‘distancemetric’ ‘iter.max’ ‘nstart’ ‘algorithm’ ‘trace’
Argument items with no description in Rd file 'mnplots.Rd':
  ‘Vmse’ ‘mseCache’ ‘subplotdim’ ‘subplotind’ ‘minimiseDistance’
Argument items with no description in Rd file 'mseclusters.Rd':
  ‘X’ ‘B’ ‘normalise’
Argument items with no description in Rd file 'normaliseMatrix.Rd':
  ‘X’ ‘type’
Argument items with no description in Rd file 'partMat2clustVec.rd':
  ‘U’ ‘skipValidity’
Argument items with no description in Rd file 'permutations.Rd':
  ‘n’
Argument items with no description in Rd file 'relabelClusts.Rd':
  ‘ref’ ‘input’ ‘technique’ ‘X’ ‘distCriterion’
Documented arguments not in \usage in Rd file 'sqrtm.Rd':
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘ungroup.Rd’
Documented arguments not in \usage in Rd file 'MortSmooth_tpower.Rd':
  ‘vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 548 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘uniswappeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: swap_statistics
> ### Title: Get statistics on the swaps data for a given address or
> ###   addresses
> ### Aliases: swap_statistics
> 
> ### ** Examples
> 
> 
> addresses <- c("0xb1b117a45aD71d408eb55475FC3A65454edCc94A",
+ "0x41D2a18E1DdACdAbFDdADB62e9AEE67c63070b76",
+ "0x0De20c4bDBE0d0EEFFd2956Be4c148CA86C6cC45")
> 
> swap_data <- swaps(addresses)
Error in `.data$Address`:
! Column `Address` not found in `.data`.
Backtrace:
     ▆
  1. ├─uniswappeR::swaps(addresses)
  2. │ └─swaps %>% select(.data$Address, everything())
  3. ├─dplyr::select(., .data$Address, everything())
  4. ├─dplyr:::select.data.frame(., .data$Address, everything())
  5. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
  6. │   └─tidyselect:::eval_select_impl(...)
  7. │     ├─tidyselect:::with_subscript_errors(...)
  8. │     │ └─rlang::try_fetch(...)
  9. │     │   └─base::withCallingHandlers(...)
 10. │     └─tidyselect:::vars_select_eval(...)
 11. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 12. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
 13. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 14. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
 15. │               └─base::eval(expr, data_mask)
 16. │                 └─base::eval(expr, data_mask)
 17. │                   ├─Address
 18. │                   └─rlang:::`$.rlang_data_pronoun`(.data, Address)
 19. │                     └─rlang:::data_pronoun_get(...)
 20. └─rlang:::abort_data_pronoun(x, call = y)
 21.   └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
Execution halted
'LazyData' is specified without a 'data' directory
Undeclared package ‘mirt’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.4Mb
    libs   2.3Mb
GNU make is a SystemRequirements.
Note: found 3347 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 7872 marked UTF-8 strings
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Undeclared package ‘httr’ in Rd xrefs
Note: found 488 marked UTF-8 strings
Package suggested but not available for checking: ‘USA.state.boundaries.data’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘pROC’ in Rd xrefs
Undeclared package ‘devtools’ in Rd xrefs
Documented arguments not in \usage in Rd file 'use_course_details.Rd':
  ‘destdir’ ‘zipfile’

Documented arguments not in \usage in Rd file 'write-this.Rd':
  ‘contents’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   6.6Mb
Note: found 1 marked UTF-8 string
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Note: found 50 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'parallel' 'xml2'
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'countDNAPatternInAlt.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'countDNAPatternInAltOneVariant.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'getAltSequence.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'getCodonInAlt.Rd':
  ‘trascriptsTable’ ‘codonPositionsColumnn’

Documented arguments not in \usage in Rd file 'getCodonInAltOneVariant.Rd':
  ‘trascriptsTable’ ‘codonPositionsColumnn’

Documented arguments not in \usage in Rd file 'getTSSKozakOneVariant.Rd':
  ‘variantsTable’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘badger’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'validate_extend.Rd':
  ‘varlist:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘factoextra’ in Rd xrefs
GNU make is a SystemRequirements.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   7.5Mb
'LazyData' is specified without a 'data' directory
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DT’ ‘maps’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘coda’ in Rd xrefs
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
S3 methods shown with full name in Rd file 'syntab.Rd':
  ‘print.syntab’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 128 marked UTF-8 strings
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/vein.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    help   3.1Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Argument items with no description in Rd file 'learnPartitionWithLLR.Rd':
  ‘type’ ‘procedure’ ‘ql’ ‘qq’ ‘BinaryLearningProcedure’
Argument items with no description in Rd file 'plotClassifRule.Rd':
  ‘object’
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'boxplot_VICI.Rd':
  ‘res_2plot’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘leaflet’ ‘mapview’
  All declared Imports should be used.
Note: found 60 marked UTF-8 strings
Note: found 468 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'draw_map_shiny.Rd':
  ‘rigth.lim’

Documented arguments not in \usage in Rd file 'map_summary.Rd':
  ‘rigth.lim’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘readr’ ‘uuid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Undeclared package ‘mi’ in Rd xrefs
Note: found 2754 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared packages ‘foreach’, ‘copula’ in Rd xrefs
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.8Mb
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
Undeclared package ‘rms’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   7.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       5.4Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
Documented arguments not in \usage in Rd file 'cpp_vol2bird_version.Rd':
  ‘path’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Note: found 4954 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'blendColor.Rd':
  ‘color’ ‘percent’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘dtw’ in Rd xrefs
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   8.6Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Undeclared package ‘readr’ in Rd xrefs
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Undeclared package ‘progress’ in Rd xrefs
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘tibble’ in Rd xrefs
Undeclared package ‘RCurl’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get.wal.mipmap.heights.Rd':
  ‘height_mm’

Documented arguments not in \usage in Rd file 'get.wal.mipmap.widths.Rd':
  ‘width_mm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   6.4Mb
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    help   3.9Mb
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'WaveDjF.Rd':
  ‘y_fft’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Auto-generated content requiring editing in Rd file 'maxithresh.Rd':
  \details: ‘~~ If necessary, more details than the description above ~~’
  \arguments: data: ‘~~Describe \code{data} here~~’
  \arguments: g: ‘~~Describe \code{g} here~~’
  \arguments: L: ‘~~Describe \code{L} here~~’
  \arguments: F: ‘~~Describe \code{F} here~~’
  \arguments: eta: ‘~~Describe \code{eta} here~~’
'LazyData' is specified without a 'data' directory
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘StratigrapheR’ in Rd xrefs
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 3133 marked UTF-8 strings
Note: found 4413 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building ‘wcde.Rmd’ using rmarkdown

Quitting from lines 54-62 [unnamed-chunk-4] (wcde.Rmd)
Error: processing vignette 'wcde.Rmd' failed with diagnostics:
ℹ In argument: `d = purrr::map(.x = u, .f = ~read_with_progress(f =
  .x))`.
Caused by error in `purrr::map()`:
ℹ In index: 1.
Caused by error in `open.connection()`:
! HTTP error 404.
--- failed re-building ‘wcde.Rmd’

SUMMARY: processing the following file failed:
  ‘wcde.Rmd’

Error: Vignette re-building failed.
Execution halted
Invalid package aliases in Rd file 'wce-package.Rd':
  ‘wce-package’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Note: found 1668 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘prepr’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
Undeclared package ‘purrr’ in Rd xrefs
Documented arguments not in \usage in Rd file 'read_img.Rd':
  ‘imgfile’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘here’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘weightedCL/libs/weightedCL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Argument items with no description in Rd file 'zdifference_ordinal.Rd':
  ‘na.rm’
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'QIC.gee.Rd':
  ‘QIC.gee’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
Note: found 4102 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'remove_empty.Rd':
  ‘quiet’

Documented arguments not in \usage in Rd file 'undoHistory.Rd':
  ‘class’ ‘btn_class’ ‘back_text’ ‘fwd_text’ ‘back_title’ ‘fwd_title’
  ‘back_icon’ ‘fwd_icon’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Package suggested but not available for checking: ‘rgdal’
Documented arguments not in \usage in Rd file 'displayDataTable.Rd':
  ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pageviews’
Package suggested but not available for checking: ‘pageviews’
Undeclared package ‘httr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘plotly’ ‘shinythemes’
  All declared Imports should be used.
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 1 marked UTF-8 string
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 3881 marked UTF-8 strings
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 933 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Note: found 3 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Undeclared package ‘lubridate’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'new_givens_path.Rd':
  ‘generate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Undeclared packages ‘wpp2010’, ‘wpp2012’ in Rd xrefs
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
Undeclared package ‘baytrends’ in Rd xrefs
Found the following significant warnings:
  dataobj.c:27:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  dataobj.c:34:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  dataobj.c:126:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  dataobj.c:633:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  dataobj.c:768:23: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  dataobj.c:774:23: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  dataobj.c:842:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  dataobj.c:868:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/wrassp.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'sample_me.Rd':
  ‘middle_name’ ‘M_rs’ ‘M_rf’ ‘M_rm’ ‘alpha’ ‘me_race’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'Cut.off.Rd':
  ‘main’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    bin   5.7Mb
Undeclared package ‘RSiena’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
Undeclared package ‘rlang’ in Rd xrefs
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    java  24.5Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rbokeh’
checkRd: (-1) read.npc.vpc.results.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) read.npc.vpc.results.Rd:19: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_
checkRd: (-1) read.npc.vpc.results.Rd:22: Escaped LaTeX specials: \_
Documented arguments not in \usage in Rd file 'xpose.create.title.Rd':
  ‘plot.text’ ‘main’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'check_problem.Rd':
  ‘xpdb’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘viridis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
Invalid package aliases in Rd file 'XRjulia-package.Rd':
  ‘XRjulia-package’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Argument items with no description in Rd file 'getCondition.Rd':
  ‘object’
Argument items with no description in Rd file 'screen.Rd':
  ‘fac’ ‘condition’ ‘position’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
'LazyData' is specified without a 'data' directory
Undeclared package ‘parsnip’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'IC.Rd':
  ‘\dots’
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Note: found 76 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'ZIBseq-package.Rd':
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~ ~~ \code{\link...’
Undeclared package ‘dplyr’ in Rd xrefs
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 47 marked UTF-8 strings
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 146804 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘rlang’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Undeclared package ‘loo’ in Rd xrefs
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 134469 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Found the following files/directories:
  ‘acceldata2.RData’
File ‘acc/libs/acc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'ADMM_EN2.Rd':
  ‘alpha’

Documented arguments not in \usage in Rd file 'ADMM_EN_SMW.Rd':
  ‘alpha’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'testRmACD.Rd':
  ‘pStar’
File ‘ACDm/libs/ACDm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'fitSnpNmfArray.Rd':
  ‘maxIter’ ‘acc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
‘configure’: /bin/bash is not portable
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppProgress’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'd1.Rd':
  ‘The’ ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 305 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'AdaptGauss-package.Rd':
  ‘MultiModal-package’
Invalid package aliases in Rd file 'aslm-package.Rd':
  ‘aslm-package’ ‘asggm-package’
Argument items with no description in Rd file 'asggm-internal.Rd':
  ‘ansL’ ‘kNodes’ ‘spP’
Specified C++11: please drop specification unless essential
Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'print.aTest.Rd':
  ‘how’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'ae_count.Rd':
  ‘patients’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/admiralonco.Rcheck/00install.out’ for details.
Note: found 12 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building ‘adce.Rmd’ using rmarkdown

Quitting from lines 135-146 [unnamed-chunk-8] (adce.Rmd)
Error: processing vignette 'adce.Rmd' failed with diagnostics:
argument "join_type" is missing, with no default
--- failed re-building ‘adce.Rmd’

--- re-building ‘adface.Rmd’ using rmarkdown

Quitting from lines 233-247 [unnamed-chunk-13] (adface.Rmd)
Error: processing vignette 'adface.Rmd' failed with diagnostics:
argument "join_type" is missing, with no default
--- failed re-building ‘adface.Rmd’

--- re-building ‘adis.Rmd’ using rmarkdown

Quitting from lines 551-562 [unnamed-chunk-19] (adis.Rmd)
Error: processing vignette 'adis.Rmd' failed with diagnostics:
argument "join_type" is missing, with no default
--- failed re-building ‘adis.Rmd’

--- re-building ‘admiralvaccine.Rmd’ using rmarkdown
--- finished re-building ‘admiralvaccine.Rmd’

--- re-building ‘adsl.Rmd’ using rmarkdown
--- finished re-building ‘adsl.Rmd’

SUMMARY: processing the following files failed:
  ‘adce.Rmd’ ‘adface.Rmd’ ‘adis.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘docstring’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rgdal’
Package which this enhances but not available for checking: ‘asreml’
Specified C++11: please drop specification unless essential
File ‘ahaz/libs/ahaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’
  ‘utils’
  All declared Imports should be used.
Invalid package aliases in Rd file 'aire.zmvm-deprecated.Rd':
  ‘aire.zmvm-deprecated-package’
Note: found 53 marked UTF-8 strings
Note: found 17 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 710 marked UTF-8 strings
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
File ‘AlgDesign/libs/AlgDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 115 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘alphabetr/libs/alphabetr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'gs.Rd':
  ‘x’ ‘parallel’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
Argument items with no description in Rd file 'MLS.Rd':
  ‘MSE1’
'LazyData' is specified without a 'data' directory
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'amelia.package.Rd':
  ‘amelia-package’
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘network’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'check_factors.Rd':
  ‘object’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'rowVars.Rd':
  \arguments: \dots: ‘~~Describe \code{\dots} here~~’
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Note: found 237 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'crawl_interpolation.Rd':
  ‘pt.colors’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mcclust’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'alternate.sol3.Rd':
  ‘lambda0’

Documented arguments not in \usage in Rd file 'check.group.Rd':
  ‘k’

Documented arguments not in \usage in Rd file 'getrow3.Rd':
  ‘lambda0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 4 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'apci.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.bar.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.heatmap.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.hexagram.Rd':
  ‘first_age’ ‘first_period’ ‘interval’ ‘first_age_isoline’
  ‘first_period_isoline’ ‘isoline_interval’ ‘line_width’ ‘line_color’
  ‘label_size’ ‘label_color’ ‘scale_units’ ‘wrap_cohort_labels’
  ‘quantile’
Argument items with no description in Rd file 'apci.plot.raw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'cohortdeviation.Rd':
  ‘\dots’
Argument items with no description in Rd file 'compute_xcoordinate.Rd':
  ‘p’
Argument items with no description in Rd file 'compute_ycoordinate.Rd':
  ‘p’ ‘a’
Argument items with no description in Rd file 'maineffect.Rd':
  ‘\dots’
Argument items with no description in Rd file 'temp_model.Rd':
  ‘\dots’
Argument items with no description in Rd file 'tests.Rd':
  ‘\dots’
Namespaces in Imports field not imported from:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'apercu.Rd':
  ‘c’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
Note: found 76 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘bannerCommenter’ ‘config’ ‘feather’ ‘here’ ‘knitr’ ‘log4r’ ‘ps’
  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Argument items with no description in Rd file 'dynamac_pkg_bounds_test.Rd':
  ‘obs’ ‘fstat’ ‘tstat’ ‘case’ ‘k’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Documented arguments not in \usage in Rd file 'allocateFromCdf.AromaUnitTabularBinaryFile.Rd':
  ‘path’ ‘tags’ ‘footer’

Documented arguments not in \usage in Rd file 'byChipType.DChipSnpInformation.Rd':
  ‘rootPath’ ‘pattern’ ‘verbose’

Documented arguments not in \usage in Rd file 'byChipType.UgpGenomeInformation.Rd':
  ‘version’

Documented arguments not in \usage in Rd file 'calculateResidualSet.FirmaModel.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'findByChipType.AromaChipTypeAnnotationFile.Rd':
  ‘chipType’ ‘tags’

Documented arguments not in \usage in Rd file 'fit.SmoothMultiarrayModel.Rd':
  ‘data’

Documented arguments not in \usage in Rd file 'getCellIndices.ExonChipEffectFile.Rd':
  ‘units’

Documented arguments not in \usage in Rd file 'getImage.AffymetrixCelFile.Rd':
  ‘palette’

Documented arguments not in \usage in Rd file 'getOutputDataSet.Transform.Rd':
  ‘force’

Documented arguments not in \usage in Rd file 'getUnitTypes.AffymetrixCdfFile.Rd':
  ‘map’

Documented arguments not in \usage in Rd file 'plotMvsX.AffymetrixCelFile.Rd':
  ‘xlim’ ‘xlab’

Documented arguments not in \usage in Rd file 'process.BackgroundCorrection.Rd':
  ‘force’ ‘verbose’

Documented arguments not in \usage in Rd file 'readUnits.CnagCfhFile.Rd':
  ‘cdf’

Documented arguments not in \usage in Rd file 'setArrays.ArrayExplorer.Rd':
  ‘arrays’

Documented arguments not in \usage in Rd file 'setRestructor.AffymetrixCdfFile.Rd':
  ‘units’

Documented arguments not in \usage in Rd file 'setupExampleData.Rd':
  ‘dirs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'fitOne.MultiSourceCopyNumberNormalization.Rd':
  ‘name’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Documented arguments not in \usage in Rd file 'fit.CopyNumberSegmentationModel.Rd':
  ‘chromosome’

Documented arguments not in \usage in Rd file 'getPath.Explorer.Rd':
  ‘create’

Documented arguments not in \usage in Rd file 'process.AromaTransform.Rd':
  ‘force’ ‘verbose’

Documented arguments not in \usage in Rd file 'process.ChromosomeExplorer.Rd':
  ‘chromosome’

Documented arguments not in \usage in Rd file 'process.Explorer.Rd':
  ‘arrays’ ‘verbose’

Documented arguments not in \usage in Rd file 'setArrays.Explorer.Rd':
  ‘arrays’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 1409 marked UTF-8 strings
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'RweaveAsciiSetup.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveOrg.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweavePandoc.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveReST.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveT2t.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveTextile.Rd':
  ‘stylepath’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ash/libs/ash.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  MSTOpt.cpp:20:43: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wformat=]
  MSTOpt.cpp:593:49: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
  genetic_map_DH.cpp:191:31: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wformat=]
  genetic_map_DH.cpp:233:19: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
  genetic_map_DH.cpp:470:17: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
  genetic_map_DH.cpp:477:17: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wformat=]
  linkage_group_DH.cpp:123:31: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/ASMap.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Package which this enhances but not available for checking: ‘asreml’
Documented arguments not in \usage in Rd file 'check.args_.Rd':
  ‘rename_’ ‘arg.update_’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Unknown packages ‘assertive.properties’, ‘assertive.types’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘asteRiskData’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘lubridate’ ‘openair’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.rsp’
  All declared Imports should be used.
Unknown package ‘snpar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 54582 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Note: found 610 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘readxl’ ‘reshape2’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘rclipboard’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MixAll’ ‘dplyr’ ‘lqmm’ ‘matrixcalc’ ‘rmutil’ ‘rootSolve’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Package suggested but not available for checking: ‘lixoftConnectors’
Note: found 64209 marked UTF-8 strings
Note: found 133353 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'write.narrative.Rd':
  ‘trials:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 260 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘fdpbandsdata’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 148 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Note: found 13825 marked UTF-8 strings
File ‘Barnard/libs/Barnard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'BartMixVs-package.Rd':
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
File ‘base64enc/libs/base64enc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘rgdal’
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Earlier versions
Namespaces in Imports field not imported from:
  ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘vtable’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
File ‘batman/libs/batman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 490 marked UTF-8 strings
GNU make is a SystemRequirements.
Invalid package aliases in Rd file 'bayesANOVA-package.Rd':
  ‘bayesANOVA-package’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
File ‘BayesComm/libs/BayesComm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘StanHeaders’ ‘astsa’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppParallel’ ‘mlbench’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
File ‘bayesianETAS/libs/bayesianETAS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘MCMCpack’ ‘R2WinBUGS’ ‘R2jags’ ‘carData’ ‘rjags’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
Note: found 1924 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘matrixcalc’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'hmmeantemp.Rd':
  ‘dat’
Found the following significant warnings:
  mbart.cpp:406:18: warning: format '%d' expects argument of type 'int', but argument 2 has type 'ivs' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/BayesTree.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
File ‘BayesTree/libs/BayesTree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 385 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘BCBCSF/libs/BCBCSF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘fabiabreast.txt’
checkRd: (-1) tlsce.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:93: Escaped LaTeX specials: \_
S3 methods shown with full name in Rd file 'export.bce.Rd':
  ‘export.bce’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  HelperVariables.h:135:15: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=]
  Params.h:122:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'R_xlen_t' {aka 'long int'} [-Wformat=]
  Graph.h:186:66: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::vector<Node>::size_type' {aka 'long unsigned int'} [-Wformat=]
  Cbcpgraph.cpp:58:66: warning: format '%f' expects a matching 'double' argument [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/bcp.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 72 marked UTF-8 strings
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 2666 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
Argument items with no description in Rd file 'bdw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plot.bdw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.bdw.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
Note: found 107 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘forecast’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘BenfordTests/libs/BenfordTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘BiDAG’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 42 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘betategarch/libs/betategarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'print_summary_gibbs_psd_help.Rd':
  ‘flag=T:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 379 marked UTF-8 strings
Note: found 1227 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
Note: found 582 marked UTF-8 strings
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'h.pr.u.Rd':
  ‘z’ ‘ih’ ‘mu’ ‘sigma’ ‘pk’ ‘K’ ‘H’ ‘n’
Argument items with no description in Rd file 'hatpai.u.Rd':
  ‘z’ ‘hk1’ ‘hk0’ ‘ph1’ ‘ph0’ ‘sigma1’ ‘sigma0’ ‘mu1’ ‘mu0’ ‘pai’ ‘H’
  ‘n’
Argument items with no description in Rd file 'ind.u.Rd':
  ‘pr’
Argument items with no description in Rd file 'lambda.u.Rd':
  ‘nu’
Argument items with no description in Rd file 'mu.k.u.Rd':
  ‘k’ ‘ik’ ‘z’ ‘sigma’ ‘mu0’
Argument items with no description in Rd file 'nu.u.Rd':
  ‘ind’ ‘tau’ ‘H’
Argument items with no description in Rd file 'pai.u.Rd':
  ‘b’ ‘a.pai’ ‘b.pai’
Argument items with no description in Rd file 'sig.k.u.Rd':
  ‘k’ ‘ik’ ‘z’ ‘mu0’ ‘a0’ ‘b0’
Argument items with no description in Rd file 'z.pr.u.Rd':
  ‘z’ ‘hk’ ‘mu’ ‘sigma’ ‘ph’ ‘H’ ‘n’
File ‘BiasedUrn/libs/BiasedUrn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
Note: found 1904 marked UTF-8 strings
Note: found 573 marked UTF-8 strings
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DAAG’ ‘datasets’ ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RBGL’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘lavaan.survey’
Unknown package ‘lavaan.survey’ in Rd xrefs
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Package suggested but not available for checking: ‘ffbase’
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Invalid package aliases in Rd file 'package_bigdist.Rd':
  ‘package_bigdist-package’
Note: found 940 marked Latin-1 strings
Specified C++11: please drop specification unless essential
File ‘biglm/libs/biglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 660 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘binom/libs/binom.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'select.cfs.Rd':
  ‘select.cfs’

S3 methods shown with full name in Rd file 'select.fast.filter.Rd':
  ‘select.fast.filter’

S3 methods shown with full name in Rd file 'select.forward.Corr.Rd':
  ‘select.forward.Corr’

S3 methods shown with full name in Rd file 'select.forward.wrapper.Rd':
  ‘select.forward.wrapper’

S3 methods shown with full name in Rd file 'select.inf.chi2.Rd':
  ‘select.inf.chi2’

S3 methods shown with full name in Rd file 'select.inf.gain.Rd':
  ‘select.inf.gain’

S3 methods shown with full name in Rd file 'select.inf.symm.Rd':
  ‘select.inf.symm’

S3 methods shown with full name in Rd file 'select.process.Rd':
  ‘select.process’

S3 methods shown with full name in Rd file 'select.relief.Rd':
  ‘select.relief’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
Documented arguments not in \usage in Rd file 'predict2.em.Rd':
  ‘na.rm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘bioPN/libs/bioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Invalid package aliases in Rd file 'bios2cor-package.Rd':
  ‘bios2cor-package’
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 46 marked UTF-8 strings
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 516 marked UTF-8 strings
Argument items with no description in Rd file 'ONA_compiled.Rd':
  ‘ATN’
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘digest’ ‘ergm’ ‘foreign’ ‘gWidgets2’ ‘gWidgets2tcltk’ ‘haven’
  ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Argument items with no description in Rd file 'export.dyadic.Rd':
  ‘blauObj’
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘blockTools/libs/blockTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'id2rownum.Rd':
  ‘ids’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 21550 marked UTF-8 strings
Package suggested but not available for checking: ‘sangerseqR’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘HSAUR3’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘bootruin/libs/bootruin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'check_inputs.Rd':
  ‘h_rs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
Documented arguments not in \usage in Rd file 'InternalFunctions.Rd':
  ‘metric’ ‘matrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'info.Rd':
  ‘mod_spec’ ‘pkg_spec’

Documented arguments not in \usage in Rd file 'path.Rd':
  ‘args’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'b_samp.Rd':
  ‘Y’

Documented arguments not in \usage in Rd file 'betaBlock.Rd':
  ‘Y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Documented arguments not in \usage in Rd file 'utils.Rd':
  ‘max.len’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘Branching/libs/Branching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'availability.int.Rd':
  ‘v.set’ ‘dir.set’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'subset.int.Rd':
  ‘subset.int’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 87 marked UTF-8 strings
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘glmmADMB’
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Running examples in ‘BRVM-Ex.R’ failed
The error most likely occurred in:

> ### Name: BRVM_company_rank
> ### Title: BRVM Companies Rank - Get all tickers rank according to last
> ###   quotation
> ### Aliases: BRVM_company_rank
> 
> ### ** Examples
> 
> 
> BRVM_company_rank()
Make sure you have an active internet connection
> comp.rank<-BRVM_company_rank()
Make sure you have an active internet connection
> comp.rank<-comp.rank%>%
+ dplyr::arrange(desc(percent_change))
Error in UseMethod("arrange") : 
  no applicable method for 'arrange' applied to an object of class "NULL"
Calls: %>% -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'table.Rd':
  ‘headTitles’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Argument items with no description in Rd file 'plot.bshazard.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.bshazard.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.bshazard.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘grDevices’ ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/bsts.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 89 marked UTF-8 strings
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘magrittr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'count.Rd':
  ‘.data’

Documented arguments not in \usage in Rd file 'unite.Rd':
  ‘.data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'calcIntegralSurv2_cpp.Rd':
  ‘dsurvival’

Documented arguments not in \usage in Rd file 'dot-calcIntegralCif_cpp.Rd':
  ‘cif’ ‘CIF_t’

Documented arguments not in \usage in Rd file 'validFCTs.Rd':
  ‘super.classes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘bvarsv/libs/bvarsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
File ‘bvls/libs/bvls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 179 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Note: found 58 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'get_result.Rd':
  ‘out’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘CAMAN/libs/CAMAN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 287 marked UTF-8 strings
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Note: found 2992 marked UTF-8 strings
Note: found 23 marked UTF-8 strings
Argument items with no description in Rd file 'makeEventHistory.Rd':
  ‘type’
Argument items with no description in Rd file 'plotSeqCount.Rd':
  ‘segColors’
Found the following files/directories:
  ‘MDA231_tree.pdf’
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘methods’ ‘readr’ ‘recipes’ ‘sf’ ‘stringr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘rnaturalearthhires’
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'EcoLinkPredict.Rd':
  ‘EcoLinkPredict-package’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'validate_cover_cats.Rd':
  ‘cats_target’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'add_catmaply_slider.Rd':
  ‘text_font_color’ ‘categorical_col’

Documented arguments not in \usage in Rd file 'add_catmaply_traces.Rd':
  ‘categorical_col’

Documented arguments not in \usage in Rd file 'catmaply_annotations.Rd':
  ‘fig’ ‘text_font_color’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘epitools’ ‘forcats’ ‘purrr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CBPS’ ‘spelling’
  All declared Imports should be used.
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hotcold.csv’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'buildModel.Rd':
  ‘x’ ‘y’

Documented arguments not in \usage in Rd file 'modelKrigingInternalPredictor.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'selfAdapt.Rd':
  ‘nvaleus’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
Documented arguments not in \usage in Rd file 'evaluate_rule.Rd':
  ‘class’

Documented arguments not in \usage in Rd file 'tree_leaf_nodes.Rd':
  ‘classes.’ ‘invert.’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'CensMFM-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Documented arguments not in \usage in Rd file 'blackboost_train.Rd':
  ‘x’ ‘y’

Documented arguments not in \usage in Rd file 'survival_prob_mboost.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'centralplot.Rd':
  ‘alpha’
'LazyData' is specified without a 'data' directory
Note: found 104 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘batchtools’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘htmltools’
  ‘jsonlite’ ‘magrittr’ ‘methods’ ‘plotly’ ‘reshape’ ‘rlang’ ‘shiny’
  ‘shinyWidgets’ ‘shinyjqui’ ‘shinyjs’ ‘shinymaterial’ ‘sortable’ ‘ssh’
  ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major refactoring of the code
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'create_epa.Rd':
  ‘clean_pbp_dat’ ‘df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
File ‘cgAUC/libs/cgAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in Rd file 'select.cglasso.Rd':
  ‘select.cglasso’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Objects in \usage without \alias in Rd file 'influence-methods.Rd':
  ‘influence’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file 'jumpointsVar-package.Rd':
  ‘jumpointsVar-package’
Objects in \usage without \alias in Rd file 'jumpointsVar-internal.Rd':
  ‘seg.lm.fit0.gamma’ ‘max.rss’ ‘print.jumpointsVar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'jumpointsVar-internal.Rd':
  ‘max.rss’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bench’ ‘ggplot2’
  All declared Imports should be used.
Invalid package aliases in Rd file 'ChangePointAnalyzer-package.Rd':
  ‘ChangePointAnalyzer-package’
Auto-generated content requiring editing in Rd file 'ChangePointAnalyzer-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Documented arguments not in \usage in Rd file 'multiplierDSeqfun.Rd':
  ‘MC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘darts’
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Note: found 200 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'dot-chkArgs.Rd':
  ‘mode.’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 8119 marked UTF-8 strings
Invalid package aliases in Rd file 'ChIPtest-package.Rd':
  ‘ChIPtest_1.0-package’
File ‘ChIPtest/libs/ChIPtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
Objects in \usage without \alias in Rd file 'choplump-internal.Rd':
  ‘chooseMatrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'SearchEmptyClusters.Rd':
  ‘oldcluster’ ‘SSminvec’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 28982 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘circlize’ ‘utils’
  All declared Imports should be used.
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘networkD3’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 29 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 9 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ClickClust/libs/ClickClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1 marked UTF-8 string
Note: found 27934 marked UTF-8 strings
Note: found 10332 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 8737 marked UTF-8 strings
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
File ‘clogitboost/libs/clogitboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘clogitL1/libs/clogitL1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'clpm-internal.Rd':
  ‘lpm.newton2’ ‘lpm.fit’ ‘lpm.newton’ ‘L_lambda’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'auxiliary_functions.Rd':
  ‘edelist’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Objects in \usage without \alias in Rd file 'clustEff-internal.Rd':
  ‘.get_ave_sil_width’ ‘.get_withinSS’ ‘print.clustEff’
  ‘print.summary.clustEff’ ‘print.fpcac’ ‘print.summary.fpcac’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘clusterhap_reports’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'calculate_connectivity.Rd':
  ‘datdf’

Documented arguments not in \usage in Rd file 'dunn_metric.Rd':
  ‘distance’ ‘method’

Documented arguments not in \usage in Rd file 'evaluate_all_column_dataset.Rd':
  ‘data’

Documented arguments not in \usage in Rd file 'information_external.Rd':
  ‘info’

Documented arguments not in \usage in Rd file 'information_internal.Rd':
  ‘info’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘clustering.sc.dp/libs/clustering.sc.dp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ClusterStability/libs/ClusterStability.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 5626 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘clv/libs/clv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MPV’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 4622 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
File ‘cmprsk/libs/cmprsk.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘FNN’ ‘R.utils’ ‘SearchTrees’ ‘colorspace’ ‘colourpicker’
  ‘data.table’ ‘maps’ ‘ncdf4’ ‘raster’ ‘shinyFiles’ ‘shinyWidgets’
  ‘shinyjs’ ‘shinythemes’ ‘tcltk’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tobit1’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
Package suggested but not available for checking: ‘PopGenome’
Documented arguments not in \usage in Rd file 'feat_sample.Rd':
  ‘locus_group’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'get_superior.Rd':
  ‘stirng’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘disttree’
Documented arguments not in \usage in Rd file 'lb_calculation.Rd':
  ‘qu.param’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 14729 marked UTF-8 strings
Package which this enhances but not available for checking: ‘rkward’
Documented arguments not in \usage in Rd file 'cocorresp-internal.Rd':
  ‘Y’ ‘eps’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘rkward’
Note: found 27 marked UTF-8 strings
Package suggested but not available for checking: ‘userfriendlyscience’
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
Note: found 30244 marked UTF-8 strings
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Note: found 6 marked UTF-8 strings
Package suggested but not available for checking: ‘bvpSolve’
'LazyData' is specified without a 'data' directory
File ‘coenoflex/libs/coenoflex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4186 marked UTF-8 strings
Note: found 89 marked Latin-1 strings
  Note: found 1203 marked UTF-8 strings
File ‘collUtils/libs/collUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 742 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Note: found 2 marked UTF-8 strings
Unexported object imported by a ':::' call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'summary.CommunityClimateInput.Rd':
  ‘object’ ‘\dots’
Argument items with no description in Rd file 'summary.CommunityClimateStatistics.Rd':
  ‘object’ ‘\dots’
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
Objects in \usage without \alias in Rd file 'comf-internal.Rd':
  ‘calcet’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘CAM’
File ‘compareC/libs/compareC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'CopulaSelection.Rd':
  ‘rhoType’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Rd files without \alias:
  ‘CompoundEvents-package.Rd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘ConConPiWiFun/libs/ConConPiWiFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 92 marked UTF-8 strings
Auto-generated content requiring editing in Rd file 'concordancer-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘base’ ‘lwgeom’ ‘s2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'postProcessSys.Rd':
  ‘myFile’

