'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
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:
90  226 0.0006970650
91  229 0.0006351396
92  233 0.0005787156
93  233 0.0005273041
94  235 0.0004804598
95  237 0.0004377771
96  237 0.0003988862
97  239 0.0003634503
98  243 0.0003311623
99  245 0.0003017428
100 246 0.0002749368
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  2.27 0.38 2.64 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
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: \_
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:  111.64 963.42 1092.91 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
Documented arguments not in \usage in Rd file 'traits.Rd':
  'efo_id' 'trait' 'uri'

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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
'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: \&
Found the following significant warnings:
  HARDataCreationC.cpp:43:31: 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/HARModel.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  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.
Running examples in 'hexfont-Ex.R' failed
The error most likely occurred in:

> ### Name: unifont
> ### Title: Load Unifont font
> ### Aliases: unifont
> 
> ### ** Examples
> 
> # Much faster to load only the subset of GNU Unifont one needs
> # Mandarin Chinese
> if (require("bittermelon")) {
+   s <- "\uff32\u5f88\u68d2\uff01"
+   font <- unifont(ucp = str2ucp(s))
+   bm <- as_bm_bitmap(s, font = font)
+   print(bm, px = px_ascii)
+ }
Loading required package: bittermelon

Attaching package: 'bittermelon'

The following object is masked from 'package:base':

    which

Error in vector("list", n_orig - n_combining) : vector size cannot be NA
Calls: as_bm_bitmap -> as_bm_bitmap.character -> lapply -> FUN
Execution halted
'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: \&
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: \&
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: '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: \#
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
'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: \&
'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          1.5Mb
    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: \^ \^
'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: \&
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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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: 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
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.1Mb
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
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'depth'
'LazyData' is specified without a 'data' directory
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    gdal   3.0Mb
    libs  17.4Mb
    proj   8.3Mb
'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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'quitte'
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(magclass)
  > 
  > test_check("magclass")
  Error in R_nc4_open: NetCDF: Unknown file format
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 726 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • quitte cannot be loaded (2): 'test-as.magpie.R:22:3', 'test-as.magpie.R:63:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-readwritemagpie.R:87:3'): handling of spatial data works ───────
  Error in `ncdf4::nc_open(filename, readunlim = FALSE, suppress_dimvals = TRUE)`: Error in nc_open trying to open file D:\temp\RtmpMV5CcU\test.nc (return_on_error= FALSE )
  Backtrace:
       ▆
    1. ├─testthat::expect_no_warning(write.magpie(m10, file.path(td, "test.nc"))) at test-readwritemagpie.R:87:3
    2. │ └─testthat:::expect_no_(...)
    3. │   └─testthat:::quasi_capture(enquo(object), NULL, capture)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─rlang::try_fetch(...)
    6. │     │   └─base::withCallingHandlers(...)
    7. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    8. └─magclass::write.magpie(m10, file.path(td, "test.nc"))
    9.   ├─magclass:::suppressSpecificWarnings(...)
   10.   │ └─base::withCallingHandlers(...)
   11.   ├─raster::writeRaster(...)
   12.   └─raster::writeRaster(...)
   13.     └─raster (local) .local(x, filename, ...)
   14.       └─raster:::.stopWriteCDF(b)
   15.         ├─raster::brick(x@file@name)
   16.         └─raster::brick(x@file@name)
   17.           └─raster:::.rasterObjectFromFile(...)
   18.             └─raster:::.rasterObjectFromCDF(...)
   19.               └─ncdf4::nc_open(filename, readunlim = FALSE, suppress_dimvals = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 726 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'doMC'
installed size is 65.4Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs  58.7Mb
'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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
Warning in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) :
  invalid non-character version specification 'x' (type: double)
Warning in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) :
  invalid non-character version specification 'x' (type: double)
Warning in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) :
  invalid non-character version specification 'x' (type: double)
Warning in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) :
  invalid non-character version specification 'x' (type: double)

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.
Argument items with no description in Rd file 'alignPeaks.Rd':
  '\dots'
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'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:
    data   1.2Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
Specified C++11: please drop specification unless essential
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs          3.2Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug Fixes
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    res   3.8Mb
Specified C++11: please drop specification unless essential
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  mapget.c:251:16: warning: too many arguments for format [-Wformat-extra-args]
  mapget.c:325:12: warning: too many arguments for format [-Wformat-extra-args]
  mapget.c:354:14: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.4/maps.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
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: \_
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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs       1.3Mb
'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
'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 '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'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   1.7Mb
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
Running examples in 'matric-Ex.R' failed
The error most likely occurred in:

> ### Name: sim_read
> ### Title: Read similarity matrix.
> ### Aliases: sim_read
> 
> ### ** Examples
> 
> suppressMessages(suppressWarnings(library(magrittr)))
> population <- tibble::tibble(
+   Metadata_group = sample(c("a", "b"), 4, replace = TRUE),
+   x = rnorm(4),
+   y = x + rnorm(4) / 100,
+   z = y + rnorm(4) / 1000
+ )
> tmpdir <- tempdir()
> tmpfile_prefix <- file.path(tmpdir, "test")
> tmpfile_parquet <- file.path(tmpdir, "test.pqrquet")
> sim_df <- sim_calculate(population, method = "pearson")
> sim_df %>% sim_write(tmpfile_prefix, file_format = "csv")
INFO [2023-12-13 11:32:54] Creating D:\temp\RtmpcN8HT0/test ...
INFO [2023-12-13 11:32:54] Writing D:\temp\RtmpcN8HT0/test/test.csv ...
INFO [2023-12-13 11:32:54] Writing D:\temp\RtmpcN8HT0/test/test_metadata.csv ...
INFO [2023-12-13 11:32:54] Writing D:\temp\RtmpcN8HT0/test/test_metadata.json ...
NULL
> sim_df_csv <- sim_read(tmpfile_prefix, file_format = "csv")
INFO [2023-12-13 11:32:54] Reading D:\temp\RtmpcN8HT0/test/test.csv ...
INFO [2023-12-13 11:32:54] Reading D:\temp\RtmpcN8HT0/test/test_metadata.csv ...
INFO [2023-12-13 11:32:54] Reading D:\temp\RtmpcN8HT0/test/test_metadata.json ...
> sim_df %>% sim_write(tmpfile_parquet)
INFO [2023-12-13 11:32:54] Writing D:\temp\RtmpcN8HT0/test.pqrquet ...
NULL
> sim_df_parquet1 <- sim_read(tmpfile_parquet)
> sim_df %>% arrow::write_parquet(tmpfile_parquet)
Error: IOError: Failed to open local file 'D:/temp/RtmpcN8HT0/test.pqrquet'. Detail: [Windows error 1224] Der Vorgang ist bei einer Datei mit einem geöffneten Bereich, der einem Benutzer zugeordnet ist, nicht anwendbar.
Execution halted
Running 'testthat.R' [70s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(matric)
  > 
  > test_check("matric")
  
  Attaching package: 'purrr'
  
  The following object is masked from 'package:testthat':
  
      is_null
  
  The following object is masked from 'package:base':
  
      %||%
  
  [ FAIL 1 | WARN 66 | SKIP 0 | PASS 93 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-sim_read-write.R:98:3'): `sim_read` works ──────────────────────
  Error: IOError: Failed to open local file 'D:/temp/RtmpKmB7XY/test.parquet'. Detail: [Windows error 1224] Der Vorgang ist bei einer Datei mit einem geöffneten Bereich, der einem Benutzer zugeordnet ist, nicht anwendbar.
  
  Backtrace:
      ▆
   1. ├─sim_df %>% sim_write(tmp_parquet_file) at test-sim_read-write.R:98:3
   2. ├─matric::sim_write(., tmp_parquet_file)
   3. │ └─sim_df %>% arrow::write_parquet(output)
   4. └─arrow::write_parquet(., output)
   5.   └─arrow:::make_output_stream(sink)
   6.     └─FileOutputStream$create(x)
   7.       └─arrow:::io___FileOutputStream__Open(clean_path_abs(path))
  