Documented arguments not in \usage in Rd file 'theta_ll.Rd':
  ‘params’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
File ‘ConsReg/libs/ConsReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
File ‘contoureR/libs/contoureR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'print_table.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'coopProductGame-package.Rd':
  ‘coopProducGame-package’
Note: found 144 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'ft.Rd':
  ‘theta’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘cord/libs/cord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Note: found 1187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 438 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xcms’
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
Note: found 59 marked UTF-8 strings
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9044 marked UTF-8 strings
Note: found 140280 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
File ‘covBM/libs/covBM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘covfefe_inauguration.txt’
Note: found 1934235 marked UTF-8 strings
Note: found 2385 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Note: found 213180 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘gsl’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘CoxPlus/libs/CoxPlus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘BEST’
Found the following significant warnings:
  cpglmm.c:272:17: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  cpglmm.c:272:17: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  cpglmm.c:1095:17: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  cpglmm.c:1095:17: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/cplm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
File ‘cpm/libs/cpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘credule/libs/credule.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 37 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer3’
Namespaces in Imports field not imported from:
  ‘DT’ ‘gbm’
  All declared Imports should be used.
Packages suggested but not available for checking: 'conos', 'pagoda2'
Documented arguments not in \usage in Rd file 'pinvGamma.Rd':
  ‘logical;’

Documented arguments not in \usage in Rd file 'qinvGamma.Rd':
  ‘logical;’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
‘cleanup’: /bin/bash is not portable
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘crrSC/libs/crrSC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 500 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘geosphere’ ‘mapdata’ ‘maps’ ‘marmap’ ‘shinydashboard’
  ‘shinyjs’ ‘stringr’ ‘swfscDAS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgeos’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘future’
  All declared Imports should be used.
Note: found 282 marked UTF-8 strings
Note: found 3031 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'tool.Rd':
  ‘seq’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'ctqr-internal.Rd':
  ‘findagoodestimator’ ‘safe.pch’ ‘quickpred’ ‘check.in.ctqr’ ‘start’
  ‘ee.u’ ‘ee.cens’ ‘ee.cens.trunc’ ‘ee.icens’ ‘qr.gs’ ‘nobs.ctqr’
  ‘vcov.ctqr’ ‘coef.ctqr’ ‘print.ctqr’ ‘summary.ctqr’
  ‘print.summary.ctqr’ ‘firstep.ct’ ‘firstep.ic’ ‘asy.qr.ct’
  ‘asy.qr.ic’ ‘safesolve’ ‘regularize_corr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'ctqr-internal.Rd':
  ‘qr.gs’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 1350 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘par-7269706c6579’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Hello.csv’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'chi2cub2cov.Rd':
  ‘covar’

Documented arguments not in \usage in Rd file 'cubpq.Rd':
  ‘summary’

Documented arguments not in \usage in Rd file 'cubshe.Rd':
  ‘makeplot’ ‘summary’

Documented arguments not in \usage in Rd file 'kkk.Rd':
  ‘Vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 459 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Documented arguments not in \usage in Rd file 'cvRiskPlot.Rd':
  ‘estimator’

Documented arguments not in \usage in Rd file 'matrixMetrics.Rd':
  ‘estimator’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘RGtk2’
Documented arguments not in \usage in Rd file 'compute_stat.Rd':
  ‘K_0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
File ‘cycleRtools/libs/cycleRtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 469 marked UTF-8 strings
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'tree.filter.Rd':
  ‘nodeList’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 109157 marked UTF-8 strings
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
Note: found 2020 marked UTF-8 strings
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 212 marked Latin-1 strings
  Note: found 12719 marked UTF-8 strings
File ‘DALY/libs/DALY.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'mm_run_reg.Rd':
  ‘all_params’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
Invalid package aliases in Rd file 'dap-package.Rd':
  ‘dap-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'plotDataExplorer.single.Rd':
  ‘obj’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘my new data set.rds’
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
Note: found 72720 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Documented arguments not in \usage in Rd file 'dotgetJSONValue.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 8 marked Latin-1 strings
Note: found 2596 marked UTF-8 strings
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 54339 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dblog’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in Rd file 'dbglm-internal.Rd':
  ‘dbglm.iteration’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘html5’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘lubridate’ ‘tseries’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'a_dcc_mat_est.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'dcc_mat_est.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'deco_mat_est.Rd':
  ‘param’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 122 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 38 marked UTF-8 strings
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  difeq.c:268:69: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  dopri.c:332:68: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  r_difeq.c:214:59: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  r_difeq.c:223:52: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  r_dopri.c:93:59: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  util.c:36:38: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/dde.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinydisconnect’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'DDPNA-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
Argument items with no description in Rd file 'DEP_Mod_net_plot.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
Note: found 53 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'getTriContextFraction.Rd':
  ‘trimer.counts.ref’

Documented arguments not in \usage in Rd file 'norm.it.Rd':
  ‘trimer.counts’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'degreenet-internal.Rd':
  ‘range’ ‘lims’
Objects in \usage without \alias in Rd file 'degreenet-internal.Rd':
  ‘bootstrapyule’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘smd_table.docx’
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'boot_f_cor.Rd':
  ‘fun’

Documented arguments not in \usage in Rd file 'boot_f_pcor.Rd':
  ‘fun’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Note: found 3 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: found 2534 marked UTF-8 strings
Rd files without \alias:
  ‘densityClust-package.Rd’
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Package suggested but not available for checking: ‘Rdonlp2’
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘Rdonlp2’
Specified C++11: please drop specification unless essential
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 5764 marked UTF-8 strings
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.N’ ‘.Nmiss’ ‘.Q1’ ‘.Q3’ ‘.factorN’ ‘.factorNmiss’ ‘.factorQ1’
  ‘.factorQ3’ ‘.factormax’ ‘.factormean’ ‘.factormedian’ ‘.factormin’
  ‘.factorsd’ ‘.max’ ‘.mean’ ‘.median’ ‘.min’ ‘.sd’
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
Note: found 47 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘dhlabR-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_collocations
> ### Title: Get collocations for word in corpus
> ### Aliases: get_collocations
> 
> ### ** Examples
> 
> pids <- c("URN:NBN:no-nb_digibok_2008051404065", "URN:NBN:no-nb_digibok_2010092120011")
> word <- "."
> collocations <- get_collocations(pids, word)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [api.nb.no] Connection timeout after 10001 ms
Calls: get_collocations ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Documented arguments not in \usage in Rd file 'encode_unit.Rd':
  ‘original’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 8014 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘diffIRT/libs/diffIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'Nortonbass_startvalgen.Rd':
  ‘param’ ‘startvalgen’

Documented arguments not in \usage in Rd file 'seqdiffusion.Rd':
  ‘w’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘gurobi’
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘discreteMTP’
Unknown package ‘discreteMTP’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'RV.Rd':
  ‘RV-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
Note: found 270 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Missing link or links in Rd file 'ds.Rd':
  ‘[mrds:mrds-opt]{mrds-opt}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘distr.Rnw’ using knitr

Quitting from lines 1036-1040 [examdcP] (distr.Rnw)
Error: processing vignette 'distr.Rnw' failed with diagnostics:
error in evaluating the argument 'object' in selecting a method for function 'decomposePM': unable to find an inherited method for function 'r' for signature 'object = "numeric"'
--- failed re-building ‘distr.Rnw’

SUMMARY: processing the following file failed:
  ‘distr.Rnw’

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in Rd file 'internals.Rd':
  ‘namestoGather’ ‘namestoGatherNS’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'internalmleHelpers.Rd':
  ‘validity.check’

Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.csimpsum’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘distrMod-Ex.R’ failed
The error most likely occurred in:

> ### Name: BinomFamily
> ### Title: Generating function for Binomial families
> ### Aliases: BinomFamily
> ### Keywords: models
> 
> ### ** Examples
> 
> (B1 <- BinomFamily(size = 25, prob = 0.25))
Warning in .local(.Object, ...) : you have to specify slot r at least
Error: unable to find an inherited method for function ‘r’ for signature ‘object = "numeric"’
Execution halted
'LazyData' is specified without a 'data' directory
Assignments in \usage in Rd file 'internalGenerics.Rd':
  x <- samplesize(object, value)

Documented arguments not in \usage in Rd file 'internals.Rd':
  ‘DClass’
Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.consolidategaps’ ‘.List’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘distr-Ex.R’ failed
The error most likely occurred in:

> ### Name: Binom-class
> ### Title: Class "Binom"
> ### Aliases: Binom-class Binom initialize,Binom-method
> ### Keywords: distribution
> 
> ### ** Examples
> 
> B <- Binom(prob=0.5,size=1) # B is a binomial distribution with prob=0.5 and size=1.
> r(B)(1) # # one random number generated from this distribution, e.g. 1
[1] 0
> d(B)(1) # Density of this distribution is  0.5 for x=1.
[1] 0.5
> p(B)(0.4) # Probability that x<0.4 is 0.5.
[1] 0.5
> q(B)(.1) # x=0 is the smallest value x such that p(B)(x)>=0.1.
[1] 0
> ## in RStudio or Jupyter IRKernel, use q.l(.)(.) instead of q(.)(.)
> size(B) # size of this distribution is 1.
[1] 1
> size(B) <- 2 # size of this distribution is now 2.
> C <- Binom(prob = 0.5, size = 1) # C is a binomial distribution with prob=0.5 and size=1.
> D <- Binom(prob = 0.6, size = 1) # D is a binomial distribution with prob=0.6 and size=1.
> E <- B + C # E is a binomial distribution with prob=0.5 and size=3.
> F <- B + D # F is an object of class LatticeDistribution.
Warning in .local(.Object, ...) : you have to specify slot r at least
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'object' in selecting a method for function 'prob': unable to find an inherited method for function ‘r’ for signature ‘object = "numeric"’
Calls: + ... initialize -> initialize -> .local -> table -> r -> <Anonymous>
Execution halted
Running examples in ‘distrTeach-Ex.R’ failed
The error most likely occurred in:

> ### Name: illustrateCLT
> ### Title: Functions for Illustrating the CLT
> ### Aliases: illustrateCLT illustrateCLT.tcl
> ### Keywords: distribution methods dynamic
> 
> ### ** Examples
> 
> distroptions("DefaultNrFFTGridPointsExponent" = 13)
> illustrateCLT(Distr = Unif(), len = 10)
> distroptions("DefaultNrFFTGridPointsExponent" = 12)
> illustrateCLT(Distr = Pois(lambda = 2), len = 10)
Error: unable to find an inherited method for function ‘r’ for signature ‘object = "numeric"’
Execution halted
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'diveMove-internal.Rd':
  ‘.diveMatches’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘truncnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggmulti’ ‘loon’ ‘loon.data’ ‘loon.ggplot’ ‘loon.shiny’ ‘loon.tourr’
  ‘stats’ ‘zenplots’
  All declared Imports should be used.
Found the following significant warnings:
  GslOdeBase.cpp:47:49: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  GslOdeBase.cpp:47:57: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wformat=]
  GslOdeBase.cpp:102:37: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  GslOdeBase.cpp:102:50: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wformat=]
  TimeMachine.cpp:39:22: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  TimeMachine.cpp:39:46: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/diversitree.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Package suggested but not available for checking: ‘BOLTSSIRR’
Package suggested but not available for checking: ‘rgdal’
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘dkDNA/libs/dkDNA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
Invalid package aliases in Rd file 'dmaiIntro.Rd':
  ‘dmaiIntro-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'dml_bagging.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_boosting.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_ensemble_lm.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_ensemble_rf.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_neural_network.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_random_forest.Rd':
  ‘y,x,d,data,sed’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'dnapath2-package.Rd':
  ‘dnapath2-package’
Auto-generated content requiring editing in Rd file 'dnapath2-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Note: found 175 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
S3 methods shown with full name in Rd file 'add.joint.mean.many.Rd':
  ‘all.cond.mean.PO’ ‘all.cond.mean2.PO’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'derivType.Rd':
  ‘L’ ‘mu’ ‘eps’
Argument items with no description in Rd file 'getNewParams.SC.Rd':
  ‘n.fft’
Argument items with no description in Rd file 'graph.CTMC.Rd':
  ‘\dots’
Argument items with no description in Rd file 'num.deriv.Rd':
  ‘\dots’
Argument items with no description in Rd file 'power.coef.one.Rd':
  ‘\dots’
Documented arguments not in \usage in Rd file 'concDict.Rd':
  ‘text’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Note: found 9796 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'check_results.Rd':
  ‘error_on_failure’ ‘error_on_warning’

Documented arguments not in \usage in Rd file 'function_get_comments.Rd':
  ‘thresholds’

Documented arguments not in \usage in Rd file 'vignette_results_display.Rd':
  ‘vignette_results’ ‘error_on_failure’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Note: found 100 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DT’ ‘DoseFinding’ ‘Rsolnp’ ‘ggplot2’ ‘kableExtra’ ‘knitr’
  ‘latticeExtra’ ‘purrr’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  ‘stringr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
Note: found 2 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Unknown package ‘broomExtra’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘ggplot2’ ‘nloptr’
  All declared Imports should be used.
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'forecastCovCompiled.Rd':
  ‘obj’ ‘zero’ ‘trend’ ‘estimation.sample’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘dse/libs/dse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 386 marked UTF-8 strings
Note: found 4891 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
'LazyData' is specified without a 'data' directory
Note: found 281 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Objects in \usage without \alias in Rd file 'd.spls.norm1.Rd':
  ‘d.spls.norm2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘dualtrees/libs/dualtrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2854 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GenEst’ ‘expint’ ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘NatureSounds’ ‘av’ ‘magrittr’ ‘stats’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'dynConfiR-package.Rd':
  ‘dynWEV-package’
Package suggested but not available for checking: ‘lle’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
File ‘dynpred/libs/dynpred.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Namespace in Imports field not imported from: ‘qcr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'e.cluster.decision.Rd':
  ‘reg_data’ ‘log.lambda’
Argument items with no description in Rd file 'e.cluster.dendrogram.Rd':
  ‘echelon.obj’ ‘n.sim’ ‘cluster.legend.pos’ ‘cluster_reg’ ‘p_rank’
  ‘para’
Argument items with no description in Rd file 'e.cluster.map.Rd':
  ‘x’ ‘c_separates’ ‘locs’ ‘coo’ ‘rin’ ‘p_rank’ ‘cluster_reg’ ‘n.sim’
  ‘cluster.type’
Argument items with no description in Rd file 'e.dendrogram.Rd':
  ‘peaks’ ‘locs’ ‘x’ ‘separates’ ‘c_separates’ ‘number’ ‘parents’
  ‘pare_locs’ ‘progeny’ ‘symbols’ ‘col.symbols’ ‘cex.symbols’ ‘lwd’
  ‘col’ ‘ens’ ‘adj.ens’ ‘col.ens’ ‘cex.ens’ ‘limb’
Argument items with no description in Rd file 'e.dendrogram.axis.Rd':
  ‘main’ ‘ylab’ ‘yaxes’ ‘ylim’ ‘xaxes’ ‘xdper’ ‘dmai’ ‘peaks’ ‘x’
Argument items with no description in Rd file 'e.main.Rd':
  ‘x’ ‘rin’ ‘T’
Argument items with no description in Rd file 'e.monte.bin.Rd':
  ‘rin’ ‘cas’ ‘pop’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd file 'e.monte.poi.Rd':
  ‘rin’ ‘cas’ ‘pop’ ‘ex’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd file 'e.profile.Rd':
  ‘peaks’ ‘parents’ ‘separates’
Argument items with no description in Rd file 'e.scan.Rd':
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’
Argument items with no description in Rd file 'e.scan.pop.Rd':
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’ ‘pop’
Argument items with no description in Rd file 'nlimb.Rd':
  ‘x’ ‘k2’
'LazyData' is specified without a 'data' directory
Note: found 1281 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 42 marked UTF-8 strings
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 6 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
Note: found 74 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'fcf.env.Rd':
  ‘vars’

Documented arguments not in \usage in Rd file 'getlevels.Rd':
  ‘editarray’

Documented arguments not in \usage in Rd file 'parseCatEdit.Rd':
  ‘e’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 136358 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Package suggested but not available for checking: ‘lavaan.survey’
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'rotate_to_equilibrium.Rd':
  ‘xy_may’

Documented arguments not in \usage in Rd file 'wide.dyads.to.edgelist.Rd':
  ‘fist.var’

Documented arguments not in \usage in Rd file 'wide.to.long.Rd':
  ‘last.col’ ‘ego.vars’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 7 marked UTF-8 strings
Invalid package aliases in Rd file 'HOF-package.Rd':
  ‘HOF-package’
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'colBoxplot4.Rd':
  ‘id’

Documented arguments not in \usage in Rd file 'elaborator_server.Rd':
  ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘elsa/libs/elsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Note: found 155 marked UTF-8 strings
Note: found 50 marked Latin-1 strings
Found the following significant warnings:
  emd-rubner.c:810:20: warning: 'minI' is used uninitialized [-Wuninitialized]
  emd-rubner.c:810:26: warning: 'minJ' is used uninitialized [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/emdist.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
License stub is invalid DCF.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Found the following significant warnings:
  bitstring.h:28:54: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/emoa.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
File ‘emoa/libs/emoa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 16919 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 23639 marked Latin-1 strings
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘enc-package.Rd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Note: found 2 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’
  All declared Imports should be used.
File ‘EntropyEstimation/libs/EntropyEstimation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'xcms', 'MSnbase'
Package suggested but not available for checking: ‘RStoolbox’
Documented arguments not in \usage in Rd file 'div_plot.Rd':
  ‘plot_cols’

Documented arguments not in \usage in Rd file 'seq_plot.Rd':
  ‘plot_cols’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Auto-generated content requiring editing in Rd file 'EnviroPRA-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
Found export directives that require package ‘methods’:
  ‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Note: found 1 marked Latin-1 string
  Note: found 1508 marked UTF-8 strings
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘epidict’
Documented arguments not in \usage in Rd file 'dots_to_charlist.Rd':
  ‘call’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
S3 methods shown with full name in Rd file 'addDrug.Lexis.Rd':
  ‘addDrug.Lexis’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘episcan_1geno_cc.txt’ ‘episcan_1geno_quant.txt’
  ‘episcan_2geno_cc.txt’ ‘episcan_2geno_quant.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘knitr’ ‘plyr’ ‘tidyverse’ ‘xml2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xts’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 15 marked UTF-8 strings
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'equateMultiple-package.Rd':
  ‘EquateMultiple-package’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
File ‘equivalence/libs/equivalence.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'subnetwork_templates.Rd':
  ‘nams.vattr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
S3 methods shown with full name in Rd file 'summary.error_interval.Rd':
  ‘summary.error_interval’

S3 methods shown with full name in Rd file 'summary.measure.Rd':
  ‘summary.measure’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'esaBcv_package.Rd':
  ‘esaBcv_package-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'ETAS-internal.Rd':
  ‘Smooth.catalog’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Documented arguments not in \usage in Rd file 'poly_clip.Rd':
  ‘x’ ‘y’

Documented arguments not in \usage in Rd file 'setup_gpar.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'setup_grobs.Rd':
  ‘centers’

Documented arguments not in \usage in Rd file 'update_list.Rd':
  ‘x’ ‘val’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 1350 marked UTF-8 strings
Note: found 1054 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘forcats’ ‘rqPen’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘curl’ ‘scales’ ‘stringr’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'doHttrRequest.Rd':
  ‘params’ ‘customConfig’

Documented arguments not in \usage in Rd file 'errorMessage.Rd':
  ‘test_me’

Documented arguments not in \usage in Rd file 'isError.Rd':
  ‘test_me’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘sample .nwk’
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'borrOrderingInternal.Rd':
  ‘n.cntrl’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘ExactData’
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 342 marked UTF-8 strings
Unknown package ‘iptools’ in Rd xrefs
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘exif/libs/exif.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  error.c:45:23: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/ExomeDepth.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cec2013’
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
Argument items with no description in Rd file 'plot.expectreg.Rd':
  ‘\dots’
Argument items with no description in Rd file 'update.expectreg.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘ggpmisc’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
Argument items with no description in Rd file 'fbvpot.Rd':
  ‘cutoff’
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Documented arguments not in \usage in Rd file 'getQQLimit.Rd':
  ‘N’ ‘rho’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘extremis/libs/extremis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘exuberdata’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'complete.log.likelihood_Sj.Rd':
  ‘z’
Auto-generated content requiring editing in Rd file 'getStuffForDIC.Rd':
  \details: ‘If necessary, more details than the description above’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'procrustes_switching.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_exact.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_full_sa.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_partial_sa.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'weighted_procrustes_switching.Rd':
  \details: ‘If necessary, more details than the description above.’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘base’ ‘data.table’
  All declared Imports should be used.
Note: found 55 marked UTF-8 strings
File ‘falcon/libs/falcon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'dot-get_default_sign_size.Rd':
  ‘outcome_type’

Documented arguments not in \usage in Rd file 'dot-get_iteration_data.Rd':
  ‘file_dir’

Documented arguments not in \usage in Rd file 'extract_model_vimp.Rd':
  ‘feature_similarity_table’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ezprof.c:55:38: warning: format '%f' expects argument of type 'double', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
  ezprof.c:57:38: warning: format '%f' expects argument of type 'double', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/fanc.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'cache.Rd':
  ‘data’ ‘reset’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 179 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1430 marked UTF-8 strings
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘FastBandChol/libs/FastBandChol.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
File ‘fastcmh/libs/fastcmh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'kkk.Rd':
  ‘Vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
File ‘fastdigest/libs/fastdigest.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'Get_C_R_K_Q.Rd':
  ‘have_noise’

Documented arguments not in \usage in Rd file 'Sample_KF_post.Rd':
  ‘C0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘FastGP/libs/FastGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘coxKM’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
Rd files without \alias:
  ‘FastPCS-package.Rd’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Invalid package aliases in Rd file 'FastRCS-package.Rd':
  ‘FastPCS-package’
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
File ‘FastRWeb/libs/null.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'bin.Rd':
  ‘Integer’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘NNLM’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘collapse’ ‘data.table’ ‘kit’ ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
Unexported object imported by a ':::' call: ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  Density_Estimation/Source/../../Skeletons/Include/../../Density_Estimation/Include/Data_Problem_imp.h:174:24: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<Point<2>, std::allocator<Point<2> > >::size_type' {aka 'long unsigned int'} [-Wformat=]
  Density_Estimation/Source/../../Skeletons/Include/../../Density_Estimation/Include/Data_Problem_imp.h:174:24: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<Point<3>, std::allocator<Point<3> > >::size_type' {aka 'long unsigned int'} [-Wformat=]
  FPCA/Source/Mixed_FE_FPCA.cpp:290:251: warning: format '%d' expects argument of type 'int', but argument 2 has type '__gnu_cxx::__alloc_traits<std::allocator<double>, double>::value_type' {aka 'double'} [-Wformat=]
  Inference/Source/Inference_Data.cpp:271:21: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
  C_Libraries/triangle.c:1426:9: warning: too many arguments for format [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-devel/fdaPDE.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘FastGP’ ‘MASS’ ‘fdapace’
  All declared Imports should be used.
Argument items with no description in Rd file 'getbasispenalty.Rd':
  ‘Lfdobj’
Note: found 76 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘FD/libs/FD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘vert.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.txt’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘e1071’ ‘lattice’ ‘randomForest’ ‘tibble’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 20 marked UTF-8 strings
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
File ‘fechner/libs/fechner.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘panelView’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New Stuff
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 43825 marked UTF-8 strings
Note: found 134 marked UTF-8 strings
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'checkStream.Rd':
  ‘skipChecks’

Documented arguments not in \usage in Rd file 'cpp_detectCUSUMMeanSinglePrechange.Rd':
  ‘BL’

Documented arguments not in \usage in Rd file 'cpp_detectEWMAMeanSinglePrechange.Rd':
  ‘BL’

Documented arguments not in \usage in Rd file 'makeStreamMeanChangeR.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'update_Omega.Rd':
  ‘m_new’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  fftw.c:112:34: warning: format '%x' expects argument of type 'unsigned int', but argument 2 has type 'double (*)[2]' [-Wformat=]
  fftw.c:113:34: warning: format '%x' expects argument of type 'unsigned int', but argument 2 has type 'double (*)[2]' [-Wformat=]
  fftw.c:114:34: warning: format '%x' expects argument of type 'unsigned int', but argument 2 has type 'fftw_plan' {aka 'struct fftw_plan_s *'} [-Wformat=]
  fftw.c:115:34: warning: format '%x' expects argument of type 'unsigned int', but argument 2 has type 'fftw_plan' {aka 'struct fftw_plan_s *'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/fftw.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'recode_subquad.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MicrobeDS’
Invalid package aliases in Rd file 'filename.Rd':
  ‘filename-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 222 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘diveRsity’
Unknown package ‘diveRsity’ in Rd xrefs
Found the following files/directories:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Found the following significant warnings:
  finite_moment_test.cpp:412:22: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/finity.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 7 marked UTF-8 strings
Specified C++11: please drop specification unless essential
File ‘fishMod/libs/fishMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'plot_data_type.Rd':
  ‘client_id’ ‘client_secret’ ‘refresh_token’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'nCDunnett', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Note: found 584 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
File ‘flashClust/libs/flashClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) cclust.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) randIndex.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:28: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘flock/libs/flock.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 3549 marked UTF-8 strings
Packages suggested but not available for checking: 'gpls', 'vbmp'
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  FLSAGeneral.cc:248:66: warning: format '%d' expects argument of type 'int', but argument 5 has type 'std::set<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
  FLSAGeneral.cc:248:70: warning: format '%d' expects argument of type 'int', but argument 6 has type 'std::set<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
  FLSAGeneral.cc:280:63: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=]
  FLSAGeneral.cc:369:62: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::set<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
  FLSAGeneral.cc:369:65: warning: format '%d' expects argument of type 'int', but argument 5 has type 'std::set<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
  MaxFlowGraph.cc:560:43: warning: format '%d' expects argument of type 'int', but argument 2 has type '__gnu_cxx::__normal_iterator<std::vector<MaxFlowEdge>*, std::vector<std::vector<MaxFlowEdge> > >::difference_type' {aka 'long int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/flsa.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘flux.CH4.txt’
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'hl.factor.number.Rd':
  ‘w’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  ANN.cpp:173:23: warning: too many arguments for format [-Wformat-extra-args]
  ANN.cpp:181:26: warning: too many arguments for format [-Wformat-extra-args]
  KNN_cover_tree.cpp:103:18: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wformat=]
  KNN_cover_tree.cpp:156:18: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<Id_dist>::size_type' {aka 'long unsigned int'} [-Wformat=]
  KNN_cover_tree.cpp:221:20: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<Id_dist>::size_type' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/FNN.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 446 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 234 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 31 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘LaplacesDemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
File ‘fpow/libs/fpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘fractional/libs/fractional.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'assert.surface.Rd':
  ‘surf’

Documented arguments not in \usage in Rd file 'check.dtype.for.data.Rd':
  ‘silent’

Documented arguments not in \usage in Rd file 'fread3.Rd':
  ‘filehandle:’

Documented arguments not in \usage in Rd file 'fwrite3.Rd':
  ‘filehandle:’ ‘data:’

Documented arguments not in \usage in Rd file 'polygon.soup.to.indexed.mesh.Rd':
  ‘face_vertex_coords’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'freqdom.transpose.Rd':
  ‘S’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 50 marked UTF-8 strings
Package suggested but not available for checking: ‘dggrids’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'draw.colorbar.Rd':
  ‘coloredmesh’

Documented arguments not in \usage in Rd file 'extend_neighbors.Rd':
  ‘min_dotp_threshold’

Documented arguments not in \usage in Rd file 'surf.sphere.spatialfilter.Rd':
  ‘gaussian_weight’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Argument items with no description in Rd file 'fsdam.Rd':
  ‘verbose’ ‘which’
Argument items with no description in Rd file 'plot.classes.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.fsim.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.sfpl.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.sfplsim.FASSMR.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.summary.mfplsim.Rd':
  ‘\dots’
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'imp_small_gaps_WMA.Rd':
  ‘Data’ ‘univariate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 39 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Note: found 7921 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Objects in \usage without \alias in Rd file 'funData-constructor.Rd':
  ‘funData’

Objects in \usage without \alias in Rd file 'irregFunData-constructor.Rd':
  ‘irregFunData’

Objects in \usage without \alias in Rd file 'multiFunData-constructor.Rd':
  ‘multiFunData’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'plot.funData.Rd':
  ‘plot.funData’

S3 methods shown with full name in Rd file 'plot.irregFunData.Rd':
  ‘plot.irregFunData’

S3 methods shown with full name in Rd file 'plot.multiFunData.Rd':
  ‘plot.multiFunData’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 120 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 36 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'build_limits_lookup.Rd':
  ‘min_preds’ ‘max_preds’ ‘min_ratio’ ‘max_ratio’ ‘draw_unadjusted’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
Documented arguments not in \usage in Rd file 'loggedOutput.Rd':
  ‘future’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘futureheatwaves/libs/futureheatwaves.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'mandelbrot.Rd':
  ‘Z’ ‘xmid’ ‘ymid’ ‘side’ ‘resolution’ ‘maxIter’ ‘tau’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'GAabbreviate-internal.Rd':
  ‘GAabbreviation-package’
File ‘gafit/libs/gafit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘gargle’ ‘getProxy’ ‘rappsflyer’ ‘rfacebookstat’ ‘rgoogleads’
  ‘rmytarget’ ‘rvkstat’ ‘ryandexdirect’ ‘rym’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘webshot’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'splitQTL_comment.Rd':
  ‘output_qtls’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
Invalid package aliases in Rd file 'gamlss.mx.package.Rd':
  ‘gamlss.mix-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
Documented arguments not in \usage in Rd file 'as.gapdata.Rd':
  ‘labels_df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++14: please drop specification unless essential
':::' call which should be '::': ‘graphics:::grid’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'lrr_plot.Rd':
  ‘plot_cols’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
Found the following significant warnings:
  node_categorical.cpp:42:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_categorical.cpp:45:19: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_categorical.cpp:52:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_categorical.cpp:55:19: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_continuous.cpp:37:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_continuous.cpp:43:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/gbm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘gbp/libs/gbp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'align_peaks.Rd':
  ‘gc_peak_df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘gputools’
Package suggested but not available for checking: ‘paleofire’
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘GCPM/libs/GCPM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
File ‘GEEaSPU/libs/GEEaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Objects in \usage without \alias in Rd file 'geepack-internal.Rd':
  ‘genZcor’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
File ‘gelnet/libs/gelnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Auto-generated content requiring editing in Rd file 'gemlog-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Invalid package aliases in Rd file 'GenBinom-package.Rd':
  ‘GenbinomApps-package’
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘genderdata’
Documented arguments not in \usage in Rd file 'CirDisp.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'CirKurt.Rd':
  ‘x’ ‘na.rm’

Documented arguments not in \usage in Rd file 'CirSD.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'CirSkew.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'CirVar.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'MeanDir.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'impact.Rd':
  ‘na.rm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'expand.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'grapes-bq-grapes.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'grapes-bt-grapes.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'stftcalc.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘R.utils’ ‘markdown’
  All declared Imports should be used.
Package suggested but not available for checking: ‘maptools’
Package suggested but not available for checking: ‘rrvgo’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'generalizedwendland-internal.Rd':
  ‘numint.abstol (default: 1e-3)’ ‘numint.reltol (default: 1e-3)’
  ‘numint.qag_key (default: 0)’ ‘numint.subintervals (default: 0)’
  ‘interp.method (default: 'none')’ ‘interp.num_support (default: 0)’
  ‘cov.reparameterize (default: TRUE)’ ‘cov.eps (default:
  .Machine$double.eps^0.5)’ ‘cov.d_value (default: 2)’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
  ‘reshape2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'GenlibR-package.Rd':
  ‘GenlibR-package’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Note: found 58 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 80 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 646 marked UTF-8 strings
Note: found 87001 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'variables_query-method.Rd':
  ‘variables’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘RandomFields’
Unknown package ‘RandomFields’ in Rd xrefs
Note: found 4 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Note: found 64 marked Latin-1 strings
  Note: found 25 marked UTF-8 strings
Package suggested but not available for checking: ‘rgdal’
Namespaces in Imports field not imported from:
  ‘DT’ ‘GWmodel’ ‘beepr’ ‘cartography’ ‘dplyr’ ‘raster’ ‘readxl’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinyjs’ ‘sp’
  ‘spdep’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pipeR’ ‘rlang’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RGtk2’
Namespaces in Imports field not imported from:
  ‘googlesheets4’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘gfpop.data’
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'attract_by_distance.Rd':
  ‘prop_start’ ‘prop_end’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'labels.rpart.Rd':
  ‘pretty:’

Documented arguments not in \usage in Rd file 'rpart_labels.Rd':
  ‘model’ ‘...’

Documented arguments not in \usage in Rd file 'rpart_segments.Rd':
  ‘model’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'interpolateDataFrame.Rd':
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': ‘scales:::censor’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘productplots:::bound’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
Argument items with no description in Rd file 'isADMG.Rd':
  ‘amat’
Argument items with no description in Rd file 'isAG.Rd':
  ‘amat’
Namespaces in Imports field not imported from:
  ‘sna’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Invalid package aliases in Rd file 'package-ggparallel.Rd':
  ‘package-ggparallel-package’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lixoftConnectors’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'operator.Rd':
  ‘x’ ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 35 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘RPostgres’ ‘colourpicker’ ‘dplyr’
  ‘ggpmisc’ ‘ggpubr’ ‘ggrepel’ ‘gridExtra’ ‘markdown’ ‘plotly’
  ‘quantreg’ ‘rlang’ ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘survival’
  ‘survminer’ ‘table1’ ‘tidyr’ ‘zoo’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 6242 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘nomogramFormula’ ‘survival’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘utils’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'ggplot_gtable.Rd':
  ‘plot’

Documented arguments not in \usage in Rd file 'undocumented.Rd':
  ‘latex’ ‘ggplot’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 138 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
Documented arguments not in \usage in Rd file 'add_scale.Rd':
  ‘domain’

Documented arguments not in \usage in Rd file 'bin_vector.Rd':
  ‘width’ ‘origin’ ‘closed’ ‘pad’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 208 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘class’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
Note: found 553 marked UTF-8 strings
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Unknown package ‘IC2’ in Rd xrefs
Specified C++11: please drop specification unless essential
File ‘GiRaF/libs/GiRaF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1178 marked UTF-8 strings
Note: found 866 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MCMCpack’ ‘ggplot2’ ‘moments’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mlr3proba’
Argument items with no description in Rd file 'GLD.lm.full.surv.Rd':
  ‘maxit’
Argument items with no description in Rd file 'GLD.lm.surv.Rd':
  ‘maxit’
Documented arguments not in \usage in Rd file 'getBeta.Rd':
  ‘thetaConrol’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘gllm/libs/gllm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GLMaSPU/libs/GLMaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ordinal’
  All declared Imports should be used.
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘AER’ ‘MASS’ ‘Matrix’ ‘censReg’ ‘effects’ ‘foreign’ ‘lme4’ ‘lmtest’
  ‘nnet’ ‘pBrackets’ ‘plm’ ‘pscl’ ‘sandwich’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'glmpathcr-internal.Rd':
  ‘fit’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
File ‘globalOptTests/libs/globalOptTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rnaturalearthdata’
  All declared Imports should be used.
Note: found 1191 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'fun.svd_1.Rd':
  ‘X’

Documented arguments not in \usage in Rd file 'fun.svd_2.Rd':
  ‘X’

Documented arguments not in \usage in Rd file 'fun.svd_3.Rd':
  ‘X’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 2629 marked UTF-8 strings
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 1352 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘goodpractice-package.Rd’
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘ganalytics’
Documented arguments not in \usage in Rd file 'doHttrRequest.Rd':
  ‘session’ ‘params’

Documented arguments not in \usage in Rd file 'get_google_token.Rd':
  ‘shiny_return_token’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘future’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Documented arguments not in \usage in Rd file 'estimate_noise_nn.Rd':
  ‘n_thread’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
Package suggested but not available for checking: ‘maptools’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘gplm/libs/gplm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Note: found 5030 marked UTF-8 strings
Package suggested but not available for checking: ‘monocle’
Package unavailable to check Rd xrefs: ‘monocle’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘PairedData’ ‘RColorBrewer’ ‘agricolae’ ‘corrplot’ ‘desplot’
  ‘dplyr’ ‘ggplot2’ ‘ggpubr’ ‘gridGraphics’ ‘gtools’ ‘kableExtra’
  ‘knitr’ ‘magrittr’ ‘pastecs’ ‘reshape2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘summarytools’
  All declared Imports should be used.
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'HistPCA.Rd':
  ‘ggplot’
Specified C++11: please drop specification unless essential
Note: found 14768 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 989 marked UTF-8 strings
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'prCaSetRownames.Rd':
  ‘rownames.fn’

Documented arguments not in \usage in Rd file 'prClearPCAclass.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
S3 methods shown with full name in Rd file 'groc.fit.Rd':
  ‘groc.fit’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘rjags’
  All declared Imports should be used.
File ‘grove/libs/grove.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'fit_grp.Rd':
  ‘grplasso-package’
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
File ‘grr/libs/grr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
Objects in \usage without \alias in Rd file 'GSA.internal.Rd':
  ‘est.s0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file 'gsb-package.Rd':
  ‘gsb-package’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
File ‘gsmoothr/libs/gsmoothr.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 146 marked UTF-8 strings
Note: found 269 marked UTF-8 strings
Note: found 42384 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RRprof.out’
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
Note: found 20255 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘GWASExactHW/libs/GWASExactHW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 275 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘attempt’ ‘corpcor’ ‘glue’ ‘htmltools’ ‘pkgload’ ‘processx’
  ‘tools’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rgeos’
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘gsubfn’ ‘stringr’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.ga.breed’ ‘.ga.fitness’ ‘.ga.init’ ‘.ga.mutate’ ‘.ga.step’
  ‘.ga.weight’
Note: found 7592 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'modeling-package.Rd':
  ‘modeling-package’
checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) HWClrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
File ‘hawkes/libs/hawkes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Note: found 3 marked UTF-8 strings
Note: found 104392 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  datatype_export.c:67:13: warning: ISO C does not support the 'I' printf flag [-Wformat=]
  datatype_export.c:67:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'hid_t' {aka 'long int'} [-Wformat=]
  convert.c:261:63: warning: format '%d' expects argument of type 'int', but argument 2 has type 'R_xlen_t' {aka 'long int'} [-Wformat=]
  convert.c:261:76: warning: format '%d' expects argument of type 'int', but argument 3 has type 'R_xlen_t' {aka 'long int'} [-Wformat=]
  Wrapper_manual_H5T.c:76:57: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/hdf5r.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
Documented arguments not in \usage in Rd file 'check_arg_for_hyperslab_func.Rd':
  ‘cur_arg’

Documented arguments not in \usage in Rd file 'extract_dim.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘HDGLM/libs/HDGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘ggjoy’ ‘isotone’ ‘png’ ‘questionr’ ‘rprojroot’
  ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘TidyDensity’ ‘healthyR’ ‘healthyR.ai’ ‘healthyR.data’ ‘healthyR.ts’
  ‘tidyAML’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'compute_counts.Rd':
  ‘init’ ‘inflow’

Documented arguments not in \usage in Rd file 'compute_values.Rd':
  ‘counts’

Documented arguments not in \usage in Rd file 'create_demographic_table.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'eval_strategy_newdata.Rd':
  ‘model’

Documented arguments not in \usage in Rd file 'get_state_value_names.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  MHproposal.c:24:49: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  MHproposal.c:37:54: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  changestats.c:1465:38: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  changestats.c:1517:34: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  h_ergm.c:1910:84: warning: format '%i' expects a matching 'int' argument [-Wformat=]
  model.c:57:58: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  model.c:68:58: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/hergm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'check.Rd':
  ‘inner_class’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'check_known_repos.Rd':
  ‘known_packages’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Found the following significant warnings:
  rcpp_internals.cpp:65:34: warning: format '%d' expects argument of type 'int', but argument 2 has type 'Rcpp::traits::storage_type<14>::type' {aka 'double'} [-Wformat=]
  rcpp_internals.cpp:65:55: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Rcpp::traits::storage_type<14>::type' {aka 'double'} [-Wformat=]
  rcpp_internals.cpp:65:80: warning: format '%d' expects argument of type 'int', but argument 4 has type 'Rcpp::traits::storage_type<14>::type' {aka 'double'} [-Wformat=]
  rcpp_internals.cpp:65:100: warning: format '%d' expects argument of type 'int', but argument 5 has type 'Rcpp::traits::storage_type<14>::type' {aka 'double'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/HHG.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'HH-defunct.Rd':
  ‘anova.mean’ ‘print.glht.mmc.multicomp’ ‘coef.arima.HH’ ‘glht.mmc’
  ‘plot.odds.ratio’ ‘persp.plane’ ‘persp.floor’ ‘persp.back.wall.x’
  ‘persp.back.wall.y’ ‘persp.setup’ ‘plot.hov’ ‘plot.hov.bf’
  ‘plot.matchMMC’ ‘seqplot.forecast’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'residual.plots.lattice.Rd':
  ‘X’
File ‘HiCseg/libs/HiCseg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found export directives that require package ‘methods’:
  ‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
File ‘HiDimDA/libs/HiDimDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RiskPortfolios’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'qcplate.Rd':
  ‘dat’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘colorfulVennPlot’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'HistDAWass-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
Invalid package aliases in Rd file 'histogram-package.Rd':
  ‘histogramtools-package’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
Package which this enhances but not available for checking: ‘HadoopStreaming’
Note: found 9638 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
html_describe_con: multiple local function definitions for ‘g’ with
  different formal arguments
Documented arguments not in \usage in Rd file 'bootstrapfun.Rd':
  ‘DoF’ ‘n_sample’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
Auto-generated content requiring editing in Rd file 'HMVD-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Invalid package aliases in Rd file 'hoardeR-package.Rd':
  ‘R/hoardeR-package’
Argument items with no description in Rd file 'bid2.Rd':
  ‘numattable1’ ‘playerseats1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’ ‘round1’
  ‘ntable1’ ‘decision1’
Argument items with no description in Rd file 'calcwin1.Rd':
  ‘numattable1’ ‘playerseats1’ ‘b3’ ‘b7’
Argument items with no description in Rd file 'mycount1.Rd':
  ‘x’
Argument items with no description in Rd file 'mygraphics1.Rd':
  ‘numattable1’ ‘playerseats1’ ‘chips1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’
  ‘b5’ ‘b6’ ‘b7’ ‘chips2’ ‘ntable1’ ‘myfast1’ ‘chipstart1’ ‘name1’
  ‘lowercut1’
Argument items with no description in Rd file 'nothing1.Rd':
  ‘x’
Argument items with no description in Rd file 'onepair1.Rd':
  ‘x’
Argument items with no description in Rd file 'straight1.Rd':
  ‘x’
Argument items with no description in Rd file 'straightdraw1.Rd':
  ‘x’
Argument items with no description in Rd file 'strflsh1.Rd':
  ‘x’ ‘y’
Argument items with no description in Rd file 'trip1.Rd':
  ‘x’
Argument items with no description in Rd file 'twopair1.Rd':
  ‘x’
Argument items with no description in Rd file 'writebets1.Rd':
  ‘b9’ ‘y1’ ‘numattable1’ ‘b3’ ‘playerseats1’ ‘chips1’ ‘chips2’ ‘over1’
  ‘myfast1’ ‘name1’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'plot.hopitCP.Rd':
  ‘plotf’

Documented arguments not in \usage in Rd file 'sigma.hopit.Rd':
  ‘model’

Documented arguments not in \usage in Rd file 'summary.hopit.Rd':
  ‘control’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 124 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘hpoPlot-package.Rd’
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'dot-E3.Rd':
  ‘i’ ‘M’

Documented arguments not in \usage in Rd file 'dot-E4.Rd':
  ‘i’ ‘M’

Documented arguments not in \usage in Rd file 'hrm.0w.2s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.0w.3s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.0w.4s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.0w.5s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.1f.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.1w.0f.Rd':
  ‘factor1’

Documented arguments not in \usage in Rd file 'hrm.2w.2f.Rd':
  ‘factor’

Documented arguments not in \usage in Rd file 'hrm.mv.1w.1f.Rd':
  ‘H’ ‘text’

Documented arguments not in \usage in Rd file 'hrm.mv.internal.Rd':
  ‘alpha’ ‘H’ ‘text’

Documented arguments not in \usage in Rd file 'hrm.test.1.none.Rd':
  ‘factor1’ ‘factor2’

Documented arguments not in \usage in Rd file 'hrm.test.1.one.Rd':
  ‘group’ ‘factor2’

Documented arguments not in \usage in Rd file 'hrm.test.2.one.Rd':
  ‘factor2’

Documented arguments not in \usage in Rd file 'hrm.test.2.two.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.test.3.three.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.test.4.four.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.test.5.five.Rd':
  ‘group’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘quantreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'imageplot.Rd':
  ‘\dots’
File ‘hsphase/libs/hsphase.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'FramedHTML.Rd':
  ‘DiagnosticsPath’
Namespaces in Imports field not imported from:
  ‘recipes’ ‘tune’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'as-redactor.Rd':
  ‘expr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘humaniformat/libs/humaniformat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘xml2’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘microViz’
Invalid package aliases in Rd file 'HydroMe-package.Rd':
  ‘HydroMe2-package’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'flowCore', 'rgeos'
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
Documented arguments not in \usage in Rd file 'read.txt.Witec.Rd':
  ‘nwl’ ‘remove.zerospc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 38558 marked UTF-8 strings
Note: found 1058038 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
Note: found 359 marked UTF-8 strings
Objects in \usage without \alias in Rd file 'btibgen.Rd':
  ‘ibdgen’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'pairSum.Rd':
  ‘cov1’ ‘cov2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘ibmcraftr/libs/ibmcraftr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘SparkR’
Specified C++11: please drop specification unless essential
File ‘ibm/libs/ibm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'GetCustomKmerCounts.Rd':
  ‘custom.range’

Documented arguments not in \usage in Rd file 'GetMutationLoadsFromStrelkaIDVCFs.Rd':
  ‘list.of.vcfs’

Documented arguments not in \usage in Rd file 'GetMutationLoadsFromStrelkaSBSVCFs.Rd':
  ‘split.vcfs’

Documented arguments not in \usage in Rd file 'PlotPPM.Rd':
  ‘pwm’

Documented arguments not in \usage in Rd file 'PlotPPMToPdf.Rd':
  ‘list.of.pwm’

Documented arguments not in \usage in Rd file 'ReadStrelkaSBSVCF.Rd':
  ‘suppress.discarded.variants.warnings’

Documented arguments not in \usage in Rd file 'ReadVCF.Rd':
  ‘num.of.cores’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 356712 marked UTF-8 strings
Package suggested but not available for checking: ‘icd’
Note: found 55 marked UTF-8 strings
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Found the following significant warnings:
  icenReg_files/basicUtilities.cpp:589:69: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/icenReg.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Namespaces in Imports field not imported from:
  ‘digest’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 10 marked UTF-8 strings
Found the following files/directories:
  ‘Crashpad’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'pkg-internal.Rd':
  ‘iplotMain’ ‘segments.circle’ ‘griddat’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'pkg-internal.Rd':
  ‘plot.page’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
File ‘ieeeround/libs/ieeeround.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 366 marked UTF-8 strings
Note: found 40 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘IFCdata’
File ‘IFP/libs/IFP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'dot-compl.Rd':
  ‘imgfile’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'image-package.Rd':
  ‘image-package’
Specified C++11: please drop specification unless essential
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
Documented arguments not in \usage in Rd file 'new_impactr_peaks.Rd':
  ‘acc_signal:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘haven’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pscl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘imputeYn-package.Rd’
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 151 marked UTF-8 strings
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘gurobi’
File ‘infotheo/libs/infotheo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
'LazyData' is specified without a 'data' directory
File ‘INLAspacetime/libs/INLAspacetime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
File ‘INSPIRE/libs/INSPIRE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘pkgbuild’
Package suggested but not available for checking: ‘cmdstanr’
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘splines2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘readxl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'IntervalSurgeon-package.Rd':
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'selectRuleRRF.Rd':
  ‘target’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'rawAvgCost-deprecated.Rd':
  ‘cost.transf’ ‘in.millions’ ‘confidence.interval’ ‘minimum.year’
  ‘maximum.year’ ‘final.year’ ‘incomplete.year.threshold’
  ‘incomplete.year.weights’ ‘gam.k’ ‘mars.nprune’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 12106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fdrtool’ ‘nimble’
  All declared Imports should be used.
Package suggested but not available for checking: ‘surveyspec’
Note: found 102 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'chars_collapse.Rd':
  ‘collapse’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’
File ‘iotools/libs/iotools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gmodels’ ‘lmtest’ ‘testthat’ ‘tidyverse’ ‘zoo’
  All declared Imports should be used.
Note: found 46 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  templates/Rip-bsearch-template.c:889:18: warning: too many arguments for format [-Wformat-extra-args]
  Rip-match.c:467:13: warning: too many arguments for format [-Wformat-extra-args]
  Rip-match.c:1125:15: warning: too many arguments for format [-Wformat-extra-args]
  Rip-match.c:1173:13: warning: too many arguments for format [-Wformat-extra-args]
  Rip-match.c:1407:15: warning: too many arguments for format [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-devel/IP.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
Invalid package aliases in Rd file 'iprior_package.Rd':
  ‘iprior_package-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
Argument items with no description in Rd file 'mrbayes.Rd':
  ‘unlink’ ‘constraint’
Argument items with no description in Rd file 'mrbayes.lset.Rd':
  ‘partition’
Argument items with no description in Rd file 'multistate.Rd':
  ‘model’
File ‘iRafNet/libs/iRafNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘glmnet’
  All declared Imports should be used.
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'print.cat_output.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'sub-subset-Itempool-numeric-missing-method.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'sub-subset-Response_set-numeric-missing-method.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'sub-subset-Testlet-numeric-missing-method.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'print.Item.Rd':
  ‘print.Item’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 117 marked UTF-8 strings
Package suggested but not available for checking: ‘xcms’
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
Note: found 104 marked UTF-8 strings
File ‘isingLenzMC/libs/isingLenzMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Objects in \usage without \alias in Rd file 'islasso-internal.Rd':
  ‘modelX’ ‘.checkinput’ ‘.startpoint’ ‘.islasso’
  ‘checkinput.islasso.path’ ‘startpoint.islasso.path’
  ‘islasso.path.fit.glm’ ‘islasso.path.fitter2’ ‘interpolate’ ‘makeHyp’
  ‘printHyp’ ‘cislasso’ ‘ci.fitted.islasso’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'dot-assignmentMaker.Rd':
  ‘.precip_raster’ ‘.precip_SD_raster’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 7542 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 87 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Found the following files/directories:
  ‘RMTplot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Note: found 58 marked UTF-8 strings
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Invalid package aliases in Rd file 'ivprobit-package.Rd':
  ‘ivProbit-package’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Rd files without \alias:
  ‘jackknifeKME-package.Rd’
Namespaces in Imports field not imported from:
  ‘fBasics’ ‘reshape’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Note: found 2261 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 1984 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘mcmcplots’ ‘tidyverse’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘GA’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ids’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Note: found 87 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 16726 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘dplyr’ ‘emmeans’ ‘ggrepel’ ‘ggridges’ ‘lavaan’
  ‘multcomp’ ‘mvnormtest’ ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘remMap’
Documented arguments not in \usage in Rd file 'paste_coef.Rd':
  ‘parlemts’

Documented arguments not in \usage in Rd file 'paste_linpred.Rd':
  ‘parlemts’ ‘matname’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
Note: found 925830 marked UTF-8 strings
Note: found 176 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 17 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Superpower’ ‘pwr’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 111752 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘kappalab/libs/kappalab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Rd files without \alias:
  ‘karaoke-package.Rd’
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
Namespace in Imports field not imported from: ‘gifski’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘EQL’ ‘univariateML’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
prepare_Rd: NEWS.Rd:58: Dropping empty section ‘kelvin INITIAL VERSION 1.0-0 (2012-05-30)’
'LazyData' is specified without a 'data' directory
File ‘Kendall/libs/Kendall.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
File ‘KERE/libs/KERE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Argument items with no description in Rd file 'covQualNested.Rd':
  ‘covBet’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘KernSmoothIRT/libs/KernSmoothIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
S3 methods shown with full name in Rd file 'bw.abram.temp.Rd':
  ‘bw.abram.temp’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'calc_PGtheta_R.Rd':
  ‘model’ ‘iter’

Documented arguments not in \usage in Rd file 'make_wsz_cpp.Rd':
  ‘info’ ‘initialized’

Documented arguments not in \usage in Rd file 'read_dfm_cpp.Rd':
  ‘W_raw’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘Rsamtools’ ‘rtracklayer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fitdistrplus’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘kknn/libs/kknn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘rkward’
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘SnowballC’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
S3 methods shown with full name in Rd file 'unlist.constr.Rd':
  ‘unlist.constr’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘maptools’
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Killed after ’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'knotR-package.Rd':
  ‘knot-package’
Note: found 9 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘mice’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘kriging/libs/kriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
Package suggested but not available for checking: ‘FactoClass’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
File ‘labdsv/libs/labdsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Note: found 6 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘LassoNet/libs/LassoNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lassoshooting/libs/lassoshooting.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘ergm.userterms’
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package ‘ergm.userterms’ in Rd xrefs
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘akmedoids’
Unknown package ‘akmedoids’ in Rd xrefs
Objects in \usage without \alias in Rd file 'latrend-generics.Rd':
  ‘nClusters’ ‘clusterProportions’ ‘clusterTrajectories’ ‘compose’
  ‘converged’ ‘externalMetric’ ‘estimationTime’ ‘fit’
  ‘fittedTrajectories’ ‘getArgumentDefaults’ ‘getArgumentExclusions’
  ‘getLabel’ ‘getLcMethod’ ‘getName’ ‘getShortName’ ‘idVariable’
  ‘metric’ ‘plotFittedTrajectories’ ‘plotClusterTrajectories’ ‘postFit’
  ‘postprob’ ‘predictAssignments’ ‘predictForCluster’ ‘predictPostprob’
  ‘prepareData’ ‘preFit’ ‘qqPlot’ ‘responseVariable’ ‘strip’
  ‘timeVariable’ ‘trajectoryAssignments’ ‘validate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'moments2.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'skeleton.Rd':
  ‘endogeneous’ ‘...’

Documented arguments not in \usage in Rd file 'vcov2-internal.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
Packages suggested but not available for checking: 'xcms', 'MSnbase'
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘chinese.misc’ ‘dplyr’ ‘factoextra’ ‘glasso’
  ‘highcharter’ ‘htmlwidgets’ ‘ldatuning’ ‘qgraph’ ‘quanteda’ ‘rvest’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinycssloaders’
  ‘shinydashboard’ ‘shinyjs’ ‘stringr’ ‘textmineR’ ‘textplot’ ‘tidyr’
  ‘topicmodels’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'dot-choose_best_subjects.Rd':
  ‘best’ ‘candidate’

Documented arguments not in \usage in Rd file 'dot-normalize_props.Rd':
  ‘keep_all_items’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'top.topic.words.Rd':
  ‘alpha’
File ‘lda/libs/lda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘beepr’ ‘broom’ ‘chinese.misc’ ‘dplyr’ ‘highcharter’
  ‘htmlwidgets’ ‘ldatuning’ ‘parallel’ ‘plotly’ ‘purrr’ ‘quanteda’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinycssloaders’ ‘shinyjs’
  ‘stringr’ ‘textmineR’ ‘tidyr’ ‘tidytext’ ‘topicmodels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RcppProgress’ ‘rgen’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 75 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'LEANR-package.Rd':
  ‘LEAN-package’
checkRd: (-1) leaps.Rd:38: Escaped LaTeX specials: \&
File ‘leaps/libs/leaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 78 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Invalid package aliases in Rd file 'learnn.Rd':
  ‘learnn-package’
Documented arguments not in \usage in Rd file 'backward_step.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in Rd file 'backward_step_IM.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in Rd file 'forward_step.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in Rd file 'forward_step_IM.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘maptools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_generic.Rd':
  ‘mismatch’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 3 marked UTF-8 strings
Found the following significant warnings:
  utils.c:34:68: warning: format '%d' expects argument of type 'int', but argument 3 has type 'mybigint_t' {aka 'long int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/lfe.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
File ‘lgarch/libs/lgarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Note: found 22 marked UTF-8 strings
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) LIMEcoli.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) Read.Rd:88: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:92: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:98: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:104: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:105: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:106: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:107: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:108: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:109: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:110: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:111: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:112: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:114: Escaped LaTeX specials: \# \#
Specified C++11: please drop specification unless essential
S3 methods shown with full name in Rd file 'BIC.threshold.Rd':
  ‘BIC.threshold’

S3 methods shown with full name in Rd file 'BIC.threshold.ggm.Rd':
  ‘BIC.threshold.ggm’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘linERR/libs/linERR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 60714 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'MassAcylCer.Rd':
  ‘glccer’

Documented arguments not in \usage in Rd file 'MassPEo.Rd':
  ‘PEp’

Documented arguments not in \usage in Rd file 'findMS2precursor.Rd':
  ‘minint’ ‘maxint’

Documented arguments not in \usage in Rd file 'joinAnnotationResults.Rd':
  ‘simplifyAnnotation’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_variable.Rd':
  ‘x’ ‘name’ ‘mustExist’ ‘create’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  combine.c:664:43: warning: format '%g' expects argument of type 'double', but argument 2 has type 'int' [-Wformat=]
  combine.c:664:15: warning: too many arguments for format [-Wformat-extra-args]
  subroutines.c:57:15: warning: too many arguments for format [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-devel/list.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
'LazyData' is specified without a 'data' directory
Note: found 888 marked UTF-8 strings
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
File ‘ljr/libs/ljr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘agridat’ ‘ggplot2’ ‘maps’ ‘sf’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
File ‘lmPerm/libs/lmPerm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tTestTable.rda’
Note: found 1 marked UTF-8 string
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘base’ ‘qpdf’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) SPSloess.Rd:71: Escaped LaTeX specials: \^ \^
File ‘localgauss/libs/localgauss.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) ACS.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) EmployedACS.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSale.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCA.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCanton.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleNY.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:24: Escaped LaTeX specials: \$
checkRd: (-1) SalaryGender.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) SandP500.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts2.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) TrafficFlow.Rd:18: Escaped LaTeX specials: \#
Invalid package aliases in Rd file 'Lock5Data-package.Rd':
  ‘Lock5Data-package’
Namespace in Imports field not imported from: ‘lestat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’
Note: skipping ‘locuszoomr.Rmd’ due to unavailable dependencies:
  'EnsDb.Hsapiens.v75'
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'spec.emb.Rd':
  ‘A’
File ‘loe/libs/loe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 12 marked UTF-8 strings
File ‘logisticPCA/libs/logisticPCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'dlogitnorm.Rd':
  ‘sigma’
Argument items with no description in Rd file 'invlogit.Rd':
  ‘q’ ‘\dots’
Argument items with no description in Rd file 'logit.Rd':
  ‘p’ ‘\dots’
Argument items with no description in Rd file 'plogitnorm.Rd':
  ‘sigma’ ‘\dots’
Argument items with no description in Rd file 'qlogitnorm.Rd':
  ‘sigma’ ‘\dots’
Argument items with no description in Rd file 'twCoefLogitnorm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'twCoefLogitnormE.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Argument items with no description in Rd file 'levopt.Rd':
  ‘x’ ‘alpha’ ‘fmax’ ‘tm’
Argument items with no description in Rd file 'pershow.Rd':
  ‘object’
Argument items with no description in Rd file 'norpt.Rd':
  ‘alist’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.nri.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.s.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.s.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) nri.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) roc.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) roc.s.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.s.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 994 marked Latin-1 strings
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'LoopAnalyst-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'importance_sampling.array.Rd':
  ‘is_method’

Documented arguments not in \usage in Rd file 'importance_sampling.default.Rd':
  ‘is_method’

Documented arguments not in \usage in Rd file 'importance_sampling.matrix.Rd':
  ‘is_method’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
File ‘lorec/libs/lorec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'LotkasXX.Rd':
  ‘Table’
Argument items with no description in Rd file 'LotkasXY.Rd':
  ‘Table’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘lowmemtkmeans/libs/lowmemtkmeans.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'followx.Rd':
  ‘Xi’ ‘x0’ ‘h’ ‘t0’ ‘iter’ ‘way’ ‘weights’ ‘pen’ ‘phi’
  ‘lasteigenvector’ ‘rho0’ ‘boundary’ ‘convergence.at’ ‘cross’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
File ‘LRcontrast/libs/LRcontrast.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kerdiest’
Note: found 55 marked UTF-8 strings
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
Note: found 2096 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘Icens’ ‘interval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ltsa/libs/ltsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rpostgis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'setlogdata.Rd':
  ‘logdata’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘depth’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘orthogene’
Namespace in Imports field not imported from: ‘fmsb’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘orthogene’
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ngram’ ‘shinythemes’ ‘topicmodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shinythemes’ ‘topicmodels’
  All declared Imports should be used.
Note: found 134 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘rlang’ ‘torch’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 27 marked UTF-8 strings
Packages suggested but not available for checking: 'lpjmlkit', 'quitte'
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Argument items with no description in Rd file 'plot.magree.Rd':
  ‘xlab’ ‘ylab’ ‘main’ ‘\dots’
Argument items with no description in Rd file 'print.summary.magree.Rd':
  ‘x’ ‘\dots’
Argument items with no description in Rd file 'summary.magree.Rd':
  ‘object’ ‘\dots’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocCheck’
Note: found 41 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘nomnoml’
  All declared Imports should be used.
Argument items with no description in Rd file 'alignPeaks.Rd':
  ‘\dots’
Note: found 17524 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 55 marked UTF-8 strings
Note: found 3 marked UTF-8 strings
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 3058 marked UTF-8 strings
Note: found 11396 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
Note: found 25892 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘pbmcapply’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 55 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 1056 marked UTF-8 strings
Note: found 13138 marked UTF-8 strings
Note: found 1810 marked UTF-8 strings
Note: found 1 marked UTF-8 string
GNU make is a SystemRequirements.
checkRd: (-1) Interpolation-class.Rd:41: Escaped LaTeX specials: \#
checkRd: (-1) MareyMap-class.Rd:85: Escaped LaTeX specials: \_
checkRd: (-1) MareyMap-methods.Rd:11: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) MareyMap-methods.Rd:12: Escaped LaTeX specials: \_
checkRd: (-1) SpeciesMaps-methods.Rd:11: Escaped LaTeX specials: \_
checkRd: (-1) interpolation-methods.Rd:13: Escaped LaTeX specials: \_
Note: found 5210 marked UTF-8 strings
Argument items with no description in Rd file 'bias.factor.Rd':
  ‘RRud’ ‘RReu’ ‘rr’ ‘s2’
'LazyData' is specified without a 'data' directory
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'mark_my_dir.Rd':
  ‘mark_file’

Documented arguments not in \usage in Rd file 'path_type.Rd':
  ‘github_token’

Documented arguments not in \usage in Rd file 'read_assignment_yml.Rd':
  ‘path’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘marssTMB’
Objects in \usage without \alias in Rd file 'utility_functions.Rd':
  ‘fully.spec.x’ ‘marssMODEL.to.list’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'NewPackage-package.Rd':
  ‘NewPackage-package’
Auto-generated content requiring editing in Rd file 'NewPackage-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘utilities.R’
'LazyData' is specified without a 'data' directory
checkRd: (-1) maxControl.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 18 marked UTF-8 strings
Note: found 54 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘effsize’ ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 6 marked Latin-1 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
File ‘mbrglm/libs/mbrglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lars’ ‘methods’ ‘parallel’ ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'mccca-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
File ‘mcclust/libs/mcclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘mcemGLM/libs/mcemGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘boot.heterogeneity’
  All declared Imports should be used.
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
Note: found 46 marked UTF-8 strings
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  cHDPHSMMnegbin.cc:570:28: warning: too many arguments for format [-Wformat-extra-args]
  cHMMpanelRE.cc:406:16: warning: too many arguments for format [-Wformat-extra-args]
  cHMMpanelRE.cc:407:16: warning: too many arguments for format [-Wformat-extra-args]
  cHMMpanelRE.cc:408:16: warning: too many arguments for format [-Wformat-extra-args]
  cHMMpanelRE.cc:409:16: warning: too many arguments for format [-Wformat-extra-args]
  cHMMpanelRE.cc:410:16: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCoprobitChange.cc:49:13: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCpaircompare2d.cc:448:15: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCpaircompare2d.cc:449:15: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCpaircompare2d.cc:450:15: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCpaircompare2dDP.cc:765:25: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCpaircompare2dDP.cc:766:25: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCpaircompare2dDP.cc:767:25: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCprobitres.cc:147:13: warning: too many arguments for format [-Wformat-extra-args]
  cMCMCprobitres.cc:148:13: warning: too many arguments for format [-Wformat-extra-args]
  cSSVSquantreg.cc:262:24: warning: format '%f' expects argument of type 'double', but argument 2 has type 'int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/MCMCpack.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘cmdstanr’
Note: found 496 marked UTF-8 strings
Found the following significant warnings:
  nsga2.c:300:13: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  nsga2.c:300:13: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  nsga2.c:306:13: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  nsga2.c:306:13: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  nsga2.c:336:15: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  nsga2.c:336:15: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  nsga2.c:342:15: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  nsga2.c:342:15: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/mco.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'geom_cp_density.Rd':
  ‘include’

Documented arguments not in \usage in Rd file 'get_simulate.Rd':
  ‘par_trials’ ‘pars_pop’ ‘pars_varying’

Documented arguments not in \usage in Rd file 'pp_eval.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2866 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MethylCapSig’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘MediaK/libs/MediaK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘vroom’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'buildModelMatrix.Rd':
  ‘character’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: found 37 marked UTF-8 strings
Packages suggested but not available for checking: 'ropls', 'xcms'
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Invalid package aliases in Rd file 'taxa-package.Rd':
  ‘taxa-package’
Documented arguments not in \usage in Rd file 'limited_print.Rd':
  ‘trunc’

Documented arguments not in \usage in Rd file 'parse_heirarchies_to_taxonomy.Rd':
  ‘A’

Documented arguments not in \usage in Rd file 'parse_raw_heirarchies_to_taxonomy.Rd':
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘gbm’ ‘ggplot2’ ‘graphics’ ‘randomForest’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'ClusterMF-deprecated.Rd':
  ‘formula’ ‘data’ ‘vi’ ‘study’ ‘whichweights’ ‘num.trees’ ‘mtry’
  ‘method’ ‘tau2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking: 'Rcgmin', 'Rvmmin'
Unknown packages ‘Rcgmin’, ‘Rvmmin’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
Suggests orphaned package: ‘udunits2’
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmerTest’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'plot.metaplot_gtable.Rd':
  ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ade4’ ‘dendextend’ ‘ggforce’ ‘ggrepel’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Note: found 1496 marked UTF-8 strings
Note: found 3300 marked UTF-8 strings
Specified C++11: please drop specification unless essential
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Note: found 6 marked UTF-8 strings
Note: found 7 marked Latin-1 strings
  Note: found 14 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Argument items with no description in Rd file 'predict.mfp.Rd':
  ‘safe’
Namespace in Imports field not imported from: ‘fs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘boot’ ‘energy’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  matrix.c:144:17: warning: too many arguments for format [-Wformat-extra-args]
  misc.c:31:25: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/mgcv.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
File ‘MGL/libs/MGL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘reticulate’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'Rpackage-package.Rd':
  ‘Rpackage-package’
Auto-generated content requiring editing in Rd file 'Rpackage-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
File ‘mhsmm/libs/mhsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'DAPAR', 'ProteoMM'
S3 methods shown with full name in Rd file 'complete.miceadds.Rd':
  ‘complete.mids.nmi’ ‘complete.mids.1chain’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Note: found 9345 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'changeDevSettings.Rd':
  ‘defaultsSettings’