  [ FAIL 1 | WARN 66 | SKIP 0 | PASS 93 ]
  Error: Test failures
  Execution halted
'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
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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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...'
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.5Mb
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: \#
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
Found the following significant warnings:
  datablock.h:124:42: warning: pointer used after 'void operator delete(void*)' [-Wuse-after-free]
  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 'd:/Rcompile/CRANpkg/local/4.4/MCMCpack.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
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  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Package suggested but not available for checking: 'cmdstanr'
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 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 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 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 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 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 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 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 long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/mco.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 '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
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
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'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'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  unicode_fopen.h:37:52: warning: conversion lacks type at end of format [-Wformat=]
  unicode_fopen.h:37:14: warning: too many arguments for format [-Wformat-extra-args]
  unicode_fopen.h:59:52: warning: conversion lacks type at end of format [-Wformat=]
  unicode_fopen.h:59:14: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.4/meltr.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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
    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 '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
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
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
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 '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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    help   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
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
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.2Mb
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
Package suggested but not available for checking: 'INLA'
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:
> ### ** Examples
> 
> weighted_var(1:10)
[1] 9.166667
> weighted_var(1:10, w = NULL)
[1] 9.166667
> weighted_var(1:10, w = rep(1, 10))
[1] 9.166667
> weighted_var(1:10, w = 1:10)
[1] 6.875
> weighted_var(1:10, w = 1:10, method = "ML")
[1] 6
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  0.74 0.02 0.75 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 ?) ========
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.8Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'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'
'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 long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/mgcv.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
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...'
'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.
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
'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: 'microcontax.data'
Package unavailable to check Rd xrefs: 'microcontax.data'
'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 '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.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    5.5Mb
    lib    1.2Mb
    libs   1.2Mb
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
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
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
'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 'd:/Rcompile/CRANpkg/local/4.4/minimaxdesign.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
':::' call which should be '::': 'parallel:::detectCores'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
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
Package suggested but not available for checking: 'BRugs'
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.
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: \&
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/MixAll.Rcheck/00install.out' for details.
Documented arguments not in \usage in Rd file 'mixAR-internal.Rd':
  'p' 'value' 'tau' 'etk' 'parscore' 'sigma' 'logpdf'

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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 '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: \&
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: \&
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: Escaped LaTeX specials: \&
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
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    include   9.7Mb
    libs     16.9Mb
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'
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
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
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
'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++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
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'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
Rd files without \alias:
  'mnlfa-package.Rd'
'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.
Package suggested but not available for checking: '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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
Argument items with no description in Rd file 'as.difftime.rd':
  'tim' 'format'
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   1.5Mb
'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.
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.
'LazyData' is specified without a 'data' directory
'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: \$
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
'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
Argument items with no description in Rd file 'msda.Rd':
  'sml'
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   4.5Mb
    libs   1.2Mb
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
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.
'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 unsigned 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 unsigned int' [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/mssm.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
'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
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: \&
'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.
'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
Specified C++11: please drop specification unless essential
'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:
1,1,2,2 
2,1,1,2 
> 
> ## an example with letters
> x = letters[1:4]
> m2 = initMC(x)
> nextPerm(m2)
[1] "d" "c" "b" "a"
> nextPerm(m2)
[1] "a" "d" "c" "b"
> ## and so on
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  0.61 0.06 0.68 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 ?) ========
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'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   7.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'rrelaxiv'
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Specified C++11: please drop specification unless essential
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
Running 'spelling.R' [0s]
  Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mustashe)
  > 
  > test_check("mustashe")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 60 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-unstash.R:2:3'): unstashing works ──────────────────────────────
  Error in `value[[3L]](cond)`: 
  'mustashe' is unable to create a directory to stash your objects.
  Please create the directory manually using:
  