Documented arguments not in \usage in Rd file 'getResultPerScheme.Rd':
  ‘criteria’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘curl’ ‘jsonlite’ ‘parallel’ ‘tools’ ‘vctrs’
  All declared Imports should be used.
Argument items with no description in Rd file 'micSimParallel.Rd':
  ‘transitionMatrix’ ‘absStates’ ‘varInitStates’ ‘initStatesProb’
  ‘fixInitStates’ ‘maxAge’ ‘simHorizon’ ‘fertTr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'MIDASwrappeR-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Package suggested but not available for checking: ‘midfielddata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'getvol.Rd':
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  subfunc.cpp:322:20: warning: 'arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/minimaxdesign.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘gmp’ ‘jpeg’
  All declared Imports should be used.
':::' call which should be '::': ‘parallel:::detectCores’
  See the note in ?`:::` about the use of this operator.
Namespaces in Imports field not imported from:
  ‘markdown’ ‘metafor’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pracma’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
File ‘MiSPU/libs/MiSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'logAdd.Rd':
  ‘x’ ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
Argument items with no description in Rd file 'randomizationTest.Rd':
  ‘R’
checkRd: (-1) AKMCS.Rd:215: Escaped LaTeX specials: \&
checkRd: (-1) BMP.Rd:164: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:151: Escaped LaTeX specials: \&
checkRd: (-1) MP.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) MetropolisHastings.Rd:58: Escaped LaTeX specials: \&
checkRd: (-1) SubsetSimulation.Rd:152: Escaped LaTeX specials: \&
checkRd: (-1) oscillator_d6.Rd:14: Escaped LaTeX specials: \&
Packages suggested but not available for checking:
  'karyoploteR', 'regioneR'
Found the following files/directories:
  ‘par-7269706c6579’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'rigaussian.Rd':
  ‘mu’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'Sn_A.Rd':
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
File ‘mixexp/libs/mixexp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
Auto-generated content requiring editing in Rd file 'mixl-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
Specified C++11: please drop specification unless essential
checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) mixmeta.ml.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mixRasch’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ashr’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘ConfusionTableR’ ‘OddsPlotty’ ‘caret’ ‘dplyr’ ‘ggplot2’ ‘parsnip’
  ‘ranger’ ‘recipes’ ‘rsample’ ‘varhandle’ ‘workflows’
  All declared Imports should be used.
checkRd: (-1) gp.list.Rd:16: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
Namespaces in Imports field not imported from:
  ‘ClusterR’ ‘MASS’ ‘Rdpack’ ‘multiwave’ ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘randomForest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Metrics’ ‘data.table’ ‘dplyr’ ‘mlr3’ ‘mlr3learners’
  ‘mlr3measures’ ‘mlr3pipelines’ ‘patchwork’ ‘plyr’ ‘purrr’
  ‘shinyWidgets’ ‘shinyalert’ ‘shinydashboard’ ‘shinyjs’ ‘stats’
  ‘stringr’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'cpoTemplate.Rd':
  ‘affect.names’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'mlVARsim0.Rd':
  ‘nPerson’ ‘nNode’ ‘nTime’ ‘sparsity’ ‘parRange’ ‘propPositive’
  ‘diagPositive’ ‘diagIncluded’ ‘sdRange’ ‘shrinkFactor’
  ‘residualStyle’ ‘residualShared’ ‘residualSDrange’ ‘verbose’
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘DT’ ‘XML’ ‘caTools’ ‘data.table’ ‘dplyr’ ‘ggplot2’
  ‘htmltools’ ‘leaflet’ ‘lubridate’ ‘plotly’ ‘shinyjs’ ‘stringr’ ‘xts’
  ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘doParallel’ ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘magrittr’ ‘reticulate’ ‘tensorflow’ ‘usethis’
  All declared Imports should be used.
Rd files without \alias:
  ‘mnlfa-package.Rd’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'optiSel', 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
'LazyData' is specified without a 'data' directory
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 313 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 18 marked Latin-1 strings
Documented arguments not in \usage in Rd file 'check_augment_data_specification.Rd':
  ‘strict’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘parsnip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tidymodels’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 5238 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 20578 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Warning: no function found corresponding to methods exports from ‘moko’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'as.difftime.rd':
  ‘tim’ ‘format’
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 13 marked UTF-8 strings
File ‘morse/libs/morse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 56 marked UTF-8 strings
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘NlcOptim’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'create_barrier_cs.Rd':
  ‘fields’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 3 marked UTF-8 strings
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Specified C++11: please drop specification unless essential
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
Rd files without \alias:
  ‘MPLikelihoodWB-package.Rd’
Documented arguments not in \usage in Rd file 'addHeaderToSavedata.Rd':
  ‘director’

Documented arguments not in \usage in Rd file 'extractIndirect.Rd':
  ‘curFile’

Documented arguments not in \usage in Rd file 'extractIndirect_section.Rd':
  ‘curFile’

Documented arguments not in \usage in Rd file 'graphModel.Rd':
  ‘The’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘mpmi/libs/mpmi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘mp/libs/mp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'Mqrcm-internal.Rd':
  ‘check.in’ ‘check.out’ ‘start.theta’ ‘iMqr.internal’ ‘cov.theta’
  ‘iobjfun’ ‘sortH’ ‘isigma’ ‘iMqr.newton’ ‘num.fun’ ‘make.bfun’
  ‘apply_bfun’ ‘p.bisec’ ‘slp.basis’ ‘is.slp’ ‘iqr.waldtest’
  ‘extract.p’ ‘pred.beta’ ‘print.iMqr’ ‘print.summary.iMqr’
  ‘terms.iMqr’ ‘model.matrix.iMqr’ ‘vcov.iMqr’ ‘nobs.iMqr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) F.huggins.estim.Rd:199: Escaped LaTeX specials: \$ \$
checkRd: (-1) F.huggins.estim.Rd:205: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:206: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:207: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:208: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:209: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:210: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:212: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:213: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:214: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:215: Escaped LaTeX specials: \$
checkRd: (-1) lines.cjs.Rd:15: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Auto-generated content requiring editing in Rd file 'mrbsizer-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rgdal', 'rgeos'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 75 marked UTF-8 strings
Argument items with no description in Rd file 'msda.Rd':
  ‘sml’
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Documented arguments not in \usage in Rd file 'CalcMPDynamics.Rd':
  ‘M_ageArray’ ‘TAC_f’ ‘E_f’ ‘SizeLim_f’ ‘FinF’ ‘Spat_targ’
  ‘CAL_binsmid’ ‘Linf’ ‘Len_age’ ‘maxage’ ‘nareas’ ‘Asize’ ‘nCALbins’
  ‘qs’ ‘qvar’ ‘qinc’

Documented arguments not in \usage in Rd file 'popdynCPP.Rd':
  ‘SSBcurr’

Documented arguments not in \usage in Rd file 'popdynOneMICE.Rd':
  ‘nyears’

Documented arguments not in \usage in Rd file 'qestMICE.Rd':
  ‘mod’ ‘plusgroup.’ ‘WtC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘test.txt’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  All declared Imports should be used.
Argument items with no description in Rd file 'DAGOSTINO.Rd':
  ‘data’
Argument items with no description in Rd file 'HZ.test.Rd':
  ‘data’
Argument items with no description in Rd file 'MardiaTest.Rd':
  ‘data’
Argument items with no description in Rd file 'Royston.test.Rd':
  ‘data’
Argument items with no description in Rd file 'gen.var.Rd':
  ‘\dots’
Argument items with no description in Rd file 'larg.ellip.Rd':
  ‘n’ ‘box’ ‘add’ ‘xlim’ ‘ylim’ ‘zlim’ ‘xlab’ ‘ylab’ ‘zlab’ ‘col’
  ‘alpha’ ‘\dots’
Argument items with no description in Rd file 'prism.Rd':
  ‘add’
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
Invalid package aliases in Rd file 'ms_sev-package.Rd':
  ‘ms_sev-package’
Found the following significant warnings:
  PF.cpp:44:43: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
  laplace.cpp:519:24: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  laplace.cpp:559:24: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  laplace.cpp:559:29: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=]
  laplace.cpp:628:24: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  laplace.cpp:630:24: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  problem_data.cpp:60:21: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/mssm.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘markdown’ ‘methods’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'data.visualisation.Rd':
  ‘lda.plot.wrap.1’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
Note: found 303 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
Note: found 2632 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'plotBoxes.Rd':
  ‘lwd’ ‘T.base’ ‘font.family’ ‘fig’ ‘mar’

Documented arguments not in \usage in Rd file 'plotLetters.Rd':
  ‘width’ ‘lwd’ ‘label.groups’ ‘T.base’ ‘orientation’

Documented arguments not in \usage in Rd file 'plotTs.Rd':
  ‘font.family’ ‘fig’ ‘mar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘MultiBD/libs/MultiBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plsgenomics’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'Trace.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'iteraite_fun_Iter.Rd':
  ‘The’

Documented arguments not in \usage in Rd file 'prepare_data.Rd':
  ‘The’

Documented arguments not in \usage in Rd file 'project.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'select_initial_Iter.Rd':
  ‘X’ ‘parametrs’

Documented arguments not in \usage in Rd file 'similarity_function.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'similarity_noncum.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 15 marked UTF-8 strings
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘fields’ ‘optmatch’ ‘rcbalance’ ‘utils’
  All declared Imports should be used.
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘poweRlaw’ ‘rmutil’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 6 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'check_mnsl.Rd':
  ‘fix’

Documented arguments not in \usage in Rd file 'text_colour.Rd':
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
Packages suggested but not available for checking: 'BioNet', 'DLBCL'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘glue’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 50 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Kendall’ ‘perm’
  All declared Imports should be used.
Note: found 63 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘mlr3learners’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
Argument items with no description in Rd file 'check_subject_pattern.Rd':
  ‘subject.vec’ ‘pattern’
Argument items with no description in Rd file 'names_or_error.Rd':
  ‘pattern’
Argument items with no description in Rd file 'only_captures.Rd':
  ‘match.mat’ ‘pattern’
Argument items with no description in Rd file 'stop_for_names.Rd':
  ‘pattern’
Note: found 47936 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Found the following files/directories:
  ‘Crashpad’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
Package suggested but not available for checking: ‘gurobi’
Packages suggested but not available for checking:
  'rgeos', 'rgdal', 'maptools'
Note: found 5 marked Latin-1 strings
  Note: found 7187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 140 marked UTF-8 strings
Invalid package aliases in Rd file 'NBBttest-package.Rd':
  ‘NBBtatest-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘rrpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘sSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magick’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'Moth.Rd':
  ‘delta.ident’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Note: found 7332 marked UTF-8 strings
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Note: found 21 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
':::' call which should be '::': ‘lhs:::maximinLHS’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_ \_
checkRd: (-1) makeNetwork.Rd:31: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
File ‘NetPreProc/libs/NetPreProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
File ‘neuroim/libs/neuroim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Note: found 318 marked UTF-8 strings
Note: found 4894 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘quickcode’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘curl’ ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nflfastR’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'NH-MSAR-package.Rd':
  ‘NH-MSAR-package’
Argument items with no description in Rd file 'ENu_graph.Rd':
  ‘N.s.data’
Argument items with no description in Rd file 'Estep.MSAR.VM.Rd':
  ‘verbose’
Auto-generated content requiring editing in Rd file 'NH-MSAR-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Argument items with no description in Rd file 'init.theta.MSAR.Rd':
  ‘\dots’
Argument items with no description in Rd file 'init.theta.MSAR.VM.Rd':
  ‘\dots’
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHSRdatasets’ ‘grid’ ‘utils’
  All declared Imports should be used.
File ‘nice/libs/nice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Found the following significant warnings:
  RcppUtils.cpp:237:72: warning: unknown conversion type character '>' in format [-Wformat=]
  RcppUtils.cpp:273:73: warning: unknown conversion type character '>' in format [-Wformat=]
  ../include/nimble/Utils.h:64:80: warning: format '%s' expects argument of type 'char*', but argument 2 has type 'SEXP' {aka 'SEXPREC*'} [-Wformat=]
  ../include/nimble/Utils.h:65:89: warning: format '%s' expects argument of type 'char*', but argument 3 has type 'SEXP' {aka 'SEXPREC*'} [-Wformat=]
  ../include/nimble/Utils.h:66:98: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
  ../include/nimble/Utils.h:65:89: warning: format '%s' expects argument of type 'char*', but argument 2 has type 'SEXP' {aka 'SEXPREC*'} [-Wformat=]
  Utils.cpp:66:26: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  ../inst/include/nimble/Utils.h:64:80: warning: format '%s' expects argument of type 'char*', but argument 2 has type 'SEXP' {aka 'SEXPREC*'} [-Wformat=]
  ../inst/include/nimble/Utils.h:65:89: warning: format '%s' expects argument of type 'char*', but argument 3 has type 'SEXP' {aka 'SEXPREC*'} [-Wformat=]
  ../inst/include/nimble/Utils.h:66:98: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
  ../inst/include/nimble/Utils.h:65:89: warning: format '%s' expects argument of type 'char*', but argument 2 has type 'SEXP' {aka 'SEXPREC*'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/nimble.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
Note: found 170 marked UTF-8 strings
Objects in \usage without \alias in Rd file 'internalRK.Rd':
  ‘brkCalc’ ‘findPowerR’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'Rvmmin', 'Rcgmin'
Specified C++11: please drop specification unless essential
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'nldoc_write_nldoc.Rd':
  ‘number_ections’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mail’
Documented arguments not in \usage in Rd file 'ccSpec.Rd':
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  logistf.c:118:58: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/nncc.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
Invalid package aliases in Rd file 'logistf-package.Rd':
  ‘logistf-package’ ‘{logistf}-package’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’ ‘forcats’
  ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘digest’ ‘hash’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'noise-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_max_stat.Rd':
  ‘statfunc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘noncompliance/libs/noncompliance.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'StatQQVPC.Rd':
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in Rd file 'StatQQnorm.Rd':
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in Rd file 'StatQQrefline.Rd':
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in Rd file 'covload.sub.table.Rd':
  ‘nrows’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'nose-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Documented arguments not in \usage in Rd file 'FunctionSanityChecks.Rd':
  ‘structure’

Documented arguments not in \usage in Rd file 'newLine.Rd':
  ‘current.in’

Documented arguments not in \usage in Rd file 'nosoiSimConstructor.Rd':
  ‘pres.time’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'read.Rd':
  ‘dots’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'Create_P.Rd':
  ‘y_zx_dependent’

Documented arguments not in \usage in Rd file 'make_proposer.Rd':
  ‘N’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘optparse’ ‘vcfR’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'exp_hclust.Rd':
  ‘df_allele’

Documented arguments not in \usage in Rd file 'log_mem.Rd':
  ‘msg’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘pedtools’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  nro_train.cpp:79:15: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/Numero.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 6409 marked UTF-8 strings
Note: found 7284 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 7 marked UTF-8 strings
Note: found 6986 marked UTF-8 strings
Note: found 1242 marked UTF-8 strings
Argument items with no description in Rd file 'plot.comphat.Rd':
  ‘\dots’
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’ ‘ggthemes’ ‘mlbench’ ‘rmarkdown’ ‘tidymodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘olctools/libs/olctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘oldbailey-Ex.R’ failed
The error most likely occurred in:

> ### Name: find_trials
> ### Title: Find Old Bailey Trials
> ### Aliases: find_trials
> 
> ### ** Examples
> 
> # Return a dataframe with 5 trials.
> trials <- find_trials(n_results = 5)
Error: lexical error: invalid char in json text.
                                       <!doctype html><html lang="en">
                     (right here) ------^
Execution halted
Error: there is no package called ‘emmeans’
Call sequence:
7: doWithOneRestart(return(expr), restart)
6: withOneRestart(expr, restarts[[1L]])
5: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Note: found 842 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘crayon’ ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘gdata’ ‘genefilter’ ‘maftools’ ‘readxl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
Note: found 32 marked UTF-8 strings
Note: found 34 marked UTF-8 strings
Rd files without \alias:
  ‘ontologyPlot-package.Rd’
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘glue’ ‘httpcode’ ‘httr’ ‘jsonlite’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
License stub is invalid DCF.
GNU make is a SystemRequirements.
Note: found 4 marked UTF-8 strings
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'unary_ops.Rd':
  ‘log10.ProcessNode’ ‘log10.ProcessGraphParameter’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 2524 marked UTF-8 strings
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
possible bashism in configure line 52 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
Package suggested but not available for checking: ‘openNLPmodels.en’
Documented arguments not in \usage in Rd file 'clique_color_pals.Rd':
  ‘aplha’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'bertinBase.Rd':
  ‘x’ ‘ratings’ ‘trim’

Documented arguments not in \usage in Rd file 'biplot3dBase2.Rd':
  ‘ext.sphere’

Documented arguments not in \usage in Rd file 'convertImportObjectToRepGridObject.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'convertScivescoImportObjectToRepGridObject.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'mapCoordinatesToColor.Rd':
  ‘color’

Documented arguments not in \usage in Rd file 'quasiDistributionDistanceSlater.Rd':
  ‘rep’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking: 'maptools', 'rgeos'
Note: found 10 marked UTF-8 strings
Note: found 167 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
File ‘OptHedging/libs/OptHedging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
File ‘optpart/libs/optpart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Package suggested but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'dsevdist.Rd':
  ‘x’ ‘sevdist’
Note: found 36 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
Documented arguments not in \usage in Rd file 'distsuml2.Rd':
  ‘partial’

Documented arguments not in \usage in Rd file 'distsumlp.Rd':
  ‘partial’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'dosepred.Rd':
  ‘w’

Documented arguments not in \usage in Rd file 'surv_dm_solver.Rd':
  ‘bw_optim’

Documented arguments not in \usage in Rd file 'surv_forward_solver.Rd':
  ‘Phit’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 5889 marked UTF-8 strings
Note: found 34 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rcplex’
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
Rd files without \alias:
  ‘otp-package.Rd’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘astsa’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'packagetracker.Rd':
  ‘packagetracker-package’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘flexsurv’ ‘nlme’ ‘tibble’ ‘tidyverse’ ‘tm’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'prediction_regression.Rd':
  ‘dataset’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 314 marked UTF-8 strings
Package which this enhances but not available for checking: ‘CorShrink’
Documented arguments not in \usage in Rd file 'other.Rd':
  ‘trial’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'dplyr_verbs.Rd':
  ‘funs’ ‘.dots’ ‘keep_attributes’

Documented arguments not in \usage in Rd file 'nest_tdc.Rd':
  ‘vars’ ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'pamr.internal.Rd':
  ‘print.nsc’ ‘print.nsccv’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘pamr/libs/pamr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'getOption2.Rd':
  ‘envvar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rgdal’
Note: found 16 marked UTF-8 strings
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'expect_missing_argument.Rd':
  ‘message’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'as_partition.Rd':
  ‘.partition_step’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'fixvar_of_red_mod.Rd':
  ‘data’

Documented arguments not in \usage in Rd file 'get_ndf.Rd':
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'vec_cast.partial_time.Rd':
  ‘vec_cast.partial_time’

S3 methods shown with full name in Rd file 'vec_cast.timespan.Rd':
  ‘vec_cast.timespan’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
Found the following files/directories:
  ‘Minimal-concordance.tex’ ‘Minimal.Rnw’ ‘Minimal.pdf’
  ‘Minimal.synctex.gz’ ‘Minimal.tex’ ‘figure’
Namespace in Imports field not imported from: ‘logger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 180 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘testthat’ ‘usethis’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘clusterProfiler’ ‘purrr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'markbouts.acclist.Rd':
  ‘extreme’
S3 methods shown with full name in Rd file 'ped.Rd':
  ‘ped.markerNames’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
---- unloading
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘pbivnorm/libs/pbivnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  PBSddesolve.c:221:23: warning: too many arguments for format [-Wformat-extra-args]
  ddeq.c:307:85: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/PBSddesolve.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Objects in \usage without \alias in Rd file 'pch-internal.Rd':
  ‘CumSum’ ‘myapply’ ‘makebreaks.ct’ ‘makebreaks.ic’ ‘pois.loglik’
  ‘icpch.loglik’ ‘convert.Surv’ ‘break.y’ ‘pois.fit’ ‘pch.fit.ct’
  ‘pch.fit.ic’ ‘newton’ ‘cleanlambda’ ‘predF.pch’ ‘predQ.pch’ ‘sim.pch’
  ‘build.splinex’ ‘predict.splinex’ ‘logLik.pch’ ‘nobs.pch’ ‘vcov.pch’
  ‘coef.pch’ ‘print.pch’ ‘summary.pch’ ‘print.summary.pch’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'getResponse.Rd':
  ‘model’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Note: found 11 marked UTF-8 strings
Objects in \usage without \alias in Rd file 'ODACATH.estimate.Rd':
  ‘ODACAT.estimate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘pdc/libs/pdc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘PythonInR’
'LazyData' is specified without a 'data' directory
File ‘pdist/libs/pdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ncvreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
File ‘PDSCE/libs/PDSCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'PoissonLoss.Rd':
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd file 'getPath.Rd':
  ‘A’
Argument items with no description in Rd file 'PoissonLoss.Rd':
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd file 'featureMatrixJoint.Rd':
  ‘profile.list’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'PoissonLoss.Rd':
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd file 'oracleModelComplexity.Rd':
  ‘bases’ ‘segments’
S3 methods shown with full name in Rd file 'format.relation.Rd':
  ‘format.relation’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘georob’
Note: found 4860 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
Specified C++11: please drop specification unless essential
File ‘PenCoxFrail/libs/PenCoxFrail.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
File ‘penMSM/libs/penMSM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘fixest’
  All declared Imports should be used.
Argument items with no description in Rd file 'lmres.Rd':
  ‘\dots’
Argument items with no description in Rd file 'simpleSlope.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.lmres.Rd':
  ‘\dots’
Note: found 4 marked UTF-8 strings
Specified C++11: please drop specification unless essential
File ‘PerfMeas/libs/PerfMeas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
Documented arguments not in \usage in Rd file 'allTrees.Rd':
  ‘dist’

Documented arguments not in \usage in Rd file 'getNode.Rd':
  ‘hc’ ‘pair’

Documented arguments not in \usage in Rd file 'switchEntries.Rd':
  ‘pair’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘mclust’
  All declared Imports should be used.
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'perspective-package.Rd':
  ‘perspective-package’
Note: found 201 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1782 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘pgee.mixed/libs/pgee.mixed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Unknown packages ‘maptools’, ‘rgdal’ in Rd xrefs
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘ph2bye/libs/ph2bye.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘animation.gif’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
Found the following files/directories:
  ‘test.pdf’
Namespaces in Imports field not imported from:
  ‘C50’ ‘HDclassif’ ‘MASS’ ‘MLmetrics’ ‘Matrix’ ‘adabag’ ‘base’
  ‘caTools’ ‘e1071’ ‘earth’ ‘evtree’ ‘frbs’ ‘glmnet’ ‘hda’ ‘ipred’
  ‘kernlab’ ‘kknn’ ‘klaR’ ‘mda’ ‘nnet’ ‘party’ ‘pls’ ‘randomForest’
  ‘rpartScore’ ‘sparseLDA’ ‘themis’
  All declared Imports should be used.
Note: found 114 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'process_season.Rd':
  ‘d’ ‘options_season’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'phm-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Note: found 13 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘tidyverse’ ‘usethis’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pinnacle.API’
Note: found 2048 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'pipegs.Rd':
  ‘pipegs-package’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'TungUbRF.Rd':
  ‘feature_num_tree’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'make_pgk_cache_subdir_for_all_relative_files.Rd':
  ‘relative_filenames’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BH’
  All declared Imports should be used.
Note: found 150 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Note: found 12992 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'plsgenomics-deprecated.Rd':
  ‘plsgenomics-deprecated-package’
Invalid package aliases in Rd file 'plsgenomics-internal.Rd':
  ‘plsgenomics-internal-package’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘ssh’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘base’ ‘grDevices’
  All declared Imports should be used.
Found the following significant warnings:
  FLSAGeneral.cc:240:66: warning: format '%d' expects argument of type 'int', but argument 5 has type 'std::set<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
  FLSAGeneral.cc:240:70: warning: format '%d' expects argument of type 'int', but argument 6 has type 'std::set<int>::size_type' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/PMA.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Package suggested but not available for checking: ‘pmartRdata’
Package suggested but not available for checking: ‘MSnbase’
Note: found 62 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'sample_store.Rd':
  ‘subjects_ids’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 7256 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 437 marked UTF-8 strings
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Note: found 21 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘formula.tools’ ‘ggplot2’ ‘gplots’ ‘graphics’ ‘purrr’
  ‘rstatix’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Note: found 52 marked UTF-8 strings
Note: found 805 marked Latin-1 strings
  Note: found 12681 marked UTF-8 strings
Package suggested but not available for checking: ‘pollimetrydata’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'genclone-method.Rd':
  ‘gen’ ‘loc’ ‘treatOther’ ‘quiet’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘population/libs/population.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing link or links in Rd file 'pop.predict.Rd':
  ‘rrBLUP’

Missing link or links in Rd file 'x.val.Rd':
  ‘rrBLUP’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘ragt2ridges’
Unknown package ‘ragt2ridges’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tradelist-class.Rd:91: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:146: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:126: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:219: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:225: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:229: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:231: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:233: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:235: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:237: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:301: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:303: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:305: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:307: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:309: Escaped LaTeX specials: \&
checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
Note: found 869 marked UTF-8 strings
Objects in \usage without \alias in Rd file 'ppmlasso-internal.Rd':
  ‘spatRes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘rpart’ ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’ ‘numDeriv’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'local_test_setup.Rd':
  ‘use_precommmit’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘ffbase’
Unknown package ‘ffbase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./include/MCMC/sampler.h:241:55: warning: format '%i' expects argument of type 'int', but argument 2 has type 'uint_fast32_t' {aka 'long unsigned int'} [-Wformat=]
  postProcess.cpp:57:51: warning: format '%i' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  postProcess.cpp:102:43: warning: format '%i' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/PReMiuM.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 96 marked UTF-8 strings
Note: found 42966 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'maptools', 'rgdal'
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 165 marked UTF-8 strings
Specified C++11: please drop specification unless essential
File ‘PRIMAL/libs/PRIMAL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'rcbc'
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'validate_inputs.Rd':
  ‘required_vars’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cin’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'bitAND.Rd':
  ‘a’ ‘b’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
File ‘prototest/libs/prototest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 12717 marked UTF-8 strings
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
Documented arguments not in \usage in Rd file 'dot-marxan_data_reader.Rd':
  ‘parameter’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘pRSR/libs/pRSR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1 marked UTF-8 string
Note: found 4 marked UTF-8 strings
Invalid package aliases in Rd file 'granova-package.Rd':
  ‘granova-package’
Documented arguments not in \usage in Rd file 'estimateDeltaLOH.PairedPSCBS.Rd':
  ‘scale’

Documented arguments not in \usage in Rd file 'getLocusData.AbstractCBS.Rd':
  ‘splitters’

Documented arguments not in \usage in Rd file 'getSegments.AbstractCBS.Rd':
  ‘simplify’ ‘splitters’

Documented arguments not in \usage in Rd file 'mergeTwoSegments.AbstractCBS.Rd':
  ‘left’ ‘update’ ‘verbose’

Documented arguments not in \usage in Rd file 'plotTracks.PairedPSCBS.Rd':
  ‘x’ ‘tracks’ ‘scatter’ ‘calls’ ‘pch’ ‘col’ ‘cex’ ‘changepoints’
  ‘grid’ ‘quantiles’ ‘xlim’ ‘Clim’ ‘Blim’ ‘xScale’ ‘add’ ‘subplots’
  ‘verbose’

Documented arguments not in \usage in Rd file 'updateMeansTogether.AbstractCBS.Rd':
  ‘idxList’ ‘verbose’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
Note: found 596 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'kepner_robinson_test_internal.Rd':
  ‘group’ ‘alternative’ ‘trend’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26 marked Latin-1 strings
File ‘pspearman/libs/pspearman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'pspline.sample.scalars.Rd':
  ‘time’

Documented arguments not in \usage in Rd file 'pspline.sample.timeseries.Rd':
  ‘time’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lifecycle’ ‘patchwork’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 107 marked UTF-8 strings
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'GetFitHReg.Rd':
  ‘z’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘ptest/libs/ptest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Invalid package aliases in Rd file 'package-ptf.Rd':
  ‘package-ptf-package’
File ‘ptinpoly/libs/ptinpoly.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'assert_correct_attributes.Rd':
  ‘expected_colnames’

Documented arguments not in \usage in Rd file 'geopath_to_tibble.Rd':
  ‘route’

Documented arguments not in \usage in Rd file 'run_to_tibble.Rd':
  ‘route’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 28898 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘itsadug’ ‘mgcv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Invalid package aliases in Rd file 'PVAClone-package.Rd':
  ‘PVA-package’ ‘pva-package’ ‘Pva-package’
File ‘PWEALL/libs/PWEALL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘progressr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) Ch0C-plot.cpd.PwrGSD.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'http_was_redirected.Rd':
  ‘response’

Documented arguments not in \usage in Rd file 'permutations.Rd':
  ‘nset’

Documented arguments not in \usage in Rd file 'pxweb_split_query.Rd':
  ‘pxweb_metadata’

Documented arguments not in \usage in Rd file 'split_dimensions_left_right.Rd':
  ‘pxq’

Documented arguments not in \usage in Rd file 'str_pad.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'lagm.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_names_MV.Rd':
  ‘path_matrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'Qest-internal.rd':
  ‘expit’ ‘logit’ ‘pmax0’ ‘num.fun’ ‘format.perc’ ‘Ltau’ ‘minabs’
  ‘invJ’ ‘tensorX’ ‘buildTau’ ‘callwtau’ ‘callQ’ ‘start.Qest’
  ‘start.Qest.family’ ‘rq.fit.br2’ ‘Qest.sgs.internal’
  ‘Qest.gs.internal’ ‘Qest.gs’ ‘Qest.newton’ ‘Qlm.bfun’ ‘start.Qlm’
  ‘scalevars.Qlm’ ‘descalecoef.Qlm’ ‘Qlm.sgs.internal’
  ‘Qlm.gs.internal’ ‘Qlm.gs’ ‘Qlm.newton’ ‘plfcox’ ‘scalevars.Qcoxph’
  ‘descalecoef.Qcoxph’ ‘check.singularities’ ‘starting.points.Qcox’
  ‘adjust.coef’ ‘agsurv.Qcoxph’ ‘coxsurv.fit.Qcoxph’ ‘seg.lm.fit1’ ‘gs’
  ‘myg’ ‘dlist’ ‘omega’ ‘choose_eps’ ‘derQtheta’ ‘der2Qtheta’ ‘intA’
  ‘findp’ ‘findAp’ ‘A_beta_fun’ ‘A_gamma_fun’ ‘A_beta_beta_fun’
  ‘A_gamma_gamma_mix_fun’ ‘A_gamma_gamma_fun’ ‘A_beta_gamma_fun’
  ‘coxBB’ ‘derQtheta.gamma’ ‘der2Qtheta.gamma’ ‘findAp.gamma’
  ‘QestGamma.ee.u’ ‘QestGamma.ee.c’ ‘QestGamma.ee.ct’ ‘tau.pois’
  ‘ppoisC’ ‘dpoisC’ ‘qpoisC.955’ ‘qpoisC.me’ ‘qpoisC.bisec’ ‘qpoisC’
  ‘derQtheta.pois’ ‘der2Qtheta.pois’ ‘findp.pois’ ‘findAp.pois’
  ‘QestPois.ee.u’ ‘QestUnif.ee.u’ ‘QestNorm.ee.u’ ‘QestNorm.ee.c’
  ‘QestNorm.ee.ct’ ‘Qest.ee.u’ ‘Qest.ee.c’ ‘Qest.ee.ct’ ‘QCox.ee.c’
  ‘QCox.ee.ct’ ‘Qlm.ee.u’ ‘Qest.covar’ ‘Qcox.covar’ ‘Qlm.covar’ ‘Loss’
  ‘coxLoss’ ‘qlmLoss’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'Qest-internal.rd':
  ‘format.perc’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spDataLarge’
Namespaces in Imports field not imported from:
  ‘rmarkdown’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'ad.simudata.Rd':
  ‘SimuNum’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘missMethods’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in Rd file 'qrcmNP-internal.Rd':
  ‘Q’ ‘funQ1’ ‘check.fun’ ‘boot’ ‘predBeta’ ‘grad3’ ‘grad2’ ‘num.int’
  ‘integr’ ‘bisec’ ‘Bfun’ ‘bfun’ ‘funGrad’ ‘Fun’ ‘armijo’ ‘check.in.2’
  ‘check.out.2’ ‘piqr.newton’ ‘piqr.ee’ ‘pciqr.ee’ ‘pctiqr.ee’
  ‘plotCoef’ ‘nonzeroCoef’ ‘cov.theta.2’ ‘plot.piqr2’
  ‘divide.et.impera.2’ ‘print.niqr’ ‘print.summary.niqr’ ‘print.piqr’
  ‘print.summary.piqr’ ‘terms.piqr’ ‘coef.piqr’ ‘model.matrix.piqr’
  ‘nobs.piqr’
Assignments in \usage in Rd file 'qrcmNP-internal.Rd':
  start.theta.niqr <- function(fun, x0, X, y, control = list()) piqr.internal(mf, 
      cl, formula.p, tol = 1e-06, maxit = 100, s, segno = 1, lambda = 0, 
      check = FALSE, A, st.theta = FALSE, theta0)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'qrcmNP-internal.Rd':
  ‘plot.piqr2’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Objects in \usage without \alias in Rd file 'qrcm-internal.Rd':
  ‘check.in.iqr’ ‘check.in0.iqrL’ ‘check.in.iqrL’ ‘check.out’
  ‘start.iqr’ ‘start.iqrL’ ‘ctiqr.internal’ ‘iqrL.internal’ ‘iqrL.fit’
  ‘iqr.ee’ ‘ciqr.ee’ ‘ctiqr.ee’ ‘iobjfun’ ‘iobjfun.ct’ ‘cov.fun.iqr’
  ‘iqrL.ee’ ‘cov.fun.iqrL’ ‘iqr.newton’ ‘divide.et.impera’
  ‘iqrL.newton’ ‘pmax0’ ‘maxind’ ‘num.fun’ ‘make.bfun’ ‘apply_bfun’
  ‘p.bisec’ ‘p.bisec.internal’ ‘slp.basis’ ‘is.slp’ ‘safesolve’
  ‘iqr.waldtest’ ‘extract.p’ ‘pred.beta’ ‘km’ ‘alpha’ ‘test.unif.ct’
  ‘findagoodestimator’ ‘quickpred’ ‘trans’ ‘alpha.bisec’
  ‘alpha.bisec.out’ ‘ks’ ‘print.iqr’ ‘print.summary.iqr’ ‘terms.iqr’
  ‘model.matrix.iqr’ ‘vcov.iqr’ ‘nobs.iqr’ ‘predict.iqrL.internal’
  ‘print.iqrL’ ‘print.summary.iqrL’ ‘terms.iqrL’ ‘model.matrix.iqrL’
  ‘vcov.iqrL’ ‘nobs.iqrL’ ‘qc.penalty’ ‘fixqc’ ‘print.qc.iqr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'qrcm-internal.Rd':
  ‘predict.iqrL.internal’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘qrencoder/libs/qrencoder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) NEWS.Rd:15: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'mmer_adapted.Rd':
  ‘void’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'export_responses_filedownload.Rd':
  ‘requestID’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'convert-wrappers.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'corpus-class.Rd':
  ‘if’

Documented arguments not in \usage in Rd file 'dfm-class.Rd':
  ‘drop_docid’

Documented arguments not in \usage in Rd file 'dictionary-class.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'matrix2fcm.Rd':
  ‘slots’

Documented arguments not in \usage in Rd file 'meta_system.Rd':
  ‘source’

Documented arguments not in \usage in Rd file 'search_index.Rd':
  ‘regex’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 4 marked UTF-8 strings
Note: found 35707 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'wordcloud_comparison.Rd':
  ‘random.color’ ‘ordered.colors’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘SparseM’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 8504 marked UTF-8 strings
Auto-generated content requiring editing in Rd file 'quhomology-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘fastshp’
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 12928 marked UTF-8 strings
Invalid package aliases in Rd file 'qut-package.Rd':
  ‘QUT-package’
Specified C++11: please drop specification unless essential
Note: found 63 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘pracma’ ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Namespaces in Imports field not imported from:
  ‘quickcode’ ‘stats’ ‘utils’
  All declared Imports should be used.
Note: found 6 marked Latin-1 strings
  Note: found 347 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘asd’ ‘cubature’ ‘data.table’ ‘ggplot2’ ‘multxpert’ ‘survival’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘comat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'print.ramchoiceRevealAtte.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.ramchoiceRevealPref.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.ramchoiceRevealPrefModel.Rd':
  ‘object’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking: 'xcms', 'MSnbase'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
Invalid package aliases in Rd file 'randtests-package.Rd':
  ‘randomtests-package’
'LazyData' is specified without a 'data' directory
Note: found 15 marked UTF-8 strings
File ‘RANKS/libs/RANKS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'get_parameters.Rd':
  ‘parameters_def’

Documented arguments not in \usage in Rd file 'print.rapi_api.Rd':
  ‘...further’

Documented arguments not in \usage in Rd file 'print.rapi_operation.Rd':
  ‘...further’

Documented arguments not in \usage in Rd file 'print.rapi_schema_function.Rd':
  ‘...further’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'RApiDatetime-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘# Optional simple examples of the most important functions’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
Objects in \usage without \alias in Rd file 'cache.Rd':
  ‘\S4method{cache}{RapData,character,ANY}’
  ‘\S4method{cache}{RapData,character,missing}’
  ‘\S4method{cache}{RapResults,character,ANY}’
  ‘\S4method{cache}{RapResults,character,missing}’

Objects in \usage without \alias in Rd file 'is.cached.Rd':
  ‘\S4method{is.cached}{RapData,character}’
  ‘\S4method{is.cached}{RapResults,character}’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'mpaRaoS.Rd':
  ‘rasterm’

Objects in \usage without \alias in Rd file 'paRaoP.Rd':
  ‘paRaoS’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'onb_from_w.Rd':
  ‘v’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'gen_fractal_perlin.Rd':
  ‘image’

Documented arguments not in \usage in Rd file 'generate_base_shape.Rd':
  ‘image’

Documented arguments not in \usage in Rd file 'generate_cloud_layer.Rd':
  ‘image’

Documented arguments not in \usage in Rd file 'make_base_triangulated.Rd':
  ‘zscale’

Documented arguments not in \usage in Rd file 'raymarch_cloud_layer.Rd':
  ‘image’

Documented arguments not in \usage in Rd file 'render_snapshot_software.Rd':
  ‘ground_size’

Documented arguments not in \usage in Rd file 'transform_into_heightmap_coords.Rd':
  ‘image’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  cdotree.cpp:33:23: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  cdotree.cpp:33:32: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  cdotree.cpp:57:23: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  cdotree.cpp:57:30: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  cdotree.cpp:57:39: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  cmbrt.cpp:149:21: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  cmbrt.cpp:161:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int' [-Wformat=]
  cmbrt.cpp:170:31: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  cpsambrt.cpp:188:21: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  cpsambrt.cpp:208:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int' [-Wformat=]
  cpsambrt.cpp:222:31: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rbart.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rex’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'Min_Max_Inverse_Scale_Vec.Rd':
  ‘mat’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'export.default.Rd':
  ‘export.default’

S3 methods shown with full name in Rd file 'export.listpoly.Rd':
  ‘export.listpoly’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 26334 marked UTF-8 strings
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’ ‘shinythemes’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘rlemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘data.csv’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'makeTitle.Rd':
  ‘string:’ ‘length:’ ‘prefix.length:’ ‘char:’

Documented arguments not in \usage in Rd file 'messageConsole.Rd':
  ‘message:’

Documented arguments not in \usage in Rd file 'tkEmptyLine.Rd':
  ‘tk.object:’ ‘row:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘outcmaesdisp.dat’
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Invalid package aliases in Rd file 'RcmdrPlugin.coin-package.Rd':
  ‘RcmdrcoinPlugin-package’
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'Rcmdr.HH-package.Rd':
  ‘Rcmdr.HH-package’
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'RcmdrPlugin.SCDA-package.Rd':
  ‘RcmdrSCDAPlugin-package’
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Note: found 345 marked UTF-8 strings
Package suggested but not available for checking: ‘conics’
Note: found 1 marked UTF-8 string
Auto-generated content requiring editing in Rd file 'RcppAnnoy-package.Rd':
  \examples: ‘# Optional simple examples of the most important functions’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
‘configure’: /bin/bash is not portable
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  ../inst/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=]
  ../inst/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rcpp.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Invalid package aliases in Rd file 'Rd2markdown-package.Rd':
  ‘Rd2markdown-package’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'h_opt_density_res.Rd':
  ‘x’ ‘dgp_F1’ ‘dgp_Fp1’ ‘f_low’ ‘f_up’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘devAll’
Documented arguments not in \usage in Rd file 'favicon.Rd':
  ‘file’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Invalid package aliases in Rd file 'rdoc_options.Rd':
  ‘rdoc_options-package’
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'RDocumentation-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DIDmultiplegt’
Note: found 5 marked UTF-8 strings
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'readAcquFile.Rd':
  ‘file’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'readmnist-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'add_docid.Rd':
  ‘impute_types’

Documented arguments not in \usage in Rd file 'texts.Rd':
  ‘spacer’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'rearrr_fn_.Rd':
  ‘overwrite’

Documented arguments not in \usage in Rd file 'rev_windows_rearranger_.Rd':
  ‘keep_windows’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1036 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'recom-package.Rd':
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Note: found 9698 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'RED.Rd':
  ‘RED-package’
Auto-generated content requiring editing in Rd file 'referenceIntervals-package.Rd':
  \references: ‘~~ Literature or other references for background information ~~’
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’ ‘scales’
  All declared Imports should be used.
Note: found 24152 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'Estep.Rd':
  ‘adaptive_quad’

Documented arguments not in \usage in Rd file 'd_bernoulli.Rd':
  ‘pred.data’ ‘num.quad’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘textshaping’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘remote/libs/remote.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:38: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:42: Escaped LaTeX specials: \$
Note: found 6034 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
File ‘repolr/libs/repolr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 25 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'gaussian_process_cv.Rd':
  ‘ncomp’

Documented arguments not in \usage in Rd file 'get_samples_from_strata.Rd':
  ‘starta’

Documented arguments not in \usage in Rd file 'ith_subsets_ortho_diss.Rd':
  ‘remove’

Documented arguments not in \usage in Rd file 'pca_nipals.Rd':
  ‘Y’

Documented arguments not in \usage in Rd file 'predict_gaussian_process.Rd':
  ‘b’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
Note: found 1172 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'get.V.Rd':
  ‘ct.lst’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘ccdata’
Rd files without \alias:
  ‘retry-package.Rd’
'LazyData' is specified without a 'data' directory
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 806 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'compareChecksum.GenericDataFile.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'dim.GenericTabularFile.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'dsApplyInPairs.GenericDataFileSet.Rd':
  ‘ds’

Documented arguments not in \usage in Rd file 'fromFile.GenericDataFile.Rd':
  ‘unknown’

Documented arguments not in \usage in Rd file 'gzip.GenericDataFile.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'readChecksum.ChecksumFile.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'writeChecksum.GenericDataFile.Rd':
  ‘verbose’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RFlocalfdr.data’ ‘vita’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  Rglpk_read_file.c:215:26: warning: format '%c' expects argument of type 'int', but argument 2 has type 'char *' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rglpk.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘attempt’ ‘curl’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1473 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'dimnames.AbstractFileArray.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'length.AbstractFileArray.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'readContiguousValues.AbstractFileArray.Rd':
  ‘length’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
File ‘RI2by2/libs/RI2by2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Specified C++11: please drop specification unless essential
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 169 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘rIsing/libs/rIsing.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 243 marked UTF-8 strings
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'inner_t_index_calculation.Rd':
  ‘param_’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Non-standard file/directory found at top level:
  ‘jri’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
Documented arguments not in \usage in Rd file 'rJava-internal.Rd':
  ‘r.convertor’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
License stub is invalid DCF.
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'rkt-package.Rd':
  ‘tkt-package’
'LazyData' is specified without a 'data' directory
File ‘rkvo/libs/rkvo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘Rlof/libs/Rlof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 31 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘RMKdiscrete/libs/RMKdiscrete.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'bind.Rd':
  ‘.single_on_bind’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Note: found 133 marked Latin-1 strings
Package suggested but not available for checking: ‘rnaturalearthhires’
Note: found 2800 marked UTF-8 strings
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
File ‘rnetcarto/libs/rnetcarto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘rngSetSeed/libs/rngSetSeed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘attention’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rgdal’
Documented arguments not in \usage in Rd file 'SanitizeURL.Rd':
  ‘bad.str’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'internal_plots.Rd':
  ‘panelFirst’

Documented arguments not in \usage in Rd file 'internals.Rd':
  ‘L2fam’
Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.evalListRec’ ‘.filterEargsWEargList’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘RobAStBase-Ex.R’ failed
The error most likely occurred in:

> ### Name: RobAStBase-package
> ### Title: Robust Asymptotic Statistics
> ### Aliases: RobAStBase-package RobAStBase
> ### Keywords: package
> 
> ### ** Examples
> 
> library(RobAStBase)
> ## some L2 differentiable parametric family from package distrMod, e.g.
> B <- BinomFamily(size = 25, prob = 0.25) 
Warning in .local(.Object, ...) : you have to specify slot r at least
Error: unable to find an inherited method for function ‘r’ for signature ‘object = "numeric"’
Execution halted
Invalid package aliases in Rd file '0RobRDA-package.Rd':
  ‘RobRDA-package’
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'internal-interpolate.Rd':
  ‘upRad.s’
Objects in \usage without \alias in Rd file 'internal-interpolate.Rd':
  ‘.getPsi.wL’ ‘.getPsi.P’

Objects in \usage without \alias in Rd file 'rescaleFunction-methods.Rd':
  ‘rescaleFunction’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'createITPSplineResult.Rd':
  ‘measure’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: found 6 marked UTF-8 strings
Specified C++11: please drop specification unless essential
File ‘robustETM/libs/robustETM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Documented arguments not in \usage in Rd file 'Sample.rgasp.Rd':
  ‘interval_data’

Objects in \usage without \alias in Rd file 'neg_log_marginal_post_approx_ref_ppgasp.Rd':
  ‘neg_log_marginal_post_approx_ref’

Objects in \usage without \alias in Rd file 'separable_multi_kernel.Rd':
  ‘separable_kernel’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'choose.test.Rd':
  ‘Xpaired’ ‘Ypaired’ ‘Xextra’ ‘Yextra’ ‘mc.rep’
Argument items with no description in Rd file 'multinom.test.Rd':
  ‘X’ ‘Y’ ‘alternative’ ‘correct’ ‘perm’ ‘mc.rep’ ‘method’ ‘verbose’
  ‘mode’ ‘useC’
Argument items with no description in Rd file 'mw.mw.2.perm.Rd':
  ‘X’ ‘Y’ ‘Xprime’ ‘Yprime’ ‘.corr’ ‘mc.rep’ ‘alternative’ ‘verbose’
Argument items with no description in Rd file 'pm.wilcox.test.Rd':
  ‘Xpaired’ ‘Ypaired’ ‘Xextra’ ‘Yextra’ ‘alternative’ ‘verbose’
Argument items with no description in Rd file 'sim.partially.matched.Rd':
  ‘meanRatio’ ‘sdRatio’ ‘within.sd’ ‘type’ ‘hyp’
Argument items with no description in Rd file 'wmw.paired.replicates.test.Rd':
  ‘X’ ‘Y’ ‘alternative’ ‘correct’ ‘perm’ ‘mc.rep’ ‘method’ ‘verbose’
  ‘mode’ ‘useC’
Problems with news in ‘NEWS.md’:
No news entries found.
Objects in \usage without \alias in Rd file 'gettptnfpfn-defunct.Rd':
  ‘gettptnfpfn’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 261 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'add_matches_columns.Rd':
  ‘Matches’

Documented arguments not in \usage in Rd file 'run_checks_two.Rd':
  ‘lookback’ ‘standard_deviaion’ ‘match_on’ ‘model_type’

Documented arguments not in \usage in Rd file 'trim_pool.Rd':
  ‘standard_deviaion’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Auto-generated content requiring editing in Rd file 'roloc-package.Rd':
  \references: ‘~~ Literature or other references for background information ~~’
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'DOLLAR.Class.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'DOLLARLT_-.Class.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'getMethods.Class.Rd':
  ‘unqiue’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ROptEstOld-Ex.R’ failed
The error most likely occurred in:

> ### Name: BinomFamily
> ### Title: Generating function for Binomial families
> ### Aliases: BinomFamily
> ### Keywords: models
> 
> ### ** Examples
> 
> (B1 <- BinomFamily(size = 25, prob = 0.25))
Warning in .local(.Object, ...) : you have to specify slot r at least
Error: unable to find an inherited method for function ‘r’ for signature ‘object = "numeric"’
Execution halted
Documented arguments not in \usage in Rd file 'internal-interpolate.Rd':
  ‘upRad.s’ ‘withSmooth’
Assignments in \usage in Rd file 'internal-interpolate.Rd':
  .readGridFromCSV <- function(fromFileCSV) .generateInterpGrid(thGrid, 
      PFam, toFileCSV = "temp.csv", getFun = .getLMGrid, ..., modifyfct, 
      nameInSysdata, GridFileName, withPrint = TRUE, len = 13)

Objects in \usage without \alias in Rd file 'internalRobestHelpers.Rd':
  ‘.constructArg.list’ ‘.fix.in.defaults’ ‘.pretreat’ ‘.check.eps’
  ‘.isOKsteps’ ‘.isOKfsCor’

Documented arguments not in \usage in Rd file 'internal_Cniperplots.Rd':
  ‘origCl’

Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.isVirginW’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘ROptEst-Ex.R’ failed
The error most likely occurred in:

> ### Name: RMXEOMSEMBREOBRE
> ### Title: Optimally robust estimation: RMXE, OMSE, MBRE, and OBRE
> ### Aliases: RMXEstimator OMSEstimator OBREstimator MBREstimator
> ### Keywords: robust
> 
> ### ** Examples
> 
> #############################
> ## 1. Binomial data
> #############################
> ## generate a sample of contaminated data
> set.seed(123)
> ind <- rbinom(100, size=1, prob=0.05)
> x <- rbinom(100, size=25, prob=(1-ind)*0.25 + ind*0.9)
> 
> ## ML-estimate
> MLE.bin <- MLEstimator(x, BinomFamily(size = 25))
Warning in .local(.Object, ...) : you have to specify slot r at least
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'object' in selecting a method for function 'startPar': unable to find an inherited method for function ‘r’ for signature ‘object = "numeric"’
Calls: MLEstimator ... initialize -> initialize -> .local -> table -> r -> <Anonymous>
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'A.Introduction-RoughSets.Rd':
  ‘A.Introduction-RoughSets-package’
Invalid package aliases in Rd file 'B.Introduction-FuzzyRoughSets.Rd':
  ‘B.Introduction-FuzzyRoughSets-package’
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following significant warnings:
  phylopars_rcpp.cpp:125:26: warning: 'void arma::set_cerr_stream(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  phylopars_rcpp.cpp:144:26: warning: 'void arma::set_cerr_stream(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  phylopars_rcpp.cpp:179:26: warning: 'void arma::set_cerr_stream(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rphylopars.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Argument items with no description in Rd file 'anova.phylopars.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'logLik.phylopars.Rd':
  ‘\dots’
Argument items with no description in Rd file 'logLik.phylopars.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.SSC.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.phylopars.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.phylopars.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.phylopars.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.phylopars.lm.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  RS-pgsql-copy.c:305:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/RPostgreSQL.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’ ‘timeDate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'rrcov-utils.Rd':
  ‘tol’ ‘sv’ ‘n’ ‘p’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 192 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'RNAPlot.Rd':
  ‘seqTF’
Argument items with no description in Rd file 'aptPlotCT.Rd':
  ‘seqTF’
Found the following files/directories:
  ‘test.bpl’ ‘test.cr’ ‘test.ct’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file '000-LB-.RspDocument.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'RspEvalDirective.Rd':
  ‘attributes’

Documented arguments not in \usage in Rd file 'RspExpression.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'RspIncludeDirective.Rd':
  ‘attributes’

Documented arguments not in \usage in Rd file 'buildNonSweaveVignette.Rd':
  ‘pathname’

Documented arguments not in \usage in Rd file 'buildNonSweaveVignettes.Rd':
  ‘path’ ‘pattern’

Documented arguments not in \usage in Rd file 'exprToCode.RspSourceCodeFactory.Rd':
  ‘expr’

Documented arguments not in \usage in Rd file 'getContent.RspText.Rd':
  ‘unescaped’

Documented arguments not in \usage in Rd file 'toSourceCode.RspSourceCodeFactory.Rd':
  ‘expr’

Documented arguments not in \usage in Rd file 'trim.RspDocument.Rd':
  ‘envir’

Documented arguments not in \usage in Rd file 'writeResponse.RspResponse.Rd':
  ‘collapse’ ‘sep’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lubridate’ ‘reshape2’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘rsdepth/libs/rsdepth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘keys’ ‘shinyWidgets’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  model/variables/BehaviorVariable.cpp:990:55: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'siena::Effect*' [-Wformat=]
  model/variables/BehaviorVariable.cpp:994:54: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'siena::Effect*' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/RSiena.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Note: found 467 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'ApiRequest.Rd':
  ‘report.description’

Documented arguments not in \usage in Rd file 'BuildLineItemSegment.Rd':
  ‘elements’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘RSKC/libs/RSKC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MatrixExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Found the following significant warnings:
  ../inst/include/rstan/io/r_ostream.hpp:48:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=]
  ../inst/include/rstan/io/r_ostream.hpp:71:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rstan.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'SetHash.Rd':
  ‘\dots’
Documented arguments not in \usage in Rd file 'calculate.var.np.Rd':
  ‘sone’ ‘szero’ ‘yone’ ‘yzero’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘RTextTools/libs/RTextTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 50 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 37 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Found the following significant warnings:
  triangle.c:1428:9: warning: too many arguments for format [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-devel/RTriangle.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
Documented arguments not in \usage in Rd file 'summary.trimbatch.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'trim_workhorse.Rd':
  ‘max_beta’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 2023 marked Latin-1 strings
  Note: found 17 marked UTF-8 strings
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘Tsttwalk.dat’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'tidy_pi_traces.Rd':
  ‘mix_indiv_tib’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'MEM_MIDAS_lr_pred_no_skew.Rd':
  ‘daily_ret’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
S3 methods shown with full name in Rd file 'printHTML.trackinfo.Rd':
  ‘printHTML.trackInfo’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘results’
Documented arguments not in \usage in Rd file 'dot-is_datetime_valid.Rd':
  ‘(`character`)’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmmADMB’
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘withr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'summary.rv.Rd':
  ‘all.levels’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'matmult.Rd':
  ‘%*%.rv’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
Note: found 16 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘rwfec/libs/rwfec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 4250 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'wind.fit_int.Rd':
  ‘X’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 12 marked UTF-8 strings
Malformed Title field: should not end in a period.
Note: found 426306 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'LoadDataFile.Rd':
  ‘remapcells’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'predict.s2netR.Rd':
  ‘...’
Argument items with no description in Rd file 'print_misc.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘CARBayesdata’ ‘MASS’ ‘nimble’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 63 marked Latin-1 strings
Note: found 4 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'file_status.Rd':
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Note: found 3 marked Latin-1 strings
Note: found 120 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'SAMM-package.Rd':
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘networkTomography’
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘FitARMA’
Specified C++11: please drop specification unless essential
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
Argument items with no description in Rd file 'creer_graphe.Rd':
  ‘groupes’
Argument items with no description in Rd file 'fichiers.Rd':
  ‘groupes’
'library' or 'require' call to ‘progress’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rgdal’
'LazyData' is specified without a 'data' directory
File ‘saturnin/libs/saturnin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘sBIC/libs/sBIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbioPN/libs/sbioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘sbmSDP/libs/sbmSDP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'item_rm_recursive.Rd':
  ‘sb_id’

Documented arguments not in \usage in Rd file 'session_age.Rd':
  ‘sb_id’ ‘...’

Documented arguments not in \usage in Rd file 'session_expired.Rd':
  ‘sb_id’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
License stub is invalid DCF.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'rrvgo', 'SingleCellSignalR'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mathjaxr’
  All declared Imports should be used.
File ‘SCEPtERbinary/libs/SCEPtERbinary.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SCEPtER/libs/SCEPtER.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'scRNAseq', 'sceasy', 'SeuratDisk', 'SeuratWrappers',
  'zellkonverter', 'GEOfastq'
Note: found 33 marked UTF-8 strings
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Note: found 464 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'conos', 'pagoda2'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'plot.Rd':
  ‘plot.discretization’

S3 methods shown with full name in Rd file 'predict.Rd':
  ‘predict.discretization’ ‘predict.reject_infered’

S3 methods shown with full name in Rd file 'summary.Rd':
  ‘summary.discretization’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RhpcBLASctl’
  All declared Imports should be used.
File ‘scout/libs/scout.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘decoupleR’
File ‘scquantum/libs/scquantum.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘crayon’ ‘knitr’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘untitled_consensus_cluster’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 51 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Found the following significant warnings:
  Suda2.h:772:68: warning: format '%f' expects argument of type 'double', but argument 3 has type 'int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/sdcMicro.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 5 marked Latin-1 strings
  Note: found 51869 marked UTF-8 strings
Packages suggested but not available for checking: 'rgdal', 'rgeos'
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Packages suggested but not available for checking: 'maptools', 'rgdal'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'parse_search_analytics.Rd':
  ‘pn’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'pipe.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘fansi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘testit’
  All declared Imports should be used.
File ‘segmag/libs/segmag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Packages suggested but not available for checking: 'spgrass6', 'rgdal'
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘webp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘editData’ ‘miniUI’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘semver/libs/semver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 836 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
Note: found 3128 marked UTF-8 strings
Note: found 182 marked UTF-8 strings
Note: found 52 marked UTF-8 strings
Auto-generated content requiring editing in Rd file 'seqCBS-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'sequential.design.Rd':
  ‘\dots’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BPCells’
Packages suggested but not available for checking:
  'BPCells', 'monocle', 'presto'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'jc_clc_perm_impl.Rd':
  ‘a’

Documented arguments not in \usage in Rd file 'local_g_spt.Rd':
  ‘n_sim’

Documented arguments not in \usage in Rd file 'permute_listw.Rd':
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  c_functions.c:279:32: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long int' [-Wformat=]
  c_functions.c:288:35: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/SFSI.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘sgeostat/libs/sgeostat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Invalid package aliases in Rd file 'package_sgmodel.Rd':
  ‘package_sgmodel-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
Note: found 14 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘billboarder’ ‘glue’ ‘scrypt’ ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘websocket’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'shiny_models.Rd':
  ‘original_data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 1231 marked UTF-8 strings
‘gs+qpdf’ made some significant size reductions:
     compacted ‘a-SightabilityModel.pdf’ from 399Kb to 140Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files,
  or build the source package with --compact-vignettes=both
Note: found 28 marked UTF-8 strings
Packages suggested but not available for checking: 'ggseqlogo', 'qlcMatrix'
Unknown package ‘ggseqlogo’ in Rd xrefs
File ‘signal/libs/signal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Found the following files/directories:
  ‘ExportFigtree1.tre’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'estThetaRow.Rd':
  ‘theta’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pedtools’ ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  misc/SimInf_clean_raw_events.c:192:66: warning: format '%i' expects argument of type 'int', but argument 2 has type 'R_xlen_t' {aka 'long int'} [-Wformat=]
  misc/SimInf_clean_raw_events.c:194:65: warning: format '%i' expects argument of type 'int', but argument 2 has type 'R_xlen_t' {aka 'long int'} [-Wformat=]
  misc/SimInf_clean_raw_events.c:196:65: warning: format '%i' expects argument of type 'int', but argument 2 has type 'R_xlen_t' {aka 'long int'} [-Wformat=]
  misc/SimInf_clean_raw_events.c:198:65: warning: format '%i' expects argument of type 'int', but argument 2 has type 'R_xlen_t' {aka 'long int'} [-Wformat=]
  misc/SimInf_clean_raw_events.c:207:31: warning: format '%i' expects argument of type 'int', but argument 2 has type 'R_xlen_t' {aka 'long int'} [-Wformat=]
  misc/SimInf_distance_matrix.c:47:55: warning: format '%i' expects argument of type 'int', but argument 2 has type 'R_xlen_t' {aka 'long int'} [-Wformat=]
  misc/SimInf_distance_matrix.c:47:64: warning: format '%i' expects argument of type 'int', but argument 3 has type 'R_xlen_t' {aka 'long int'} [-Wformat=]
  misc/SimInf_distance_matrix.c:99:61: warning: format '%i' expects argument of type 'int', but argument 2 has type 'R_xlen_t' {aka 'long int'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/SimInf.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'make_kernel_dist.Rd':
  ‘Umax’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Note: found 1 marked UTF-8 string
Packages suggested but not available for checking: 'Rcgmin', 'Rvmmin'
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Unknown packages ‘Rvmmin’, ‘Rcgmin’ in Rd xrefs
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rgdal', 'rgeos'
Documented arguments not in \usage in Rd file 'interval_labels.Rd':
  ‘format’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘simplexreg/libs/simplexreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'SimplifyStats-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Found the following significant warnings:
  calibPop.cpp:198:126: warning: format '%g' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/simPop.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘fg_step_tab_pp’
Invalid package aliases in Rd file 'SimReg-package.Rd':
  ‘SimReg3-package’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'sim_founderRVstatus.Rd':
  ‘intro_RV’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'management.prob.Rd':
  ‘...’
Argument items with no description in Rd file 'mng.tree.removal.Rd':
  ‘\dots’
Argument items with no description in Rd file 'prep.common.vars.fun.Rd':
  ‘\dots’
Argument items with no description in Rd file 'recr.BBG2008.Rd':
  ‘common.vars’
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'to_shiny_tag.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 2 marked UTF-8 strings
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
File ‘skm/libs/skm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘png’
  All declared Imports should be used.
Package suggested but not available for checking: ‘texPreview’
Unknown package ‘texPreview’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
Note: found 23 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘captioner’
File ‘SLHD/libs/SLHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘checkmate’ ‘glmnet’ ‘mice’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
File ‘slp/libs/slp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: ‘gurobi’
Auto-generated content requiring editing in Rd file 'smallstuff-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rgdal’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Unknown package ‘InformationValue’ in Rd xrefs
Note: found 1122 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'aux_cs.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gauss.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gw.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_mat.Rd':
  ‘mat_list1’ ‘mat_list2’ ‘x’ ‘y’ ‘return_single’

Documented arguments not in \usage in Rd file 'aux_matern.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_pexp.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_spher.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_tapmat.Rd':
  ‘dists’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'SMLE-package.Rd':
  ‘smle-package’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  glog.cpp:151:10: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  glog.cpp:253:10: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  glog.cpp:286:15: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  glog.cpp:320:13: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  glog.cpp:369:10: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/smog.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'smoke-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Auto-generated content requiring editing in Rd file 'smotefamily-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Found the following files/directories:
  ‘my_new_social_media_plot.png’
Objects in \usage without \alias in Rd file 'sm-internal.Rd':
  ‘sm.check.data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘evd’ ‘truncnorm’
  All declared Imports should be used.
Found the following files/directories:
  ‘.R_Test’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘flextable’ ‘htmlTable’ ‘stringr’
  All declared Imports should be used.
Note: found 938 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘lgr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.solveEnv’
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'som.nn.do.train.Rd':
  ‘model’

Documented arguments not in \usage in Rd file 'som.nn.som.internal.Rd':
  ‘rlen’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'plot.predictions.Rd':
  ‘plot.predictions’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.som.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) som.Rd:128: Escaped LaTeX specials: \_
File ‘som/libs/som.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1245 marked UTF-8 strings
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dbplyr’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'path2name.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
Package suggested but not available for checking: ‘NLMR’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘sparcl/libs/sparcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gtable’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Unknown package ‘sparsebn’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  grad_est.cpp:33:19: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  grad_est.cpp:98:19: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  grad_est.cpp:116:10: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  grad_est.cpp:133:19: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  grad_est.cpp:160:20: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  hmc4sfa.cpp:45:14: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  test_gamma_pois.cpp:30:13: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/SparseFactorAnalysis.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
File ‘SparseFactorAnalysis/libs/SparseFactorAnalysis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘sparseLTSEigen/libs/sparseLTSEigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘sparsereg/libs/sparsereg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SparseTSCGM/libs/SparseTSCGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'logit.Rd':
  ‘theta’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
Note: found 283 marked UTF-8 strings
Argument items with no description in Rd file 'binarizer.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat.data', 'spatstat',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
checkRd: (-1) NEWS.Rd:137: Escaped LaTeX specials: \&
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘spDataLarge’
Note: found 56 marked UTF-8 strings
Note: found 34 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'hazard.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 2 marked UTF-8 strings
File ‘SPECIES/libs/SPECIES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'grapes-matches-grapes.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'changeDevSettings.Rd':
  ‘defaultsSettings’

Documented arguments not in \usage in Rd file 'checkMethod.Rd':
  ‘allowedMethod’

Documented arguments not in \usage in Rd file 'convertListToS4.Rd':
  ‘names’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'i_is_index.Rd':
  ‘max_length’

Documented arguments not in \usage in Rd file 'i_read_asd_spectra.Rd':
  ‘format’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 5 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘glue’ ‘httptest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.neig’
Objects in \usage without \alias in Rd file 'add_details.Rd':
  ‘\S4method{add_details}{spflow_model}’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘sf’ ‘spData’
  All declared Imports should be used.
Note: found 189 marked UTF-8 strings
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
checkRd: (-1) PimaIndiansDiabetes_long.Rd:14: Escaped LaTeX specials: \^
checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'split_feasibility.Rd':
  ‘split_feasibility-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'obis_search.Rd':
  ‘scientificname’

Documented arguments not in \usage in Rd file 'spocc_objects.Rd':
  ‘n’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ratings.cpp:9:28: warning: format '%p' expects argument of type 'void*', but argument 3 has type 'SEXP' {aka 'SEXPREC*'} [-Wformat=]
  ratings.cpp:9:28: warning: format '%p' expects argument of type 'void*', but argument 4 has type 'Rcpp::NumericVector*' {aka 'Rcpp::Vector<14, Rcpp::PreserveStorage>*'} [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/sport.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Specified C++11: please drop specification unless essential
Note: found 7587 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'basketball_center_circle_fill.Rd':
  ‘linethickness’

Documented arguments not in \usage in Rd file 'basketball_free_throw_circle_dash.Rd':
  ‘end_angleThe’

Documented arguments not in \usage in Rd file 'basketball_painted_area.Rd':
  ‘free_throw_lane_boundary_line_thickness’

Documented arguments not in \usage in Rd file 'curling_features_set_colors.Rd':
  ‘sheet’ ‘ring_1’ ‘ring_2’ ‘ring_3’

Documented arguments not in \usage in Rd file 'football_field_border.Rd':
  ‘boundary_thickness’

Documented arguments not in \usage in Rd file 'football_field_border_outline.Rd':
  ‘boundary_thickness’

Documented arguments not in \usage in Rd file 'hockey_features_set_colors.Rd':
  ‘boards_color’ ‘center_line_color’ ‘blue_line_color’
  ‘goal_line_color’ ‘goalkeepers_restricted_area_color’
  ‘goal_crease_outline_color’ ‘goal_crease_fill_color’
  ‘referee_crease_color’ ‘center_faceoff_spot_color’
  ‘faceoff_spot_outer_ring_color’ ‘faceoff_spot_fill_color’
  ‘center_faceoff_circle_color’ ‘non_center_faceoff_circle_color’
  ‘faceoff_line_color’ ‘goal_color’ ‘goal_fill_color’

Documented arguments not in \usage in Rd file 'lacrosse_off_field_officials_box.Rd':
  ‘feature_thickness’

Documented arguments not in \usage in Rd file 'lacrosse_penalty_box_outline.Rd':
  ‘feature_thickness’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'checkFunEvalsDesignSize.Rd':
  ‘fun’ ‘upper’

Documented arguments not in \usage in Rd file 'print.spotBOModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotGaussianProcessModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotLOESS.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotLassoModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotLinearModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotRSM.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotRandomForest.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotRanger.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotSeverity.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotTreeModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'simulationSpectral.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘sampling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘rgeoda’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Note: found 199 marked UTF-8 strings
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'sim.kong.Rd':
  ‘gamma’ ‘beta’ ‘design’ ‘rho’ ‘seed’ ‘impute’ ‘ppi’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘RSQLite’ ‘dbplyr’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘arm’ ‘brms’ ‘lme4’ ‘plotly’ ‘shinyMatrix’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'sraAutoregTimeseries.Rd':
  ‘logs2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'namesMultiple.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 123 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘mice’ ‘sandwich’ ‘zoo’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'connect-report_mig-method.Rd':
  ‘h’ ‘...’