    dir.create(D:/RCompile/.mustashe)
  If that does not work, please create the directory from the command line and open an issue at: https://github.com/jhrcook/mustashe
  Backtrace:
      ▆
   1. ├─testthat::expect_null(...) at test-unstash.R:2:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─mustashe::stash(...)
   5.   └─mustashe:::check_stash_dir()
   6.     └─base::tryCatch(...)
   7.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   8.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.           └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 60 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
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: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rTubeDB'
Package unavailable to check Rd xrefs: 'rTubeDB'
'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.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'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'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs     2.4Mb
    models   1.1Mb
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'
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
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.7Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    6.5Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
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
'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  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
'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 '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
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
'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
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
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
':::' 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
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
'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 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
GNU make is a SystemRequirements.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
'LazyData' is specified without a 'data' directory
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: \&
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
'LazyData' is specified without a 'data' directory
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 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 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 'd:/Rcompile/CRANpkg/local/4.4/nimble.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    CppCode   4.7Mb
    R         7.6Mb
    include  10.5Mb
    libs      1.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Package which this enhances but not available for checking: 'jpndistrict'
Malformed Description field: should contain one or more complete sentences.
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.
'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
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.7Mb
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
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 'd:/Rcompile/CRANpkg/local/4.4/nncc.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
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'
'LazyData' is specified without a 'data' directory
'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
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.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   2.6Mb
    mods   3.3Mb
'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
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
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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.4Mb
'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
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.1Mb
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.
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 long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/Numero.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
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs   1.6Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    doc       5.7Mb
    extdata   1.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.6Mb
    test_files   4.2Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.1Mb
    libs   1.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   1.1Mb
Argument items with no description in Rd file 'plot.comphat.Rd':
  '\dots'
Rd files without \alias:
  'odbc-package.Rd'
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
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'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'
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
'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
Specified C++11: please drop specification unless essential
Rd files without \alias:
  'ontologyPlot-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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/OpenCL.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'unix'
GNU make is a SystemRequirements.
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs   19.9Mb
    share  10.2Mb
'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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    R        2.6Mb
    data     1.4Mb
    libs     4.9Mb
    models   4.8Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
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.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   1.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      1.4Mb
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
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [41s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(optimall)
  > 
  > test_check("optimall")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 212 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-optimall_shiny.R:24:1'): (code run outside of `test_that()`) ───
  Error in `get_phantom_envvars()`: `phantomjs --version` timed out.
  Backtrace:
      ▆
   1. └─shinytest::ShinyDriver$new(...) at test-optimall_shiny.R:24:1
   2.   └─shinytest (local) initialize(...)
   3.     └─shinytest:::sd_initialize(...)
   4.       └─shinytest:::get_phantomPort(timeout = phantomTimeout)
   5.         └─webdriver::run_phantomjs(timeout = timeout)
   6.           ├─withr::with_envvar(...)
   7.           │ └─withr:::get_envvar(envs = new, action = action)
   8.           │   └─withr:::as_envvars(envs)
   9.           └─webdriver:::get_phantom_envvars()
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 212 ]
  Error: Test failures
  Execution halted
'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'.
Package suggested but not available for checking: 'rrelaxiv'
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'
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'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 '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.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
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
'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:
    doc    5.0Mb
    libs   1.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rcplex'
Rd files without \alias:
  'otp-package.Rd'
'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
'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
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
checkRd: (-1) residuals_paco.Rd:10: 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
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    library  14.2Mb
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.
'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
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.8Mb
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.
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: \#
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
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'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      6.1Mb
    help   2.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    help   3.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    help   3.0Mb
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/pbdSLAP.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
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 'd:/Rcompile/CRANpkg/local/4.4/PBSddesolve.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  d:/rtools43/x86_64-w64-mingw32.static.posix/include/coin/Clp_C_Interface.h:68:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/pcaL1.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.5Mb
'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
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   8.6Mb
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
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
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.
Package suggested but not available for checking: 'PythonInR'
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs    7.4Mb
    share  12.8Mb
'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
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'
Specified C++11: please drop specification unless essential
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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   2.2Mb
Package suggested but not available for checking: 'georob'
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
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
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: \$
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checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
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checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
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checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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'
Specified C++11: please drop specification unless essential
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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: 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
Invalid package aliases in Rd file 'perspective-package.Rd':
  'perspective-package'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
'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: \_ \_
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checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
    libs      1.0Mb
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...'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
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installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'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
'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
Invalid package aliases in Rd file 'pipegs.Rd':
  'pipegs-package'
'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 '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
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    bin   8.6Mb
    doc   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
'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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tests   3.1Mb
'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
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
'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 '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
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/PMAPscore.Rcheck/00install.out' for details.
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 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 long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/PMA.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Package suggested but not available for checking: 'pmartRdata'
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
'LazyData' is specified without a 'data' directory
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'pollimetrydata'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
    libs   1.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      1.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data      2.7Mb
    extdata   3.5Mb
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: \&
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
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.
'LazyData' is specified without a 'data' directory
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.
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
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'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
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: \&
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
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
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc  10.4Mb
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
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.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata  11.6Mb
Package which this enhances but not available for checking: 'ffbase'
Unknown package 'ffbase' in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R   3.6Mb
'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:
  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 'd:/Rcompile/CRANpkg/local/4.4/PReMiuM.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
'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
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    extdata   9.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinyApp   5.4Mb
'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: 'INLA'
'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:
  'gurobi', 'Rcplex', 'rcbc'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.3Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    4.7Mb
    libs   1.6Mb
'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
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
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
Packages suggested but not available for checking: 'unix', 'cmdstanr'
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
    proj   8.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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.
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.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
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.
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
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
Found the following significant warnings:
  arch/windows/process_handles.h:100:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  arch/windows/process_handles.c:23:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/ps.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 '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.