Documented arguments not in \usage in Rd file 'print-report_mig-method.Rd':
  ‘h’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 40748 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'which_class.Rd':
  ‘character’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘reshape2’ ‘stats’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘httr’ ‘latex2exp’ ‘rstantools’ ‘tibble’ ‘tidyverse’
  ‘utils’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘starma/libs/starma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    To do
Package suggested but not available for checking: ‘starsdata’
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'statcheck-package.Rd':
  ‘{statcheck}-package’
Note: found 1 marked Latin-1 string
  Note: found 18 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Documented arguments not in \usage in Rd file 'estEffsCPP.Rd':
  ‘y’ ‘w’ ‘x’ ‘ncores’

Documented arguments not in \usage in Rd file 'updateFA.Rd':
  ‘Y’ ‘WStart’ ‘m’ ‘PStart’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘asreml’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Running examples in ‘statGraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: tang.test
> ### Title: Tang hypothesis testing for random graphs.
> ### Aliases: tang.test
> 
> ### ** Examples
> 
> set.seed(42)
> 
> ## test under H0
> lpvs <- matrix(rnorm(200), 20, 10)
> lpvs <- apply(lpvs, 2, function(x) { return (abs(x)/sqrt(sum(x^2))) })
> G1 <- igraph::sample_dot_product(lpvs)
> G2 <- igraph::sample_dot_product(lpvs)
> D1 <- tang.test(G1, G2, 5)
Error in defaults$maxiter <- .Machine$integer.max : 
  object of type 'closure' is not subsettable
Calls: tang.test -> t.embed.graph
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
'LazyData' is specified without a 'data' directory
Note: found 56 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Package suggested but not available for checking: ‘imputeMissings’
Namespaces in Imports field not imported from:
  ‘DDoutlier’ ‘car’ ‘corrplot’ ‘data.table’ ‘energy’ ‘ggplot2’
  ‘gridExtra’ ‘kableExtra’ ‘knitr’ ‘readr’ ‘reshape2’ ‘rmarkdown’
  ‘shinydisconnect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
File ‘steadyICA/libs/steadyICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘StepwiseTest/libs/StepwiseTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 534 marked UTF-8 strings
Note: found 240 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Found the following files/directories:
  ‘corrviz.html’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'd.sum.of.mixtures.EXPLN.Rd':
  ‘p.vector’
Note: found 22806 marked UTF-8 strings
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Note: found 1725 marked UTF-8 strings
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'strategicplayers-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
  \references: ‘~~ Literature or other references for background information ~~’
Found the following files/directories:
  ‘myNewStrat.R’
Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgeos’
Specified C++11: please drop specification unless essential
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_groups.Rd':
  ‘groups’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
Note: found 705 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'StructFDR-package.Rd':
  ‘TreeFDR-package’
Note: found 83 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'size.penalize.Rd':
  ‘size.penalize’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘maptools’
Documented arguments not in \usage in Rd file 'subsamp.Rd':
  ‘x:’ ‘y:’ ‘s:’ ‘m:’ ‘qnum:’ ‘wplot:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘grDevices’ ‘graphics’ ‘jsonlite’
  ‘purrr’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘SummaryLasso/libs/SummaryLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 78 marked UTF-8 strings
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'supcluster-package.Rd':
  \references: ‘~~ Literature or other references for background information ~~’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘extraTrees’
Unknown package ‘extraTrees’ in Rd xrefs
Package suggested but not available for checking: ‘extraTrees’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'check_package.Rd':
  ‘X’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
surfaceSimulate : phytransform: no visible global function definition
  for ‘rescale’
Undefined global functions or variables:
  rescale
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc'
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
File ‘survivalROC/libs/survivalROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Note: found 88 marked UTF-8 strings
Unknown package ‘survJamda’ in Rd xrefs
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tidyquant’ ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
Package suggested but not available for checking: ‘swephRdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘markdown’ ‘nextGenShinyApps’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
possible bashism in configure line 12 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 22 (echo -n):
  echo -n "  checking for OS..."
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Invalid package aliases in Rd file 'syncrng-package.Rd':
  ‘syncrng-package’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘StackImpute’ ‘arm’ ‘boot’ ‘broom’ ‘knitr’ ‘mvtnorm’
  ‘randomForest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.csv’
'LazyData' is specified without a 'data' directory
Note: found 38 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 551 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'table_params_circle.Rd':
  ‘d’

Documented arguments not in \usage in Rd file 'table_params_rect.Rd':
  ‘d’ ‘scale_breaks’ ‘r_max’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'plot.prEntries.Rd':
  ‘plot.margin’ ‘sizeAdjust’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 81 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'designMatrices.Rd':
  ‘print.designMatrices’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Note: found 301 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'default_db_ref.Rd':
  ‘name’ ‘url’ ‘desc’ ‘id_regex’

Documented arguments not in \usage in Rd file 'limited_print.Rd':
  ‘trunc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 137 marked UTF-8 strings
Note: found 30 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘reshape2’ ‘truncnorm’ ‘xtable’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  node_categorical.cpp:46:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_categorical.cpp:49:19: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_categorical.cpp:56:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_categorical.cpp:59:19: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_continuous.cpp:41:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_continuous.cpp:47:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/TDboost.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'maptools', 'R2wd'
checkRd: (-1) R2txt.Rd:164: Escaped LaTeX specials: \#
checkRd: (-1) bct.Rd:18: Escaped LaTeX specials: \^
checkRd: (-1) bct.Rd:19: Escaped LaTeX specials: \^
checkRd: (-1) ineq.Rd:10: Escaped LaTeX specials: \&
checkRd: (-1) put.points.demo.Rd:39: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:10: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:31: Escaped LaTeX specials: \^
Found the following files/directories:
  ‘Crashpad’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 56 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘par-7269706c6579’
Package suggested but not available for checking: ‘gurobi’
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'CompileLatexDir.Rd':
  ‘engine:’ ‘compile.dir:’

Documented arguments not in \usage in Rd file 'GetLayerSampleIndexes.Rd':
  ‘NamesOfListToSample’ ‘isRandomized’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
Note: found 37 marked UTF-8 strings
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘forecast’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Rd file 'textEmbedReduce.Rd':
  \usage lines wider than 90 characters:
         "https://raw.githubusercontent.com/adithya8/ContextualEmbeddingDR/master/models/fb20/scalar.csv",
         "https://raw.githubusercontent.com/adithya8/ContextualEmbeddingDR/master/models/fb20/rpca_roberta_768_D_20.csv"

These lines will be truncated in the PDF manual.
Note: found 3 marked UTF-8 strings
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Unknown package ‘textreadr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in Rd file 'timeSeries.Rd':
  ‘tbind.timeSeries’

Objects in \usage without \alias in Rd file 'tis.Rd':
  ‘tfstart.tis’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘MASS’ ‘base’ ‘graphics’ ‘janitor’ ‘rlang’ ‘testthat’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 197527 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘readr’ ‘tidyverse’ ‘usethis’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'witcher.Rd':
  ‘palettes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'poisson_likelihood.Rd':
  ‘rate_exp’ ‘rate_ref’ ‘rate_pla’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘knitr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘badger’ ‘ggplot2’ ‘lubridate’ ‘scales’ ‘xgboost’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 4546 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'gate_interactive_chr_int.Rd':
  ‘gate_list’

Documented arguments not in \usage in Rd file 'gate_programmatic.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'gate_programmatic_chr_int.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
Note: found 182 marked UTF-8 strings
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'deprecated-se.Rd':
  ‘expand_cols’

Documented arguments not in \usage in Rd file 'tidyr_legacy.Rd':
  ‘nm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'vars_select.Rd':
  ‘args’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘SingleR’
Note: found 113 marked UTF-8 strings
Note: found 34206 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 4581 marked UTF-8 strings
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'timeperiodsR-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'timeSeq_1.0.4-package.Rd':
  ‘timeSeq_1.0.4-package’
Note: found 2750 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: found 134043 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Invalid package aliases in Rd file 'tm.plugin.alceste-package.Rd':
  ‘tm.plugin.europresse-package’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvtnorm/libs/tmvtnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'TNRS_core.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
Package suggested but not available for checking: ‘corpus.JSS.papers’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
Namespace in Imports field not imported from: ‘hdi’
  All declared Imports should be used.
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'createLink.Rd':
  ‘hits’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘moveVis’
Unknown package ‘moveVis’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
Argument items with no description in Rd file 'abrams.Rd':
  ‘prior’ ‘change’
Argument items with no description in Rd file 'absoluteIncreaseALL.Rd':
  ‘storedev’ ‘\dots’
Argument items with no description in Rd file 'boundaryLineALL.Rd':
  ‘\dots’
Argument items with no description in Rd file 'growthAveragingALL.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plotFirstYears.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plotRelease.Rd':
  ‘\dots’
Argument items with no description in Rd file 'splechtnaALL.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxidata’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'seqimplic.Rd':
  ‘ylim’
Note: found 827 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in Rd file 'transport-internal.Rd':
  ‘gif.generate’ ‘plot_pgrid_wpp’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘fwelnet’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR', 'Capr'
Documented arguments not in \usage in Rd file 'clean_data.Rd':
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'correct_continuous.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'tc_correlation.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'tc_efunc.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'tc_mfunc.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'tc_response.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'truncate_input.Rd':
  ‘moving’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Package suggested but not available for checking: ‘TreeDistData’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'treemisc-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘Using_TropFishR_ELEFAN_functions.Rmd’ using rmarkdown

Quitting from lines 220-236 [unnamed-chunk-10] (Using_TropFishR_ELEFAN_functions.Rmd)
Error: processing vignette 'Using_TropFishR_ELEFAN_functions.Rmd' failed with diagnostics:
no rows to aggregate
--- failed re-building ‘Using_TropFishR_ELEFAN_functions.Rmd’

--- re-building ‘lfqData.Rmd’ using rmarkdown
--- finished re-building ‘lfqData.Rmd’

--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 147-161 [Figure 4] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
no rows to aggregate
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘Using_TropFishR_ELEFAN_functions.Rmd’ ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'dvinecopula_objective.Rd':
  ‘udata’

Documented arguments not in \usage in Rd file 'wobjective.Rd':
  ‘vt’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Objects in \usage without \alias in Rd file 'nlar.struct.Rd':
  ‘getNUsed’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
File ‘tseriesTARMA/libs/tseriesTARMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'tsibble-vctrs.Rd':
  ‘vec_ptype2.tbl_ts’ ‘vec_cast.tbl_ts’ ‘vec_cast.yearmonth’
  ‘vec_ptype2.yearmonth’ ‘vec_cast.yearquarter’
  ‘vec_ptype2.yearquarter’ ‘vec_cast.yearweek’ ‘vec_ptype2.yearweek’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'tsoutliers-package.Rd':
  ‘tsouliers-package’
'LazyData' is specified without a 'data' directory
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Invalid package aliases in Rd file 'TTAinterface-package.Rd':
  ‘TTAinterface-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 34 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Note: found 2 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘foreign’ ‘psychTools’ ‘pwr’ ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'HC.Rd':
  ‘X’ ‘K’
Argument items with no description in Rd file 'KA.Rd':
  ‘X’ ‘K’ ‘distancemetric’
Argument items with no description in Rd file 'SOMs.Rd':
  ‘X’ ‘K’ ‘topo’ ‘rlen’ ‘alpha’ ‘n.hood’
Argument items with no description in Rd file 'binarise.Rd':
  ‘U’ ‘K’ ‘technique’ ‘parameter’
Argument items with no description in Rd file 'closestToSquareFactors.Rd':
  ‘n’
Argument items with no description in Rd file 'clustDist.Rd':
  ‘U1’ ‘U2’ ‘X’ ‘criterion’
Argument items with no description in Rd file 'clustVec2partMat.Rd':
  ‘C’
Argument items with no description in Rd file 'clusterDataset.Rd':
  ‘X’ ‘K’ ‘D’ ‘methods’
Argument items with no description in Rd file 'factors.Rd':
  ‘n’ ‘primeonly’
Argument items with no description in Rd file 'fixnans.Rd':
  ‘X’ ‘type’
Argument items with no description in Rd file 'fuzzystretch.Rd':
  ‘X’ ‘x0’
Argument items with no description in Rd file 'generateCoPaM.Rd':
  ‘U’ ‘relabel_technique’ ‘w’ ‘X’ ‘distCriterion’ ‘K’ ‘GDM’
Argument items with no description in Rd file 'isValidBPM.Rd':
  ‘U’
Argument items with no description in Rd file 'isempty.Rd':
  ‘X’
Argument items with no description in Rd file 'isnullorempty.Rd':
  ‘X’
Argument items with no description in Rd file 'kmeansKA.Rd':
  ‘X’ ‘K’ ‘distancemetric’ ‘iter.max’ ‘nstart’ ‘algorithm’ ‘trace’
Argument items with no description in Rd file 'mnplots.Rd':
  ‘Vmse’ ‘mseCache’ ‘subplotdim’ ‘subplotind’ ‘minimiseDistance’
Argument items with no description in Rd file 'mseclusters.Rd':
  ‘X’ ‘B’ ‘normalise’
Argument items with no description in Rd file 'normaliseMatrix.Rd':
  ‘X’ ‘type’
Argument items with no description in Rd file 'partMat2clustVec.rd':
  ‘U’ ‘skipValidity’
Argument items with no description in Rd file 'permutations.Rd':
  ‘n’
Argument items with no description in Rd file 'relabelClusts.Rd':
  ‘ref’ ‘input’ ‘technique’ ‘X’ ‘distCriterion’
Documented arguments not in \usage in Rd file 'sqrtm.Rd':
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘ungroup.Rd’
Documented arguments not in \usage in Rd file 'MortSmooth_tpower.Rd':
  ‘vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 548 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘uniswappeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: swap_statistics
> ### Title: Get statistics on the swaps data for a given address or
> ###   addresses
> ### Aliases: swap_statistics
> 
> ### ** Examples
> 
> 
> addresses <- c("0xb1b117a45aD71d408eb55475FC3A65454edCc94A",
+ "0x41D2a18E1DdACdAbFDdADB62e9AEE67c63070b76",
+ "0x0De20c4bDBE0d0EEFFd2956Be4c148CA86C6cC45")
> 
> swap_data <- swaps(addresses)
Error in `.data$Address`:
! Column `Address` not found in `.data`.
Backtrace:
     ▆
  1. ├─uniswappeR::swaps(addresses)
  2. │ └─swaps %>% select(.data$Address, everything())
  3. ├─dplyr::select(., .data$Address, everything())
  4. ├─dplyr:::select.data.frame(., .data$Address, everything())
  5. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
  6. │   └─tidyselect:::eval_select_impl(...)
  7. │     ├─tidyselect:::with_subscript_errors(...)
  8. │     │ └─rlang::try_fetch(...)
  9. │     │   └─base::withCallingHandlers(...)
 10. │     └─tidyselect:::vars_select_eval(...)
 11. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 12. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
 13. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 14. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
 15. │               └─base::eval(expr, data_mask)
 16. │                 └─base::eval(expr, data_mask)
 17. │                   ├─Address
 18. │                   └─rlang:::`$.rlang_data_pronoun`(.data, Address)
 19. │                     └─rlang:::data_pronoun_get(...)
 20. └─rlang:::abort_data_pronoun(x, call = y)
 21.   └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: found 3347 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 7872 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Note: found 488 marked UTF-8 strings
Package suggested but not available for checking: ‘USA.state.boundaries.data’
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'use_course_details.Rd':
  ‘destdir’ ‘zipfile’

Documented arguments not in \usage in Rd file 'write-this.Rd':
  ‘contents’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
Note: found 1 marked UTF-8 string
Note: found 50 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'parallel' 'xml2'
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'countDNAPatternInAlt.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'countDNAPatternInAltOneVariant.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'getAltSequence.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'getCodonInAlt.Rd':
  ‘trascriptsTable’ ‘codonPositionsColumnn’

Documented arguments not in \usage in Rd file 'getCodonInAltOneVariant.Rd':
  ‘trascriptsTable’ ‘codonPositionsColumnn’

Documented arguments not in \usage in Rd file 'getTSSKozakOneVariant.Rd':
  ‘variantsTable’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘badger’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'validate_extend.Rd':
  ‘varlist:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DT’ ‘maps’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
S3 methods shown with full name in Rd file 'syntab.Rd':
  ‘print.syntab’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 128 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'vein-deprecated.Rd':
  ‘object’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 49 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Argument items with no description in Rd file 'learnPartitionWithLLR.Rd':
  ‘type’ ‘procedure’ ‘ql’ ‘qq’ ‘BinaryLearningProcedure’
Argument items with no description in Rd file 'plotClassifRule.Rd':
  ‘object’
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'boxplot_VICI.Rd':
  ‘res_2plot’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘leaflet’ ‘mapview’
  All declared Imports should be used.
Note: found 60 marked UTF-8 strings
Note: found 468 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'draw_map_shiny.Rd':
  ‘rigth.lim’

Documented arguments not in \usage in Rd file 'map_summary.Rd':
  ‘rigth.lim’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘readr’ ‘uuid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 2754 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'cpp_vol2bird_version.Rd':
  ‘path’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Note: found 4954 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'blendColor.Rd':
  ‘color’ ‘percent’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get.wal.mipmap.heights.Rd':
  ‘height_mm’

Documented arguments not in \usage in Rd file 'get.wal.mipmap.widths.Rd':
  ‘width_mm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'WaveDjF.Rd':
  ‘y_fft’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Auto-generated content requiring editing in Rd file 'maxithresh.Rd':
  \details: ‘~~ If necessary, more details than the description above ~~’
  \arguments: data: ‘~~Describe \code{data} here~~’
  \arguments: g: ‘~~Describe \code{g} here~~’
  \arguments: L: ‘~~Describe \code{L} here~~’
  \arguments: F: ‘~~Describe \code{F} here~~’
  \arguments: eta: ‘~~Describe \code{eta} here~~’
'LazyData' is specified without a 'data' directory
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 3133 marked UTF-8 strings
Note: found 4413 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building ‘wcde.Rmd’ using rmarkdown

Quitting from lines 54-62 [unnamed-chunk-4] (wcde.Rmd)
Error: processing vignette 'wcde.Rmd' failed with diagnostics:
ℹ In argument: `d = purrr::map(.x = u, .f = ~read_with_progress(f =
  .x))`.
Caused by error in `purrr::map()`:
ℹ In index: 1.
Caused by error in `open.connection()`:
! HTTP error 404.
--- failed re-building ‘wcde.Rmd’

SUMMARY: processing the following file failed:
  ‘wcde.Rmd’

Error: Vignette re-building failed.
Execution halted
Invalid package aliases in Rd file 'wce-package.Rd':
  ‘wce-package’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Note: found 1668 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘prepr’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'read_img.Rd':
  ‘imgfile’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘here’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘weightedCL/libs/weightedCL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Argument items with no description in Rd file 'zdifference_ordinal.Rd':
  ‘na.rm’
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'QIC.gee.Rd':
  ‘QIC.gee’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
Note: found 4102 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'remove_empty.Rd':
  ‘quiet’

Documented arguments not in \usage in Rd file 'undoHistory.Rd':
  ‘class’ ‘btn_class’ ‘back_text’ ‘fwd_text’ ‘back_title’ ‘fwd_title’
  ‘back_icon’ ‘fwd_icon’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
Documented arguments not in \usage in Rd file 'displayDataTable.Rd':
  ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pageviews’
Package suggested but not available for checking: ‘pageviews’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘plotly’ ‘shinythemes’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 3881 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 933 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Note: found 3 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'new_givens_path.Rd':
  ‘generate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  dataobj.c:772:23: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
See ‘/data/gannet/ripley/R/packages/tests-devel/wrassp.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'sample_me.Rd':
  ‘middle_name’ ‘M_rs’ ‘M_rf’ ‘M_rm’ ‘alpha’ ‘me_race’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'Cut.off.Rd':
  ‘main’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rbokeh’
checkRd: (-1) read.npc.vpc.results.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) read.npc.vpc.results.Rd:19: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_
checkRd: (-1) read.npc.vpc.results.Rd:22: Escaped LaTeX specials: \_
Documented arguments not in \usage in Rd file 'xpose.create.title.Rd':
  ‘plot.text’ ‘main’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'check_problem.Rd':
  ‘xpdb’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘viridis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
Invalid package aliases in Rd file 'XRjulia-package.Rd':
  ‘XRjulia-package’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Argument items with no description in Rd file 'getCondition.Rd':
  ‘object’
Argument items with no description in Rd file 'screen.Rd':
  ‘fac’ ‘condition’ ‘position’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'IC.Rd':
  ‘\dots’
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Note: found 76 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'ZIBseq-package.Rd':
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~ ~~ \code{\link...’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 47 marked UTF-8 strings
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 146804 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    include  12.5Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'ADMM_EN2.Rd':
  'alpha'

Documented arguments not in \usage in Rd file 'ADMM_EN_SMW.Rd':
  'alpha'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Argument items with no description in Rd file 'testRmACD.Rd':
  'pStar'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'fitSnpNmfArray.Rd':
  'maxIter' 'acc'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
Documented arguments not in \usage in Rd file 'd1.Rd':
  'The' 'A'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'AdaptGauss-package.Rd':
  'MultiModal-package'
Invalid package aliases in Rd file 'aslm-package.Rd':
  'aslm-package' 'asggm-package'
Argument items with no description in Rd file 'asggm-internal.Rd':
  'ansL' 'kNodes' 'spP'
Specified C++11: please drop specification unless essential
Unknown packages 'HI', 'MHadaptive' in Rd xrefs
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'print.aTest.Rd':
  'how'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   2.9Mb
    libs   1.2Mb
Documented arguments not in \usage in Rd file 'ae_count.Rd':
  'patients'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/admiralonco.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'adbcva.Rmd' using rmarkdown

Quitting from lines 151-181 [unnamed-chunk-6] (adbcva.Rmd)
Error: processing vignette 'adbcva.Rmd' failed with diagnostics:
The `analysis_value` argument of `derive_param_computed()` was
deprecated in admiral 0.12.0 and is now defunct.
ℹ Please use the `set_values_to` argument instead.
--- failed re-building 'adbcva.Rmd'

--- re-building 'admiralophtha.Rmd' using rmarkdown
--- finished re-building 'admiralophtha.Rmd'

--- re-building 'adoe.Rmd' using rmarkdown
--- finished re-building 'adoe.Rmd'

--- re-building 'advfq.Rmd' using rmarkdown
--- finished re-building 'advfq.Rmd'

--- re-building 'standards.Rmd' using rmarkdown
--- finished re-building 'standards.Rmd'

SUMMARY: processing the following file failed:
  'adbcva.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'adce.Rmd' using rmarkdown

Quitting from lines 135-146 [unnamed-chunk-8] (adce.Rmd)
Error: processing vignette 'adce.Rmd' failed with diagnostics:
argument "join_type" is missing, with no default
--- failed re-building 'adce.Rmd'

--- re-building 'adface.Rmd' using rmarkdown

Quitting from lines 233-247 [unnamed-chunk-13] (adface.Rmd)
Error: processing vignette 'adface.Rmd' failed with diagnostics:
argument "join_type" is missing, with no default
--- failed re-building 'adface.Rmd'

--- re-building 'adis.Rmd' using rmarkdown

Quitting from lines 551-562 [unnamed-chunk-19] (adis.Rmd)
Error: processing vignette 'adis.Rmd' failed with diagnostics:
argument "join_type" is missing, with no default
--- failed re-building 'adis.Rmd'

--- re-building 'admiralvaccine.Rmd' using rmarkdown
--- finished re-building 'admiralvaccine.Rmd'

--- re-building 'adsl.Rmd' using rmarkdown
--- finished re-building 'adsl.Rmd'

SUMMARY: processing the following files failed:
  'adce.Rmd' 'adface.Rmd' 'adis.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package which this enhances but not available for checking: 'asreml'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'aire.zmvm-deprecated.Rd':
  'aire.zmvm-deprecated-package'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'gs.Rd':
  'x' 'parallel'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
Argument items with no description in Rd file 'MLS.Rd':
  'MSE1'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'metaboliteIDmapping'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'amelia.package.Rd':
  'amelia-package'
'LazyData' is specified without a 'data' directory
'library' or 'require' call to 'network' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'check_factors.Rd':
  'object'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'rowVars.Rd':
  \arguments: \dots: '~~Describe \code{\dots} here~~'
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Problems with news in 'NEWS.md':
No news entries found.
Documented arguments not in \usage in Rd file 'crawl_interpolation.Rd':
  'pt.colors'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'alternate.sol3.Rd':
  'lambda0'

Documented arguments not in \usage in Rd file 'check.group.Rd':
  'k'

Documented arguments not in \usage in Rd file 'getrow3.Rd':
  'lambda0'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'apci.Rd':
  '\dots'
Argument items with no description in Rd file 'apci.bar.Rd':
  '\dots'
Argument items with no description in Rd file 'apci.plot.Rd':
  '\dots'
Argument items with no description in Rd file 'apci.plot.heatmap.Rd':
  '\dots'
Argument items with no description in Rd file 'apci.plot.hexagram.Rd':
  'first_age' 'first_period' 'interval' 'first_age_isoline'
  'first_period_isoline' 'isoline_interval' 'line_width' 'line_color'
  'label_size' 'label_color' 'scale_units' 'wrap_cohort_labels'
  'quantile'
Argument items with no description in Rd file 'apci.plot.raw.Rd':
  '\dots'
Argument items with no description in Rd file 'cohortdeviation.Rd':
  '\dots'
Argument items with no description in Rd file 'compute_xcoordinate.Rd':
  'p'
Argument items with no description in Rd file 'compute_ycoordinate.Rd':
  'p' 'a'
Argument items with no description in Rd file 'maineffect.Rd':
  '\dots'
Argument items with no description in Rd file 'temp_model.Rd':
  '\dots'
Argument items with no description in Rd file 'tests.Rd':
  '\dots'
Error(s) in re-building vignettes:
--- re-building 'aPEAR-vignette.Rmd' using rmarkdown

Quitting from lines 32-46 [unnamed-chunk-2] (aPEAR-vignette.Rmd)
Error: processing vignette 'aPEAR-vignette.Rmd' failed with diagnostics:
package or namespace load failed for 'clusterProfiler' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'HPO.db'
--- failed re-building 'aPEAR-vignette.Rmd'

SUMMARY: processing the following file failed:
  'aPEAR-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in Rd file 'apercu.Rd':
  'c'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    documents     2.4Mb
    libs          1.1Mb
    screenshots   1.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.6Mb
    doc    1.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found export directive that requires package 'methods':
  'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
Argument items with no description in Rd file 'dynamac_pkg_bounds_test.Rd':
  'obs' 'fstat' 'tstat' 'case' 'k'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
Documented arguments not in \usage in Rd file 'allocateFromCdf.AromaUnitTabularBinaryFile.Rd':
  'path' 'tags' 'footer'

Documented arguments not in \usage in Rd file 'byChipType.DChipSnpInformation.Rd':
  'rootPath' 'pattern' 'verbose'

Documented arguments not in \usage in Rd file 'byChipType.UgpGenomeInformation.Rd':
  'version'

Documented arguments not in \usage in Rd file 'calculateResidualSet.FirmaModel.Rd':
  'verbose'

Documented arguments not in \usage in Rd file 'findByChipType.AromaChipTypeAnnotationFile.Rd':
  'chipType' 'tags'

Documented arguments not in \usage in Rd file 'fit.SmoothMultiarrayModel.Rd':
  'data'

Documented arguments not in \usage in Rd file 'getCellIndices.ExonChipEffectFile.Rd':
  'units'

Documented arguments not in \usage in Rd file 'getImage.AffymetrixCelFile.Rd':
  'palette'

Documented arguments not in \usage in Rd file 'getOutputDataSet.Transform.Rd':
  'force'

Documented arguments not in \usage in Rd file 'getUnitTypes.AffymetrixCdfFile.Rd':
  'map'

Documented arguments not in \usage in Rd file 'plotMvsX.AffymetrixCelFile.Rd':
  'xlim' 'xlab'

Documented arguments not in \usage in Rd file 'process.BackgroundCorrection.Rd':
  'force' 'verbose'

Documented arguments not in \usage in Rd file 'readUnits.CnagCfhFile.Rd':
  'cdf'

Documented arguments not in \usage in Rd file 'setArrays.ArrayExplorer.Rd':
  'arrays'

Documented arguments not in \usage in Rd file 'setRestructor.AffymetrixCdfFile.Rd':
  'units'

Documented arguments not in \usage in Rd file 'setupExampleData.Rd':
  'dirs'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in Rd file 'fitOne.MultiSourceCopyNumberNormalization.Rd':
  'name'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Documented arguments not in \usage in Rd file 'fit.CopyNumberSegmentationModel.Rd':
  'chromosome'

Documented arguments not in \usage in Rd file 'getPath.Explorer.Rd':
  'create'

Documented arguments not in \usage in Rd file 'process.AromaTransform.Rd':
  'force' 'verbose'

Documented arguments not in \usage in Rd file 'process.ChromosomeExplorer.Rd':
  'chromosome'

Documented arguments not in \usage in Rd file 'process.Explorer.Rd':
  'arrays' 'verbose'

Documented arguments not in \usage in Rd file 'setArrays.Explorer.Rd':
  'arrays'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 42.9Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    libs  38.0Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    bin   11.3Mb
    misc   2.1Mb
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Found the following significant warnings:
  rwin.c:28:8: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  rwin.c:251:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  rwin.c:283:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  rwin.c:291:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/asciicast.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'RweaveAsciiSetup.Rd':
  'stylepath'

Documented arguments not in \usage in Rd file 'RweaveOrg.Rd':
  'stylepath'

Documented arguments not in \usage in Rd file 'RweavePandoc.Rd':
  'stylepath'

Documented arguments not in \usage in Rd file 'RweaveReST.Rd':
  'stylepath'

Documented arguments not in \usage in Rd file 'RweaveT2t.Rd':
  'stylepath'

Documented arguments not in \usage in Rd file 'RweaveTextile.Rd':
  'stylepath'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
Found the following significant warnings:
  MSTOpt.cpp:20:43: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<std::vector<double> >::size_type' {aka 'long long unsigned int'} [-Wformat=]
  MSTOpt.cpp:593:49: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  genetic_map_DH.cpp:191:31: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<std::vector<double> >::size_type' {aka 'long long unsigned int'} [-Wformat=]
  genetic_map_DH.cpp:233:19: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  genetic_map_DH.cpp:470:17: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  genetic_map_DH.cpp:477:17: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<std::vector<int> >::size_type' {aka 'long long unsigned int'} [-Wformat=]
  linkage_group_DH.cpp:123:31: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<std::vector<double> >::size_type' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/ASMap.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Package which this enhances but not available for checking: 'asreml'
Documented arguments not in \usage in Rd file 'check.args_.Rd':
  'rename_' 'arg.update_'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'asteRiskData'
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package 'snpar' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'write.narrative.Rd':
  'trials:'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'fdpbandsdata'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'BartMixVs-package.Rd':
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
Found the following significant warnings:
  cabart.cpp:289:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  cgbart.cpp:324:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  cpbart.cpp:296:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  cwbart.cpp:286:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/BART.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Earlier versions
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.8Mb
GNU make is a SystemRequirements.
Invalid package aliases in Rd file 'bayesANOVA-package.Rd':
  'bayesANOVA-package'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   5.2Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.5Mb
Package suggested but not available for checking: 'INLA'
Documented arguments not in \usage in Rd file 'Q_prime.Rd':
  'spdean'

Documented arguments not in \usage in Rd file 'neg_kappa_fn4.Rd':
  'spde_mats'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
GNU make is a SystemRequirements.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   1.8Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   5.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.9Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'hmmeantemp.Rd':
  'dat'
Found the following significant warnings:
  mbart.cpp:406:18: warning: format '%d' expects argument of type 'int', but argument 2 has type 'ivs' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/BayesTree.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.3Mb
    libs      1.4Mb
checkRd: (-1) tlsce.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:93: Escaped LaTeX specials: \_
S3 methods shown with full name in Rd file 'export.bce.Rd':
  'export.bce'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  HelperVariables.h:135:15: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=]
  Params.h:122:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  Graph.h:186:66: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::vector<Node>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  Cbcpgraph.cpp:58:66: warning: format '%f' expects a matching 'double' argument [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/bcp.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'bdw.Rd':
  '\dots'
Argument items with no description in Rd file 'plot.bdw.Rd':
  '\dots'
Argument items with no description in Rd file 'summary.bdw.Rd':
  '\dots'
Specified C++11: please drop specification unless essential
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'print_summary_gibbs_psd_help.Rd':
  'flag=T:'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is 151.7Mb
  sub-directories of 1Mb or more:
    include  150.6Mb
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'h.pr.u.Rd':
  'z' 'ih' 'mu' 'sigma' 'pk' 'K' 'H' 'n'
Argument items with no description in Rd file 'hatpai.u.Rd':
  'z' 'hk1' 'hk0' 'ph1' 'ph0' 'sigma1' 'sigma0' 'mu1' 'mu0' 'pai' 'H'
  'n'
Argument items with no description in Rd file 'ind.u.Rd':
  'pr'
Argument items with no description in Rd file 'lambda.u.Rd':
  'nu'
Argument items with no description in Rd file 'mu.k.u.Rd':
  'k' 'ik' 'z' 'sigma' 'mu0'
Argument items with no description in Rd file 'nu.u.Rd':
  'ind' 'tau' 'H'
Argument items with no description in Rd file 'pai.u.Rd':
  'b' 'a.pai' 'b.pai'
Argument items with no description in Rd file 'sig.k.u.Rd':
  'k' 'ik' 'z' 'mu0' 'a0' 'b0'
Argument items with no description in Rd file 'z.pr.u.Rd':
  'z' 'hk' 'mu' 'sigma' 'ph' 'H' 'n'
'LazyData' is specified without a 'data' directory
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found export directive that requires package 'methods':
  'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
Package suggested but not available for checking: 'ffbase'
Invalid package aliases in Rd file 'package_bigdist.Rd':
  'package_bigdist-package'
Package suggested but not available for checking: 'INLA'
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'select.cfs.Rd':
  'select.cfs'

S3 methods shown with full name in Rd file 'select.fast.filter.Rd':
  'select.fast.filter'

S3 methods shown with full name in Rd file 'select.forward.Corr.Rd':
  'select.forward.Corr'

S3 methods shown with full name in Rd file 'select.forward.wrapper.Rd':
  'select.forward.wrapper'

S3 methods shown with full name in Rd file 'select.inf.chi2.Rd':
  'select.inf.chi2'

S3 methods shown with full name in Rd file 'select.inf.gain.Rd':
  'select.inf.gain'

S3 methods shown with full name in Rd file 'select.inf.symm.Rd':
  'select.inf.symm'

S3 methods shown with full name in Rd file 'select.process.Rd':
  'select.process'

S3 methods shown with full name in Rd file 'select.relief.Rd':
  'select.relief'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
Documented arguments not in \usage in Rd file 'predict2.em.Rd':
  'na.rm'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    doc    1.1Mb
    help   1.0Mb
    libs   1.0Mb
Invalid package aliases in Rd file 'bios2cor-package.Rd':
  'bios2cor-package'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      1.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
checkRd: (-1) FighterAircraft.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'ONA_compiled.Rd':
  'ATN'
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
Argument items with no description in Rd file 'export.dyadic.Rd':
  'blauObj'
Package suggested but not available for checking: 'cmdstanr'
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    libs       4.9Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/blockcluster.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'id2rownum.Rd':
  'ids'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/BonEV.Rcheck/00install.out' for details.
installed size is 40.8Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      29.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Documented arguments not in \usage in Rd file 'check_inputs.Rd':
  'h_rs'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
Documented arguments not in \usage in Rd file 'InternalFunctions.Rd':
  'metric' 'matrix'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'info.Rd':
  'mod_spec' 'pkg_spec'

Documented arguments not in \usage in Rd file 'path.Rd':
  'args'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'b_samp.Rd':
  'Y'

Documented arguments not in \usage in Rd file 'betaBlock.Rd':
  'Y'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Documented arguments not in \usage in Rd file 'utils.Rd':
  'max.len'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'availability.int.Rd':
  'v.set' 'dir.set'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in Rd file 'subset.int.Rd':
  'subset.int'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'cmdstanr'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   3.6Mb
Package suggested but not available for checking: 'glmmADMB'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/BRugs.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'table.Rd':
  'headTitles'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Argument items with no description in Rd file 'plot.bshazard.Rd':
  '\dots'
Argument items with no description in Rd file 'print.bshazard.Rd':
  '\dots'
Argument items with no description in Rd file 'summary.bshazard.Rd':
  '\dots'
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    fonts   3.7Mb
    lib     4.5Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/bsts.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'gvcm.cat'
Specified C++11: please drop specification unless essential
Unknown package 'gvcm.cat' in Rd xrefs
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'count.Rd':
  '.data'

Documented arguments not in \usage in Rd file 'unite.Rd':
  '.data'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'calcIntegralSurv2_cpp.Rd':
  'dsurvival'

Documented arguments not in \usage in Rd file 'dot-calcIntegralCif_cpp.Rd':
  'cif' 'CIF_t'

Documented arguments not in \usage in Rd file 'validFCTs.Rd':
  'super.classes'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
Found the following significant warnings:
  WARNING: failed to apply patch d:/RCompile/CRANpkg/r_packages/patches/CRAN/Cairo.diff
See 'd:/Rcompile/CRANpkg/local/4.4/Cairo.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
Documented arguments not in \usage in Rd file 'get_result.Rd':
  'out'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'makeEventHistory.Rd':
  'type'
Argument items with no description in Rd file 'plotSeqCount.Rd':
  'segColors'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    www  12.1Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'EcoLinkPredict.Rd':
  'EcoLinkPredict-package'
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'validate_cover_cats.Rd':
  'cats_target'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc  37.7Mb
Documented arguments not in \usage in Rd file 'add_catmaply_slider.Rd':
  'text_font_color' 'categorical_col'

Documented arguments not in \usage in Rd file 'add_catmaply_traces.Rd':
  'categorical_col'

Documented arguments not in \usage in Rd file 'catmaply_annotations.Rd':
  'fig' 'text_font_color'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'rkeops'
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'buildModel.Rd':
  'x' 'y'

Documented arguments not in \usage in Rd file 'modelKrigingInternalPredictor.Rd':
  '...'

Documented arguments not in \usage in Rd file 'selfAdapt.Rd':
  'nvaleus'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in Rd file 'evaluate_rule.Rd':
  'class'

Documented arguments not in \usage in Rd file 'tree_leaf_nodes.Rd':
  'classes.' 'invert.'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Title: Add a cell type rule.
> ### Aliases: rule
> 
> ### ** Examples
> 
> # T cells are CD3E+:
> obj <- rule(simulated_umis, "T", "CD3E", ">", .1)
> # T cells are MS4A1-:
> obj <- rule(obj, "T", "MS4A1", "<", 1)
> # Tregs are a subset of T cells:
> obj <- rule(obj, "Treg", "FOXP3", ">", .1, parent="T") 
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  6.33 0.43 6.77 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
    libs   1.7Mb
Auto-generated content requiring editing in Rd file 'CensMFM-package.Rd':
  \details: '...o use the package, including the most important functions ~~'
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
Documented arguments not in \usage in Rd file 'blackboost_train.Rd':
  'x' 'y'

Documented arguments not in \usage in Rd file 'survival_prob_mboost.Rd':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'centralplot.Rd':
  'alpha'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major refactoring of the code
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'create_epa.Rd':
  'clean_pbp_dat' 'df'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    include  38.4Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in Rd file 'select.cglasso.Rd':
  'select.cglasso'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'influence-methods.Rd':
  'influence'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Invalid package aliases in Rd file 'jumpointsVar-package.Rd':
  'jumpointsVar-package'
Objects in \usage without \alias in Rd file 'jumpointsVar-internal.Rd':
  'seg.lm.fit0.gamma' 'max.rss' 'print.jumpointsVar'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in Rd file 'jumpointsVar-internal.Rd':
  'max.rss'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'ChangePointAnalyzer-package.Rd':
  'ChangePointAnalyzer-package'
Auto-generated content requiring editing in Rd file 'ChangePointAnalyzer-package.Rd':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
Documented arguments not in \usage in Rd file 'multiplierDSeqfun.Rd':
  'MC'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'darts'
Documented arguments not in \usage in Rd file 'dot-chkArgs.Rd':
  'mode.'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'countreg'
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'ChIPtest-package.Rd':
  'ChIPtest_1.0-package'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   2.2Mb
Objects in \usage without \alias in Rd file 'choplump-internal.Rd':
  'chooseMatrix'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'entab'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
Documented arguments not in \usage in Rd file 'SearchEmptyClusters.Rd':
  'oldcluster' 'SSminvec'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'cinaR.Rmd' using rmarkdown

Quitting from lines 53-55 [unnamed-chunk-5] (cinaR.Rmd)
Error: processing vignette 'cinaR.Rmd' failed with diagnostics:
there is no package called 'HPO.db'
--- failed re-building 'cinaR.Rmd'

SUMMARY: processing the following file failed:
  'cinaR.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'userfriendlyscience'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'clpm-internal.Rd':
  'lpm.newton2' 'lpm.fit' 'lpm.newton' 'L_lambda'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'auxiliary_functions.Rd':
  'edelist'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Objects in \usage without \alias in Rd file 'clustEff-internal.Rd':
  '.get_ave_sil_width' '.get_withinSS' 'print.clustEff'
  'print.summary.clustEff' 'print.fpcac' 'print.summary.fpcac'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'calculate_connectivity.Rd':
  'datdf'

Documented arguments not in \usage in Rd file 'dunn_metric.Rd':
  'distance' 'method'

Documented arguments not in \usage in Rd file 'evaluate_all_column_dataset.Rd':
  'data'

Documented arguments not in \usage in Rd file 'information_external.Rd':
  'info'

Documented arguments not in \usage in Rd file 'information_internal.Rd':
  'info'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tobit1'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Package suggested but not available for checking: 'PopGenome'
Documented arguments not in \usage in Rd file 'feat_sample.Rd':
  'locus_group'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in Rd file 'get_superior.Rd':
  'stirng'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'disttree'
Documented arguments not in \usage in Rd file 'lb_calculation.Rd':
  'qu.param'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
Documented arguments not in \usage in Rd file 'cocorresp-internal.Rd':
  'Y' 'eps'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package which this enhances but not available for checking: 'rkward'
Package suggested but not available for checking: 'userfriendlyscience'
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: spence8
> ### Title: The factor loading matrices of 8 exploratory factor analysis for
> ###   spence children anxiety scale(SCAS).
> ### Aliases: spence8
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(spence8)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.94 0.22 2.17 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   2.0Mb
Unexported object imported by a ':::' call: 'crayon:::mypaste'
  See the note in ?`:::` about the use of this operator.
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'summary.CommunityClimateInput.Rd':
  'object' '\dots'
Argument items with no description in Rd file 'summary.CommunityClimateStatistics.Rd':
  'object' '\dots'
Objects in \usage without \alias in Rd file 'comf-internal.Rd':
  'calcet'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'CAM'
Documented arguments not in \usage in Rd file 'CopulaSelection.Rd':
  'rhoType'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Rd files without \alias:
  'CompoundEvents-package.Rd'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'concordancer-package.Rd':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
'LazyData' is specified without a 'data' directory
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'checkCountsWholeNumbers.Rd':
  'aggregated.samples'

Documented arguments not in \usage in Rd file 'getGlobalClusterMarkers.Rd':
  'min.percent.samples.expression'

Documented arguments not in \usage in Rd file 'getPercentGlobalClusters.Rd':
  'min.cell.count.per.samples'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in Rd file 'postProcessSys.Rd':
  'myFile'

Documented arguments not in \usage in Rd file 'theta_ll.Rd':
  'params'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'print_table.Rd':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'coopProductGame-package.Rd':
  'coopProducGame-package'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'ft.Rd':
  'theta'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.2Mb
    doc    1.3Mb
    help   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/coursekata.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  cpglmm.c:272:17: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  cpglmm.c:272:17: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  cpglmm.c:1095:17: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  cpglmm.c:1095:17: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/cplm.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/crc32c.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
Running examples in 'crmn-Ex.R' failed
The error most likely occurred in:

> ### Name: normFit
> ### Title: Fit a normalization model
> ### Aliases: normFit
> 
> ### ** Examples
> 
> data(mix)
> nfit <- normFit(mix, "crmn", factors="type", ncomp=3)
> slplot(sFit(nfit)$fit$pc, scol=as.integer(mix$runorder))
Error in var(x) : is.atomic(y) is not TRUE
Calls: slplot -> slplot -> simpleEllipse -> var -> var -> stopifnot
Execution halted
Error(s) in re-building vignettes:
--- re-building 'crmn.Rnw' using Sweave
Loading required package: pcaMethods
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'pcaMethods'

The following object is masked from 'package:stats':

    loadings


Attaching package: 'crmn'

The following object is masked from 'package:BiocGenerics':

    normalize


Error: processing vignette 'crmn.Rnw' failed with diagnostics:
 chunk 7 (label = tz) 
Error in var(x) : is.atomic(y) is not TRUE

--- failed re-building 'crmn.Rnw'

SUMMARY: processing the following file failed:
  'crmn.Rnw'

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in Rd file 'pinvGamma.Rd':
  'logical;'

Documented arguments not in \usage in Rd file 'qinvGamma.Rd':
  'logical;'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
Documented arguments not in \usage in Rd file 'tool.Rd':
  'seq'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'ctqr-internal.Rd':
  'findagoodestimator' 'safe.pch' 'quickpred' 'check.in.ctqr' 'start'
  'ee.u' 'ee.cens' 'ee.cens.trunc' 'ee.icens' 'qr.gs' 'nobs.ctqr'
  'vcov.ctqr' 'coef.ctqr' 'print.ctqr' 'summary.ctqr'
  'print.summary.ctqr' 'firstep.ct' 'firstep.ic' 'asy.qr.ct'
  'asy.qr.ic' 'safesolve' 'regularize_corr'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in Rd file 'ctqr-internal.Rd':
  'qr.gs'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    libs   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'chi2cub2cov.Rd':
  'covar'

Documented arguments not in \usage in Rd file 'cubpq.Rd':
  'summary'

Documented arguments not in \usage in Rd file 'cubshe.Rd':
  'makeplot' 'summary'

Documented arguments not in \usage in Rd file 'kkk.Rd':
  'Vector'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.8Mb
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Documented arguments not in \usage in Rd file 'cvRiskPlot.Rd':
  'estimator'

Documented arguments not in \usage in Rd file 'matrixMetrics.Rd':
  'estimator'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package which this enhances but not available for checking: 'RGtk2'
Documented arguments not in \usage in Rd file 'compute_stat.Rd':
  'K_0'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'robustbase'
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    help   1.0Mb
    libs   1.2Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'tree.filter.Rd':
  'nodeList'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'doMC'
Documented arguments not in \usage in Rd file 'mm_run_reg.Rd':
  'all_params'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'dap-package.Rd':
  'dap-package'
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'plotDataExplorer.single.Rd':
  'obj'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Documented arguments not in \usage in Rd file 'dotgetJSONValue.Rd':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'SASxport'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dblog'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in Rd file 'dbglm-internal.Rd':
  'dbglm.iteration'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'a_dcc_mat_est.Rd':
  'param'

Documented arguments not in \usage in Rd file 'dcc_mat_est.Rd':
  'param'

Documented arguments not in \usage in Rd file 'deco_mat_est.Rd':
  'param'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'BRugs'
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  difeq.c:268:69: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  dopri.c:332:68: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  r_difeq.c:214:59: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  r_difeq.c:223:52: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  r_dopri.c:93:59: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  util.c:36:38: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/dde.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'DDPNA-package.Rd':
  \details: '...o use the package, including the most important functions ~~'
Argument items with no description in Rd file 'DEP_Mod_net_plot.Rd':
  '\dots'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'getTriContextFraction.Rd':
  'trimer.counts.ref'

Documented arguments not in \usage in Rd file 'norm.it.Rd':
  'trimer.counts'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../inst/include/barry/models/defm/defm-types.hpp:136:29: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  ../inst/include/barry/models/defm/defm-types.hpp:136:34: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  ../inst/include/barry/model-meat.hpp:1005:44: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  ../inst/include/barry/model-meat.hpp:1006:44: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  ../inst/include/barry/model-meat.hpp:1009:34: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  ../inst/include/barry/model-meat.hpp:1017:38: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  ../inst/include/barry/model-meat.hpp:1027:42: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  ../inst/include/barry/model-meat.hpp:963:27: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  ../inst/include/barry/barraydense-meat.hpp:989:27: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/defm.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'degreenet-internal.Rd':
  'range' 'lims'
Objects in \usage without \alias in Rd file 'degreenet-internal.Rd':
  'bootstrapyule'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Documented arguments not in \usage in Rd file 'boot_f_cor.Rd':
  'fun'

Documented arguments not in \usage in Rd file 'boot_f_pcor.Rd':
  'fun'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Rd files without \alias:
  'densityClust-package.Rd'
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: 'Rdonlp2'
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'Rdonlp2'
Specified C++11: please drop specification unless essential
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.N' '.Nmiss' '.Q1' '.Q3' '.factorN' '.factorNmiss' '.factorQ1'
  '.factorQ3' '.factormax' '.factormean' '.factormedian' '.factormin'
  '.factorsd' '.max' '.mean' '.median' '.min' '.sd'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
    libs   1.2Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/DFD.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'encode_unit.Rd':
  'original'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'Nortonbass_startvalgen.Rd':
  'param' 'startvalgen'

Documented arguments not in \usage in Rd file 'seqdiffusion.Rd':
  'w'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  digest.c:62:53: warning: conversion lacks type at end of format [-Wformat=]
  digest.c:62:15: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.4/digest.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'INLA'
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'discreteMTP'
Unknown package 'discreteMTP' in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'RV.Rd':
  'RV-package'
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
Package which this enhances but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
Error(s) in re-building vignettes:
--- re-building 'distr.Rnw' using knitr

Quitting from lines 1036-1040 [examdcP] (distr.Rnw)
Error: processing vignette 'distr.Rnw' failed with diagnostics:
error in evaluating the argument 'object' in selecting a method for function 'decomposePM': unable to find an inherited method for function 'r' for signature 'object = "numeric"'
--- failed re-building 'distr.Rnw'

SUMMARY: processing the following file failed:
  'distr.Rnw'

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in Rd file 'internals.Rd':
  'namestoGather' 'namestoGatherNS'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'internalmleHelpers.Rd':
  'validity.check'

Objects in \usage without \alias in Rd file 'internals.Rd':
  '.csimpsum'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'distrMod-Ex.R' failed
The error most likely occurred in:

> ### Name: BinomFamily
> ### Title: Generating function for Binomial families
> ### Aliases: BinomFamily
> ### Keywords: models
> 
> ### ** Examples
> 
> (B1 <- BinomFamily(size = 25, prob = 0.25))
Warning in .local(.Object, ...) : you have to specify slot r at least
Error: unable to find an inherited method for function 'r' for signature 'object = "numeric"'
Execution halted
'LazyData' is specified without a 'data' directory
Assignments in \usage in Rd file 'internalGenerics.Rd':
  x <- samplesize(object, value)

Documented arguments not in \usage in Rd file 'internals.Rd':
  'DClass'
Objects in \usage without \alias in Rd file 'internals.Rd':
  '.consolidategaps' '.List'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'distr-Ex.R' failed
The error most likely occurred in:

> ### Name: Binom-class
> ### Title: Class "Binom"
> ### Aliases: Binom-class Binom initialize,Binom-method
> ### Keywords: distribution
> 
> ### ** Examples
> 
> B <- Binom(prob=0.5,size=1) # B is a binomial distribution with prob=0.5 and size=1.
> r(B)(1) # # one random number generated from this distribution, e.g. 1
[1] 0
> d(B)(1) # Density of this distribution is  0.5 for x=1.
[1] 0.5
> p(B)(0.4) # Probability that x<0.4 is 0.5.
[1] 0.5
> q(B)(.1) # x=0 is the smallest value x such that p(B)(x)>=0.1.
[1] 0
> ## in RStudio or Jupyter IRKernel, use q.l(.)(.) instead of q(.)(.)
> size(B) # size of this distribution is 1.
[1] 1
> size(B) <- 2 # size of this distribution is now 2.
> C <- Binom(prob = 0.5, size = 1) # C is a binomial distribution with prob=0.5 and size=1.
> D <- Binom(prob = 0.6, size = 1) # D is a binomial distribution with prob=0.6 and size=1.
> E <- B + C # E is a binomial distribution with prob=0.5 and size=3.
> F <- B + D # F is an object of class LatticeDistribution.
Warning in .local(.Object, ...) : you have to specify slot r at least
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'object' in selecting a method for function 'prob': unable to find an inherited method for function 'r' for signature 'object = "numeric"'
Calls: + ... initialize -> initialize -> .local -> table -> r -> <Anonymous>
Execution halted
Running examples in 'distrTeach-Ex.R' failed
The error most likely occurred in:

> ### Name: illustrateCLT
> ### Title: Functions for Illustrating the CLT
> ### Aliases: illustrateCLT illustrateCLT.tcl
> ### Keywords: distribution methods dynamic
> 
> ### ** Examples
> 
> distroptions("DefaultNrFFTGridPointsExponent" = 13)
> illustrateCLT(Distr = Unif(), len = 10)
> distroptions("DefaultNrFFTGridPointsExponent" = 12)
> illustrateCLT(Distr = Pois(lambda = 2), len = 10)
Error: unable to find an inherited method for function 'r' for signature 'object = "numeric"'
Execution halted
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'diveMove-internal.Rd':
  '.diveMatches'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  GslOdeBase.cpp:47:49: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  GslOdeBase.cpp:47:57: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  GslOdeBase.cpp:102:37: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  GslOdeBase.cpp:102:50: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  TimeMachine.cpp:39:22: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  TimeMachine.cpp:39:46: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/diversitree.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used Fortran compiler: 'GNU Fortran (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Package suggested but not available for checking: 'BOLTSSIRR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
Invalid package aliases in Rd file 'dmaiIntro.Rd':
  'dmaiIntro-package'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'dml_bagging.Rd':
  'y,x,d,data,sed'
Argument items with no description in Rd file 'dml_boosting.Rd':
  'y,x,d,data,sed'
Argument items with no description in Rd file 'dml_ensemble_lm.Rd':
  'y,x,d,data,sed'
Argument items with no description in Rd file 'dml_ensemble_rf.Rd':
  'y,x,d,data,sed'
Argument items with no description in Rd file 'dml_neural_network.Rd':
  'y,x,d,data,sed'
Argument items with no description in Rd file 'dml_random_forest.Rd':
  'y,x,d,data,sed'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'dnapath2-package.Rd':
  'dnapath2-package'
Auto-generated content requiring editing in Rd file 'dnapath2-package.Rd':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '\dontrun{      ## Optional simple examples of the most impor...'
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
S3 methods shown with full name in Rd file 'add.joint.mean.many.Rd':
  'all.cond.mean.PO' 'all.cond.mean2.PO'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Argument items with no description in Rd file 'derivType.Rd':
  'L' 'mu' 'eps'
Argument items with no description in Rd file 'getNewParams.SC.Rd':
  'n.fft'
Argument items with no description in Rd file 'graph.CTMC.Rd':
  '\dots'
Argument items with no description in Rd file 'num.deriv.Rd':
  '\dots'
Argument items with no description in Rd file 'power.coef.one.Rd':
  '\dots'
Documented arguments not in \usage in Rd file 'concDict.Rd':
  'text'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'check_results.Rd':
  'error_on_failure' 'error_on_warning'

Documented arguments not in \usage in Rd file 'function_get_comments.Rd':
  'thresholds'

Documented arguments not in \usage in Rd file 'vignette_results_display.Rd':
  'vignette_results' 'error_on_failure'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   1.7Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New features
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Unknown package 'broomExtra' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/dplyr.Rcheck/00install.out' for details.
Found export directive that requires package 'methods':
  'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/DRviaSPCN.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'forecastCovCompiled.Rd':
  'obj' 'zero' 'trend' 'estimation.sample' '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'dsBaseClient'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.4Mb
GNU make is a SystemRequirements.
Objects in \usage without \alias in Rd file 'd.spls.norm1.Rd':
  'd.spls.norm2'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    R      3.3Mb
    data   8.3Mb
Package unavailable to check Rd xrefs: 'cmdstanr'
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'dynConfiR-package.Rd':
  'dynWEV-package'
Package suggested but not available for checking: 'lle'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.0Mb
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    bin       3.1Mb
    extdata   1.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'e.cluster.decision.Rd':
  'reg_data' 'log.lambda'
Argument items with no description in Rd file 'e.cluster.dendrogram.Rd':
  'echelon.obj' 'n.sim' 'cluster.legend.pos' 'cluster_reg' 'p_rank'
  'para'
Argument items with no description in Rd file 'e.cluster.map.Rd':
  'x' 'c_separates' 'locs' 'coo' 'rin' 'p_rank' 'cluster_reg' 'n.sim'
  'cluster.type'
Argument items with no description in Rd file 'e.dendrogram.Rd':
  'peaks' 'locs' 'x' 'separates' 'c_separates' 'number' 'parents'
  'pare_locs' 'progeny' 'symbols' 'col.symbols' 'cex.symbols' 'lwd'
  'col' 'ens' 'adj.ens' 'col.ens' 'cex.ens' 'limb'
Argument items with no description in Rd file 'e.dendrogram.axis.Rd':
  'main' 'ylab' 'yaxes' 'ylim' 'xaxes' 'xdper' 'dmai' 'peaks' 'x'
Argument items with no description in Rd file 'e.main.Rd':
  'x' 'rin' 'T'
Argument items with no description in Rd file 'e.monte.bin.Rd':
  'rin' 'cas' 'pop' 'n.sim' 'K' 'cluster.type'
Argument items with no description in Rd file 'e.monte.poi.Rd':
  'rin' 'cas' 'pop' 'ex' 'n.sim' 'K' 'cluster.type'
Argument items with no description in Rd file 'e.profile.Rd':
  'peaks' 'parents' 'separates'
Argument items with no description in Rd file 'e.scan.Rd':
  'x' 'locs' 'peaks' 'c_separates' 'parents' 'K'
Argument items with no description in Rd file 'e.scan.pop.Rd':
  'x' 'locs' 'peaks' 'c_separates' 'parents' 'K' 'pop'
Argument items with no description in Rd file 'nlimb.Rd':
  'x' 'k2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'fcf.env.Rd':
  'vars'

Documented arguments not in \usage in Rd file 'getlevels.Rd':
  'editarray'

Documented arguments not in \usage in Rd file 'parseCatEdit.Rd':
  'e'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'eggCountsExtra'
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'rotate_to_equilibrium.Rd':
  'xy_may'

Documented arguments not in \usage in Rd file 'wide.dyads.to.edgelist.Rd':
  'fist.var'

Documented arguments not in \usage in Rd file 'wide.to.long.Rd':
  'last.col' 'ego.vars'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Invalid package aliases in Rd file 'HOF-package.Rd':
  'HOF-package'
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   5.1Mb
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'colBoxplot4.Rd':
  'id'

Documented arguments not in \usage in Rd file 'elaborator_server.Rd':
  'id'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found export directive that requires package 'methods':
  'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
Found the following significant warnings:
  bitstring.h:28:54: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/emoa.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  'enc-package.Rd'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RStoolbox'
Documented arguments not in \usage in Rd file 'div_plot.Rd':
  'plot_cols'

Documented arguments not in \usage in Rd file 'seq_plot.Rd':
  'plot_cols'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Auto-generated content requiring editing in Rd file 'EnviroPRA-package.Rd':
  \details: '...o use the package, including the most important functions ~~'
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
'LazyData' is specified without a 'data' directory
Found export directives that require package 'methods':
  'exportClasses' 'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   2.5Mb
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'epidict'
Documented arguments not in \usage in Rd file 'dots_to_charlist.Rd':
  'call' '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.0Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
    libs   6.4Mb
GNU make is a SystemRequirements.
S3 methods shown with full name in Rd file 'addDrug.Lexis.Rd':
  'addDrug.Lexis'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'equateMultiple-package.Rd':
  'EquateMultiple-package'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'subnetwork_templates.Rd':
  'nams.vattr'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  wtedgetree.c:288:23: warning: format '%d' expects argument of type 'int', but argument 2 has type 'double' [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/ergm.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Documented arguments not in \usage in Rd file 'call.ErgmTerm.Rd':
  'A'

Objects in \usage without \alias in Rd file 'ergm-defunct.Rd':
  'sociality'

Documented arguments not in \usage in Rd file 'ergm-deprecated.Rd':
  'fname' 'varnames' 'vartypes' 'defaultvalues' 'required'
  'nw.bipartiteflag' 'requirement' 'extramessage' 'nw.directedflag' 'm'
  'response' 'new' 'from.new' 'model' 'proposal' 'eta0' 'control'
  'verbose' 'update.nws' 'Clist' 'prev.run' 'burnin' 'samplesize'
  'interval' 'maxedges' 'attrname' 'label' 'coord' 'jitter' 'thresh'
  'usearrows' 'mode' 'displayisolates' 'interactive' 'xlab' 'ylab'
  'xlim' 'ylim' 'pad' 'label.pad' 'displaylabels' 'boxed.labels'
  'label.pos' 'label.bg' 'vertex.sides' 'vertex.rot' 'arrowhead.cex'
  'label.cex' 'loop.cex' 'vertex.cex' 'edge.col' 'label.col'
  'vertex.col' 'label.border' 'vertex.border' 'edge.lty' 'label.lty'
  'vertex.lty' 'edge.lwd' 'label.lwd' 'edge.len' 'edge.curve'
  'edge.steps' 'loop.steps' 'object.scale' 'uselen' 'usecurve'
  'suppress.axes' 'vertices.last' 'layout.par' 'cex.main' 'cex.sub'
  'seed' 'latent.control' 'colornames' 'latent' 'preserve.eattr'

Documented arguments not in \usage in Rd file 'ergm_state.Rd':
  'nw'

Documented arguments not in \usage in Rd file 'nodal_attributes-API.Rd':
  'l'

Documented arguments not in \usage in Rd file 'summary.ergm_model.Rd':
  'response'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in Rd file 'summary.error_interval.Rd':
  'summary.error_interval'

S3 methods shown with full name in Rd file 'summary.measure.Rd':
  'summary.measure'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'esaBcv_package.Rd':
  'esaBcv_package-package'
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'ETAS-internal.Rd':
  'Smooth.catalog'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    libs      1.0Mb
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Documented arguments not in \usage in Rd file 'poly_clip.Rd':
  'x' 'y'

Documented arguments not in \usage in Rd file 'setup_gpar.Rd':
  'x'

Documented arguments not in \usage in Rd file 'setup_grobs.Rd':
  'centers'

Documented arguments not in \usage in Rd file 'update_list.Rd':
  'x' 'val'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
Documented arguments not in \usage in Rd file 'doHttrRequest.Rd':
  'params' 'customConfig'

Documented arguments not in \usage in Rd file 'errorMessage.Rd':
  'test_me'

Documented arguments not in \usage in Rd file 'isError.Rd':
  'test_me'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'borrOrderingInternal.Rd':
  'n.cntrl'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: 'ExactData'
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./RUtils.h:19:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  RUtils.c:144:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/excel.link.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
Unknown package 'iptools' in Rd xrefs
Package suggested but not available for checking: 'INLA'
Specified C++11: please drop specification unless essential
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    exiftool  14.1Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  error.c:45:23: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/ExomeDepth.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cec2013'
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
Argument items with no description in Rd file 'plot.expectreg.Rd':
  '\dots'
Argument items with no description in Rd file 'update.expectreg.Rd':
  '\dots'
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
Argument items with no description in Rd file 'fbvpot.Rd':
  'cutoff'
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Documented arguments not in \usage in Rd file 'getQQLimit.Rd':
  'N' 'rho'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'exuberdata'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'complete.log.likelihood_Sj.Rd':
  'z'
Auto-generated content requiring editing in Rd file 'getStuffForDIC.Rd':
  \details: 'If necessary, more details than the description above'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    minor changes
Auto-generated content requiring editing in Rd file 'procrustes_switching.Rd':
  \details: 'If necessary, more details than the description above.'
Auto-generated content requiring editing in Rd file 'rsp_exact.Rd':
  \details: 'If necessary, more details than the description above.'
Auto-generated content requiring editing in Rd file 'rsp_full_sa.Rd':
  \details: 'If necessary, more details than the description above.'
Auto-generated content requiring editing in Rd file 'rsp_partial_sa.Rd':
  \details: 'If necessary, more details than the description above.'
Auto-generated content requiring editing in Rd file 'weighted_procrustes_switching.Rd':
  \details: 'If necessary, more details than the description above.'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.0Mb
    help   1.2Mb
Documented arguments not in \usage in Rd file 'dot-get_default_sign_size.Rd':
  'outcome_type'

Documented arguments not in \usage in Rd file 'dot-get_iteration_data.Rd':
  'file_dir'

Documented arguments not in \usage in Rd file 'extract_model_vimp.Rd':
  'feature_similarity_table'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ezprof.c:55:38: warning: format '%f' expects argument of type 'double', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
  ezprof.c:57:38: warning: format '%f' expects argument of type 'double', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/fanc.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'cache.Rd':
  'data' 'reset'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
    libs   1.9Mb
Documented arguments not in \usage in Rd file 'kkk.Rd':
  'Vector'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'Get_C_R_K_Q.Rd':
  'have_noise'

Documented arguments not in \usage in Rd file 'Sample_KF_post.Rd':
  'C0'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     1.3Mb
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ica.c:100:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  ica.c:100:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/fastICA.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'coxKM'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
Rd files without \alias:
  'FastPCS-package.Rd'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Invalid package aliases in Rd file 'FastRCS-package.Rd':
  'FastPCS-package'
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    Rcgi      3.0Mb
    cgi-bin   2.8Mb
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Undefined global functions or variables:
  init run
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'bin.Rd':
  'Integer'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'NNLM'
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.5Mb
    help   2.1Mb
    libs   1.6Mb
Unexported object imported by a ':::' call: 'fdapace:::interp2lin'
  See the note in ?`:::` about the use of this operator.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'getbasispenalty.Rd':
  'Lfdobj'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New Stuff
'LazyData' is specified without a 'data' directory
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'checkStream.Rd':
  'skipChecks'

Documented arguments not in \usage in Rd file 'cpp_detectCUSUMMeanSinglePrechange.Rd':
  'BL'

Documented arguments not in \usage in Rd file 'cpp_detectEWMAMeanSinglePrechange.Rd':
  'BL'

Documented arguments not in \usage in Rd file 'makeStreamMeanChangeR.Rd':
  'x'

Documented arguments not in \usage in Rd file 'update_Omega.Rd':
  'm_new'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  fftw.c:112:34: warning: format '%x' expects argument of type 'unsigned int', but argument 2 has type 'double (*)[2]' [-Wformat=]
  fftw.c:113:34: warning: format '%x' expects argument of type 'unsigned int', but argument 2 has type 'double (*)[2]' [-Wformat=]
  fftw.c:114:34: warning: format '%x' expects argument of type 'unsigned int', but argument 2 has type 'fftw_plan' {aka 'struct fftw_plan_s *'} [-Wformat=]
  fftw.c:115:34: warning: format '%x' expects argument of type 'unsigned int', but argument 2 has type 'fftw_plan' {aka 'struct fftw_plan_s *'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/fftw.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'recode_subquad.Rd':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    extdata   2.8Mb
    libs      1.2Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'MicrobeDS'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    3.0Mb
    help   1.1Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R         4.7Mb
    doc       2.1Mb
    extdata   2.1Mb
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(filecacher)
  > 
  > test_check("filecacher")
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 152 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-file_cache.R:12:5'): file_cache with cache=NULL ──────────────
  fs::dir_exists(expected_dir) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 152 ]
  Error: Test failures
  Execution halted
Invalid package aliases in Rd file 'filename.Rd':
  'filename-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'diveRsity'
Unknown package 'diveRsity' in Rd xrefs
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Found the following significant warnings:
  finite_moment_test.cpp:412:22: warning: 'arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.4/finity.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    lib    3.0Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Documented arguments not in \usage in Rd file 'plot_data_type.Rd':
  'client_id' 'client_secret' 'refresh_token'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fivethirtyeightdata'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    3.6Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) cclust.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) randIndex.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:28: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  22.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    9.1Mb
    libs   1.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  FLSAGeneral.cc:248:66: warning: format '%d' expects argument of type 'int', but argument 5 has type 'std::set<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  FLSAGeneral.cc:248:70: warning: format '%d' expects argument of type 'int', but argument 6 has type 'std::set<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  FLSAGeneral.cc:280:63: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=]
  FLSAGeneral.cc:369:62: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::set<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  FLSAGeneral.cc:369:65: warning: format '%d' expects argument of type 'int', but argument 5 has type 'std::set<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  MaxFlowGraph.cc:560:43: warning: format '%d' expects argument of type 'int', but argument 2 has type '__gnu_cxx::__normal_iterator<std::vector<MaxFlowEdge>*, std::vector<std::vector<MaxFlowEdge> > >::difference_type' {aka 'long long int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/flsa.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'fmsb-Ex.R' failed
The error most likely occurred in:

> ### Name: WhipplesIndex
> ### Title: Whipple's Index
> ### Aliases: WhipplesIndex
> 
> ### ** Examples
> 
>  WhipplesIndex(Jpop$M2000)
$WI
[1] 99.09955

$JUDGE
[1] "highly accurate"

>  India <- read.delim("https://minato.sip21c.org/ldaR/India2011census.txt")
Warning in file(file, "rt") :
  URL 'https://minato.sip21c.org/ldaR/India2011census.txt': status was 'SSL connect error'
Error in file(file, "rt") : 
  cannot open the connection to 'https://minato.sip21c.org/ldaR/India2011census.txt'
Calls: read.delim -> read.table -> file
Execution halted
Documented arguments not in \usage in Rd file 'hl.factor.number.Rd':
  'w'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  ANN.cpp:173:23: warning: too many arguments for format [-Wformat-extra-args]
  ANN.cpp:181:26: warning: too many arguments for format [-Wformat-extra-args]
  KNN_cover_tree.cpp:103:18: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  KNN_cover_tree.cpp:156:18: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<Id_dist>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  KNN_cover_tree.cpp:221:20: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<Id_dist>::size_type' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/FNN.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  pfm-read.c:552:16: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  pfm-read.c:579:16: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  pfm-read.c:754:18: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  sfm-read.c:554:14: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'long long unsigned int' [-Wformat=]
  sfm-read.c:621:14: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'long long unsigned int' [-Wformat=]
  sfm-read.c:802:14: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'long long unsigned int' [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/foreign.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RandomFields'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   3.4Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'assert.surface.Rd':
  'surf'

Documented arguments not in \usage in Rd file 'check.dtype.for.data.Rd':
  'silent'

Documented arguments not in \usage in Rd file 'fread3.Rd':
  'filehandle:'

Documented arguments not in \usage in Rd file 'fwrite3.Rd':
  'filehandle:' 'data:'

Documented arguments not in \usage in Rd file 'polygon.soup.to.indexed.mesh.Rd':
  'face_vertex_coords'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'freqdom.transpose.Rd':
  'S'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
checkRd: (-1) NEWS.Rd:234: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:257: Escaped LaTeX specials: \_ \_
checkRd: (-1) NEWS.Rd:258: Escaped LaTeX specials: \_ \_
checkRd: (-1) NEWS.Rd:259: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:262: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:265: Escaped LaTeX specials: \_
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.8Mb
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'draw.colorbar.Rd':
  'coloredmesh'

Documented arguments not in \usage in Rd file 'extend_neighbors.Rd':
  'min_dotp_threshold'

Documented arguments not in \usage in Rd file 'surf.sphere.spatialfilter.Rd':
  'gaussian_weight'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Argument items with no description in Rd file 'fsdam.Rd':
  'verbose' 'which'
Argument items with no description in Rd file 'plot.classes.Rd':
  '\dots'
Argument items with no description in Rd file 'predict.fsim.Rd':
  '\dots'
Argument items with no description in Rd file 'predict.lm.Rd':
  '\dots'
Argument items with no description in Rd file 'predict.sfpl.Rd':
  '\dots'
Argument items with no description in Rd file 'predict.sfplsim.FASSMR.Rd':
  '\dots'
Argument items with no description in Rd file 'print.summary.mfplsim.Rd':
  '\dots'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'imp_small_gaps_WMA.Rd':
  'Data' 'univariate'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Objects in \usage without \alias in Rd file 'funData-constructor.Rd':
  'funData'

Objects in \usage without \alias in Rd file 'irregFunData-constructor.Rd':
  'irregFunData'

Objects in \usage without \alias in Rd file 'multiFunData-constructor.Rd':
  'multiFunData'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in Rd file 'plot.funData.Rd':
  'plot.funData'

S3 methods shown with full name in Rd file 'plot.irregFunData.Rd':
  'plot.irregFunData'

S3 methods shown with full name in Rd file 'plot.multiFunData.Rd':
  'plot.multiFunData'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'build_limits_lookup.Rd':
  'min_preds' 'max_preds' 'min_ratio' 'max_ratio' 'draw_unadjusted'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'loggedOutput.Rd':
  'future'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in Rd file 'mandelbrot.Rd':
  'Z' 'xmid' 'ymid' 'side' 'resolution' 'maxIter' 'tau'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   4.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
Invalid package aliases in Rd file 'GAabbreviate-internal.Rd':
  'GAabbreviation-package'
Documented arguments not in \usage in Rd file 'splitQTL_comment.Rd':
  'output_qtls'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
Invalid package aliases in Rd file 'gamlss.mx.package.Rd':
  'gamlss.mix-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
Documented arguments not in \usage in Rd file 'as.gapdata.Rd':
  'labels_df'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Specified C++14: please drop specification unless essential
installed size is 46.2Mb
  sub-directories of 1Mb or more:
    doc   44.3Mb
    libs   1.2Mb
':::' call which should be '::': 'graphics:::grid'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.8Mb
Documented arguments not in \usage in Rd file 'lrr_plot.Rd':
  'plot_cols'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  node_categorical.cpp:42:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_categorical.cpp:45:19: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_categorical.cpp:52:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_categorical.cpp:55:19: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_continuous.cpp:37:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  node_continuous.cpp:43:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/gbm.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
Package in Depends field not imported from: 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'tools:::.Rd_get_argument_names' 'tools:::RdTags' 'tools:::fetchRdDB'
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'align_peaks.Rd':
  'gc_peak_df'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'paleofire'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 104.6Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    gdal     3.0Mb
    libs    89.9Mb
    proj     8.3Mb
installed size is 101.9Mb
  sub-directories of 1Mb or more:
    gdal   3.0Mb
    libs  88.3Mb
    proj   8.3Mb
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'geepack-internal.Rd':
  'genZcor'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  ugee.c:813:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/gee.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used Fortran compiler: 'GNU Fortran (GCC) 12.3.0'
Auto-generated content requiring editing in Rd file 'gemlog-package.Rd':
  \details: '...the package, including the most important ~~ ~~ functions ~~'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.2Mb
    libs      1.1Mb
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'GenBinom-package.Rd':
  'GenbinomApps-package'
Package suggested but not available for checking: 'genderdata'
Documented arguments not in \usage in Rd file 'CirDisp.Rd':
  'x'

Documented arguments not in \usage in Rd file 'CirKurt.Rd':
  'x' 'na.rm'

Documented arguments not in \usage in Rd file 'CirSD.Rd':
  'x'

Documented arguments not in \usage in Rd file 'CirSkew.Rd':
  'x'

Documented arguments not in \usage in Rd file 'CirVar.Rd':
  'x'

Documented arguments not in \usage in Rd file 'MeanDir.Rd':
  'x'

Documented arguments not in \usage in Rd file 'impact.Rd':
  'na.rm'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in Rd file 'expand.Rd':
  'x'

Documented arguments not in \usage in Rd file 'grapes-bq-grapes.Rd':
  'x'

Documented arguments not in \usage in Rd file 'grapes-bt-grapes.Rd':
  'x'

Documented arguments not in \usage in Rd file 'stftcalc.Rd':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/genekitr.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'generalizedwendland-internal.Rd':
  'numint.abstol (default: 1e-3)' 'numint.reltol (default: 1e-3)'
  'numint.qag_key (default: 0)' 'numint.subintervals (default: 0)'
  'interp.method (default: 'none')' 'interp.num_support (default: 0)'
  'cov.reparameterize (default: TRUE)' 'cov.eps (default:
  .Machine$double.eps^0.5)' 'cov.d_value (default: 2)'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'GenlibR-package.Rd':
  'GenlibR-package'
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   3.5Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'variables_query-method.Rd':
  'variables'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'geomarocdata'
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R         9.6Mb
    extdata   2.5Mb
    help      2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'RandomFields'

Package which this enhances but not available for checking: 'INLA'
Unknown package 'RandomFields' in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'attract_by_distance.Rd':
  'prop_start' 'prop_end'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'labels.rpart.Rd':
  'pretty:'

Documented arguments not in \usage in Rd file 'rpart_labels.Rd':
  'model' '...'

Documented arguments not in \usage in Rd file 'rpart_segments.Rd':
  'model'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'interpolateDataFrame.Rd':
  'A'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   7.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': 'scales:::censor'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'productplots:::bound'
  See the note in ?`:::` about the use of this operator.
Argument items with no description in Rd file 'isADMG.Rd':
  'amat'
Argument items with no description in Rd file 'isAG.Rd':
  'amat'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'package-ggparallel.Rd':
  'package-ggparallel-package'
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   1.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.4Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'operator.Rd':
  'x' 'y'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'ggplot_gtable.Rd':
  'plot'

Documented arguments not in \usage in Rd file 'undocumented.Rd':
  'latex' 'ggplot'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   8.3Mb
Documented arguments not in \usage in Rd file 'add_scale.Rd':
  'domain'

Documented arguments not in \usage in Rd file 'bin_vector.Rd':
  'width' 'origin' 'closed' 'pad'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    Giac  17.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   2.5Mb
'LazyData' is specified without a 'data' directory
Unknown package 'IC2' in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'mlr3proba'
Argument items with no description in Rd file 'GLD.lm.full.surv.Rd':
  'maxit'
Argument items with no description in Rd file 'GLD.lm.surv.Rd':
  'maxit'
Documented arguments not in \usage in Rd file 'getBeta.Rd':
  'thetaConrol'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.0Mb
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc             1.4Mb
    libs            4.4Mb
    test_data       2.2Mb
    vignette_data   1.2Mb
Documented arguments not in \usage in Rd file 'glmpathcr-internal.Rd':
  'fit'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'fun.svd_1.Rd':
  'X'

Documented arguments not in \usage in Rd file 'fun.svd_2.Rd':
  'X'

Documented arguments not in \usage in Rd file 'fun.svd_3.Rd':
  'X'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  'goodpractice-package.Rd'
Documented arguments not in \usage in Rd file 'doHttrRequest.Rd':
  'session' 'params'

Documented arguments not in \usage in Rd file 'get_google_token.Rd':
  'shiny_return_token'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Documented arguments not in \usage in Rd file 'estimate_noise_nn.Rd':
  'n_thread'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'gvcm.cat'
Specified C++11: please drop specification unless essential
Unknown package 'gvcm.cat' in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
Running 'testthat.R' [83s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(gplsim)
  > 
  > test_check("gplsim")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 9 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-gplsim.r:22:3'): test the main functions (gplsim) with binary case ──
  as.vector(est_beta) (`actual`) not equal to `true.theta` (`expected`).
  
    `actual`: 0.8 0.5 0.4
  `expected`: 0.6 0.6 0.6
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 9 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   5.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.0Mb
    libs   1.2Mb
Argument items with no description in Rd file 'HistPCA.Rd':
  'ggplot'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'prCaSetRownames.Rd':
  'rownames.fn'

Documented arguments not in \usage in Rd file 'prClearPCAclass.Rd':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
Error(s) in re-building vignettes:
--- re-building 'example_models.Rmd' using rmarkdown
--- finished re-building 'example_models.Rmd'

--- re-building 'faq.Rmd' using rmarkdown
--- finished re-building 'faq.Rmd'

--- re-building 'get_started.Rmd' using rmarkdown

Quitting from lines 388-394 [plot_hidden] (get_started.Rmd)
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
`()` REASONS:
* Cannot currently use this function to produce a PNG file
* please install the `DiagrammeRsvg` package and retry
* pkg installed using `devtools::install_github('rich-iannone/DiagrammeRsvg')``()` REASONS:
* Cannot currently use this function to produce a PNG file
* please install the `DiagrammeRsvg` package and retry
* pkg installed using `devtools::install_github('rich-iannone/DiagrammeRsvg')`
--- failed re-building 'get_started.Rmd'

SUMMARY: processing the following file failed:
  'get_started.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'doMC'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.7Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'groc.fit.Rd':
  'groc.fit'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> cleanEx()
> nameEx("splitinput")
> ### * splitinput
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: splitinput
> ### Title: Split input data into multiple files
> ### Aliases: splitinput
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  138.87 1274.49 1433.5 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'fit_grp.Rd':
  'grplasso-package'
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Objects in \usage without \alias in Rd file 'GSA.internal.Rd':
  'est.s0'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Invalid package aliases in Rd file 'gsb-package.Rd':
  'gsb-package'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/GseaVis.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 250.2Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    java  247.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs    1.0Mb
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb
    doc     4.0Mb
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.ga.breed' '.ga.fitness' '.ga.init' '.ga.mutate' '.ga.step'
  '.ga.weight'
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'modeling-package.Rd':
  'modeling-package'
checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) HWClrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    2.6Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  Wrapper_manual_H5T.c:76:57: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long int' [-Wformat=]
  convert.c:261:63: warning: format '%d' expects argument of type 'int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  convert.c:261:76: warning: format '%d' expects argument of type 'int', but argument 3 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  1_8_16/datatype_export.c:67:13: warning: ISO C does not support the 'I' printf flag [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/hdf5r.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
Documented arguments not in \usage in Rd file 'check_arg_for_hyperslab_func.Rd':
  'cur_arg'

Documented arguments not in \usage in Rd file 'extract_dim.Rd':
  'x'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'compute_counts.Rd':
  'init' 'inflow'

Documented arguments not in \usage in Rd file 'compute_values.Rd':
  'counts'

Documented arguments not in \usage in Rd file 'create_demographic_table.Rd':
  '...'

Documented arguments not in \usage in Rd file 'eval_strategy_newdata.Rd':
  'model'

Documented arguments not in \usage in Rd file 'get_state_value_names.Rd':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  MHproposal.c:24:49: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  MHproposal.c:37:54: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  changestats.c:1465:38: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  changestats.c:1517:34: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  h_ergm.c:1910:84: warning: format '%i' expects a matching 'int' argument [-Wformat=]
  model.c:57:58: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  model.c:68:58: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/hergm.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
Documented arguments not in \usage in Rd file 'check.Rd':
  'inner_class'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'check_known_repos.Rd':
  'known_packages'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rcpp_internals.cpp:65:34: warning: format '%d' expects argument of type 'int', but argument 2 has type 'Rcpp::traits::storage_type<14>::type' {aka 'double'} [-Wformat=]
  rcpp_internals.cpp:65:55: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Rcpp::traits::storage_type<14>::type' {aka 'double'} [-Wformat=]
  rcpp_internals.cpp:65:80: warning: format '%d' expects argument of type 'int', but argument 4 has type 'Rcpp::traits::storage_type<14>::type' {aka 'double'} [-Wformat=]
  rcpp_internals.cpp:65:100: warning: format '%d' expects argument of type 'int', but argument 5 has type 'Rcpp::traits::storage_type<14>::type' {aka 'double'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/HHG.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'HH-defunct.Rd':
  'anova.mean' 'print.glht.mmc.multicomp' 'coef.arima.HH' 'glht.mmc'
  'plot.odds.ratio' 'persp.plane' 'persp.floor' 'persp.back.wall.x'
  'persp.back.wall.y' 'persp.setup' 'plot.hov' 'plot.hov.bf'
  'plot.matchMMC' 'seqplot.forecast'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Argument items with no description in Rd file 'residual.plots.lattice.Rd':
  'X'
Found export directives that require package 'methods':
  'exportClasses' 'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Argument items with no description in Rd file 'qcplate.Rd':
  'dat'
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'colorfulVennPlot'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'HistDAWass-package.Rd':
  \details: '...o use the package, including the most important functions ~~'
Invalid package aliases in Rd file 'histogram-package.Rd':
  'histogramtools-package'
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'trackr'
Package which this enhances but not available for checking: 'HadoopStreaming'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.3Mb
html_describe_con: multiple local function definitions for 'g' with
  different formal arguments
Documented arguments not in \usage in Rd file 'bootstrapfun.Rd':
  'DoF' 'n_sample'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Auto-generated content requiring editing in Rd file 'HMVD-package.Rd':
  \details: '...o use the package, including the most important functions ~~'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
Invalid package aliases in Rd file 'hoardeR-package.Rd':
  'R/hoardeR-package'
Argument items with no description in Rd file 'bid2.Rd':
  'numattable1' 'playerseats1' 'blinds1' 'dealer1' 'b3' 'b4' 'round1'
  'ntable1' 'decision1'
Argument items with no description in Rd file 'calcwin1.Rd':
  'numattable1' 'playerseats1' 'b3' 'b7'
Argument items with no description in Rd file 'mycount1.Rd':
  'x'
Argument items with no description in Rd file 'mygraphics1.Rd':
  'numattable1' 'playerseats1' 'chips1' 'blinds1' 'dealer1' 'b3' 'b4'
  'b5' 'b6' 'b7' 'chips2' 'ntable1' 'myfast1' 'chipstart1' 'name1'
  'lowercut1'
Argument items with no description in Rd file 'nothing1.Rd':
  'x'
Argument items with no description in Rd file 'onepair1.Rd':
  'x'
Argument items with no description in Rd file 'straight1.Rd':
  'x'
Argument items with no description in Rd file 'straightdraw1.Rd':
  'x'
Argument items with no description in Rd file 'strflsh1.Rd':
  'x' 'y'
Argument items with no description in Rd file 'trip1.Rd':
  'x'
Argument items with no description in Rd file 'twopair1.Rd':
  'x'
Argument items with no description in Rd file 'writebets1.Rd':
  'b9' 'y1' 'numattable1' 'b3' 'playerseats1' 'chips1' 'chips2' 'over1'
  'myfast1' 'name1'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.3Mb
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'plot.hopitCP.Rd':
  'plotf'

Documented arguments not in \usage in Rd file 'sigma.hopit.Rd':
  'model'

Documented arguments not in \usage in Rd file 'summary.hopit.Rd':
  'control'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  'hpoPlot-package.Rd'
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'dot-E3.Rd':
  'i' 'M'

Documented arguments not in \usage in Rd file 'dot-E4.Rd':
  'i' 'M'

Documented arguments not in \usage in Rd file 'hrm.0w.2s.Rd':
  'group'

Documented arguments not in \usage in Rd file 'hrm.0w.3s.Rd':
  'group'

Documented arguments not in \usage in Rd file 'hrm.0w.4s.Rd':
  'group'

Documented arguments not in \usage in Rd file 'hrm.0w.5s.Rd':
  'group'

Documented arguments not in \usage in Rd file 'hrm.1f.Rd':
  'group'

Documented arguments not in \usage in Rd file 'hrm.1w.0f.Rd':
  'factor1'

Documented arguments not in \usage in Rd file 'hrm.2w.2f.Rd':
  'factor'

Documented arguments not in \usage in Rd file 'hrm.mv.1w.1f.Rd':
  'H' 'text'

Documented arguments not in \usage in Rd file 'hrm.mv.internal.Rd':
  'alpha' 'H' 'text'

Documented arguments not in \usage in Rd file 'hrm.test.1.none.Rd':
  'factor1' 'factor2'

Documented arguments not in \usage in Rd file 'hrm.test.1.one.Rd':
  'group' 'factor2'

Documented arguments not in \usage in Rd file 'hrm.test.2.one.Rd':
  'factor2'

Documented arguments not in \usage in Rd file 'hrm.test.2.two.Rd':
  'group'

Documented arguments not in \usage in Rd file 'hrm.test.3.three.Rd':
  'group'

Documented arguments not in \usage in Rd file 'hrm.test.4.four.Rd':
  'group'

Documented arguments not in \usage in Rd file 'hrm.test.5.five.Rd':
  'group'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'imageplot.Rd':
  '\dots'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'FramedHTML.Rd':
  'DiagnosticsPath'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.3Mb
    help   1.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
Running examples in 'httpRequest-Ex.R' failed
The error most likely occurred in:

> ### Name: simplePostToHost
> ### Title: Sends Simple Post Request to HTTP Server (host)
> ### Aliases: simplePostToHost
> 
> ### ** Examples
> 
> host <- "api.scb.se"
> path <- "/OV0104/v1/doris/en/ssd"
> data <- '{"format":"json"}'
> simplePostToHost(host, path, data, contenttype="text/json")
socket error: Dies ist normalerweise ein zeitweiliger Fehler bei der Auflösung von Hostnamen. Grund ist, dass der lokale Server keine Rückmeldung vom autorisierenden Server erhalten hat
Error in make.socket(host = host, port = port, server = FALSE) : 
  socket not established
Calls: simplePostToHost -> make.socket
Execution halted
Documented arguments not in \usage in Rd file 'as-redactor.Rd':
  'expr'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'microViz'
Invalid package aliases in Rd file 'HydroMe-package.Rd':
  'HydroMe2-package'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
Documented arguments not in \usage in Rd file 'read.txt.Witec.Rd':
  'nwl' 'remove.zerospc'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in Rd file 'btibgen.Rd':
  'ibdgen'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Argument items with no description in Rd file 'pairSum.Rd':
  'cov1' 'cov2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SparkR'
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'GetCustomKmerCounts.Rd':
  'custom.range'

Documented arguments not in \usage in Rd file 'GetMutationLoadsFromStrelkaIDVCFs.Rd':
  'list.of.vcfs'

Documented arguments not in \usage in Rd file 'GetMutationLoadsFromStrelkaSBSVCFs.Rd':
  'split.vcfs'

Documented arguments not in \usage in Rd file 'PlotPPM.Rd':
  'pwm'

Documented arguments not in \usage in Rd file 'PlotPPMToPdf.Rd':
  'list.of.pwm'

Documented arguments not in \usage in Rd file 'ReadStrelkaSBSVCF.Rd':
  'suppress.discarded.variants.warnings'

Documented arguments not in \usage in Rd file 'ReadVCF.Rd':
  'num.of.cores'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'icd'
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Found the following significant warnings:
  icenReg_files/basicUtilities.cpp:589:69: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/icenReg.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rggobi'
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'pkg-internal.Rd':
  'iplotMain' 'segments.circle' 'griddat'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in Rd file 'pkg-internal.Rd':
  'plot.page'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   1.4Mb
    libs   6.2Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  harris.cpp:537:47: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<harris_corner>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  harris.cpp:606:58: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<harris_corner>::size_type' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/image.CornerDetectionHarris.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Specified C++11: please drop specification unless essential
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         1.4Mb
Documented arguments not in \usage in Rd file 'dot-compl.Rd':
  'imgfile'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.2Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     10.2Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'image-package.Rd':
  'image-package'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/immcp.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'accdata'
Documented arguments not in \usage in Rd file 'new_impactr_peaks.Rd':
  'acc_signal:'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  'imputeYn-package.Rd'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Package suggested but not available for checking: 'cmdstanr'
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'IntervalSurgeon-package.Rd':
  \seealso: 'Optional links to other man pages'
  \examples: '## Optional simple examples of the most important functions ...'
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'selectRuleRRF.Rd':
  'target'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'rawAvgCost-deprecated.Rd':
  'cost.transf' 'in.millions' 'confidence.interval' 'minimum.year'
  'maximum.year' 'final.year' 'incomplete.year.threshold'
  'incomplete.year.weights' 'gam.k' 'mars.nprune' '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'surveyspec'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'chars_collapse.Rd':
  'collapse'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  templates/Rip-bsearch-template.c:889:18: warning: too many arguments for format [-Wformat-extra-args]
  Rip-match.c:467:13: warning: too many arguments for format [-Wformat-extra-args]
  Rip-match.c:1125:15: warning: too many arguments for format [-Wformat-extra-args]
  Rip-match.c:1173:13: warning: too many arguments for format [-Wformat-extra-args]
  Rip-match.c:1407:15: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.4/IP.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Invalid package aliases in Rd file 'iprior_package.Rd':
  'iprior_package-package'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'mrbayes.Rd':
  'unlink' 'constraint'
Argument items with no description in Rd file 'mrbayes.lset.Rd':
  'partition'
Argument items with no description in Rd file 'multistate.Rd':
  'model'
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'print.cat_output.Rd':
  'object'

Documented arguments not in \usage in Rd file 'sub-subset-Itempool-numeric-missing-method.Rd':
  '...'

Documented arguments not in \usage in Rd file 'sub-subset-Response_set-numeric-missing-method.Rd':
  '...'

Documented arguments not in \usage in Rd file 'sub-subset-Testlet-numeric-missing-method.Rd':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in Rd file 'print.Item.Rd':
  'print.Item'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'islasso-internal.Rd':
  'modelX' '.checkinput' '.startpoint' '.islasso'
  'checkinput.islasso.path' 'startpoint.islasso.path'
  'islasso.path.fit.glm' 'islasso.path.fitter2' 'interpolate' 'makeHyp'
  'printHyp' 'cislasso' 'ci.fitted.islasso'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'dot-assignmentMaker.Rd':
  '.precip_raster' '.precip_SD_raster'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.3Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Package suggested but not available for checking: 'locClass'
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Invalid package aliases in Rd file 'ivprobit-package.Rd':
  'ivProbit-package'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          11.0Mb
GNU make is a SystemRequirements.
Rd files without \alias:
  'jackknifeKME-package.Rd'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   3.4Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    i18n   6.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: 'remMap'
Documented arguments not in \usage in Rd file 'paste_coef.Rd':
  'parlemts'

Documented arguments not in \usage in Rd file 'paste_linpred.Rd':
  'parlemts' 'matname'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  'karaoke-package.Rd'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
prepare_Rd: NEWS.Rd:58: Dropping empty section 'kelvin INITIAL VERSION 1.0-0 (2012-05-30)'
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'covQualNested.Rd':
  'covBet'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'bw.abram.temp.Rd':
  'bw.abram.temp'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Documented arguments not in \usage in Rd file 'calc_PGtheta_R.Rd':
  'model' 'iter'

Documented arguments not in \usage in Rd file 'make_wsz_cpp.Rd':
  'info' 'initialized'

Documented arguments not in \usage in Rd file 'read_dfm_cpp.Rd':
  'W_raw'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'unlist.constr.Rd':
  'unlist.constr'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'knotR-package.Rd':
  'knot-package'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   1.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'ergm.userterms'
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package 'ergm.userterms' in Rd xrefs
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'akmedoids'
Unknown package 'akmedoids' in Rd xrefs
Objects in \usage without \alias in Rd file 'latrend-generics.Rd':
  'nClusters' 'clusterProportions' 'clusterTrajectories' 'compose'
  'converged' 'externalMetric' 'estimationTime' 'fit'
  'fittedTrajectories' 'getArgumentDefaults' 'getArgumentExclusions'
  'getLabel' 'getLcMethod' 'getName' 'getShortName' 'idVariable'
  'metric' 'plotFittedTrajectories' 'plotClusterTrajectories' 'postFit'
  'postprob' 'predictAssignments' 'predictForCluster' 'predictPostprob'
  'prepareData' 'preFit' 'qqPlot' 'responseVariable' 'strip'
  'timeVariable' 'trajectoryAssignments' 'validate'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'moments2.Rd':
  '...'

Documented arguments not in \usage in Rd file 'skeleton.Rd':
  'endogeneous' '...'

Documented arguments not in \usage in Rd file 'vcov2-internal.Rd':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportClasses'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'dot-choose_best_subjects.Rd':
  'best' 'candidate'

Documented arguments not in \usage in Rd file 'dot-normalize_props.Rd':
  'keep_all_items'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Argument items with no description in Rd file 'top.topic.words.Rd':
  'alpha'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Invalid package aliases in Rd file 'LEANR-package.Rd':
  'LEAN-package'
checkRd: (-1) leaps.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'learnn.Rd':
  'learnn-package'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.4Mb
Package suggested but not available for checking: 'doMC'
Documented arguments not in \usage in Rd file 'backward_step.Rd':
  'empty_start_dataset' 'fit' '...'

Documented arguments not in \usage in Rd file 'backward_step_IM.Rd':
  'empty_start_dataset' 'fit' '...'

Documented arguments not in \usage in Rd file 'forward_step.Rd':
  'empty_start_dataset' 'fit' '...'

Documented arguments not in \usage in Rd file 'forward_step_IM.Rd':
  'empty_start_dataset' 'fit' '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/leidenAlg.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_generic.Rd':
  'mismatch'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  demean.c:364:42: warning: format '%d' expects argument of type 'int', but argument 2 has type 'DWORD' {aka 'long unsigned int'} [-Wformat=]
  utils.c:34:68: warning: format '%d' expects argument of type 'int', but argument 3 has type 'mybigint_t' {aka 'long long int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/lfe.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Package suggested but not available for checking: 'doMC'
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'rsyslog'
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.7Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LIMEcoli.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) Read.Rd:88: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:92: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:98: Escaped LaTeX specials: \#
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checkRd: (-1) Read.Rd:114: Escaped LaTeX specials: \# \#
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S3 methods shown with full name in Rd file 'BIC.threshold.Rd':
  'BIC.threshold'

S3 methods shown with full name in Rd file 'BIC.threshold.ggm.Rd':
  'BIC.threshold.ggm'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'MassAcylCer.Rd':
  'glccer'

Documented arguments not in \usage in Rd file 'MassPEo.Rd':
  'PEp'

Documented arguments not in \usage in Rd file 'findMS2precursor.Rd':
  'minint' 'maxint'

Documented arguments not in \usage in Rd file 'joinAnnotationResults.Rd':
  'simplifyAnnotation'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_variable.Rd':
  'x' 'name' 'mustExist' 'create'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  combine.c:664:43: warning: format '%g' expects argument of type 'double', but argument 2 has type 'int' [-Wformat=]
  combine.c:664:15: warning: too many arguments for format [-Wformat-extra-args]
  subroutines.c:57:15: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.4/list.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs       1.4Mb
    testdata   1.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R              1.2Mb
    doc-software   2.4Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/lmQCM.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) SPSloess.Rd:71: Escaped LaTeX specials: \^ \^
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'LazyData' is specified without a 'data' directory
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) ACS.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) EmployedACS.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSale.Rd:11: Escaped LaTeX specials: \$
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checkRd: (-1) StockChanges.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) TrafficFlow.Rd:18: Escaped LaTeX specials: \#
Invalid package aliases in Rd file 'Lock5Data-package.Rd':
  'Lock5Data-package'
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'spec.emb.Rd':
  'A'
Package suggested but not available for checking: 'rsyslog'
Package suggested but not available for checking: 'rsyslog'
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'dlogitnorm.Rd':
  'sigma'
Argument items with no description in Rd file 'invlogit.Rd':
  'q' '\dots'
Argument items with no description in Rd file 'logit.Rd':
  'p' '\dots'
Argument items with no description in Rd file 'plogitnorm.Rd':
  'sigma' '\dots'
Argument items with no description in Rd file 'qlogitnorm.Rd':
  'sigma' '\dots'
Argument items with no description in Rd file 'twCoefLogitnorm.Rd':
  '\dots'
Argument items with no description in Rd file 'twCoefLogitnormE.Rd':
  '\dots'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Argument items with no description in Rd file 'levopt.Rd':
  'x' 'alpha' 'fmax' 'tm'
Argument items with no description in Rd file 'pershow.Rd':
  'object'
Argument items with no description in Rd file 'norpt.Rd':
  'alist'
'LazyData' is specified without a 'data' directory
Found export directive that requires package 'methods':
  'exportMethods'
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains 'methods'.
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.nri.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.s.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.s.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) nri.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) roc.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) roc.s.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.s.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'LoopAnalyst-package.Rd':
  \details: '...the package, including the most important ~~ ~~ functions ~~'
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'importance_sampling.array.Rd':
  'is_method'

Documented arguments not in \usage in Rd file 'importance_sampling.default.Rd':
  'is_method'

Documented arguments not in \usage in Rd file 'importance_sampling.matrix.Rd':
  'is_method'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'scio'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'LotkasXX.Rd':
  'Table'
Argument items with no description in Rd file 'LotkasXY.Rd':
  'Table'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.0Mb
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'followx.Rd':
  'Xi' 'x0' 'h' 't0' 'iter' 'way' 'weights' 'pen' 'phi'
  'lasteigenvector' 'rho0' 'boundary' 'convergence.at' 'cross'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kerdiest'
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory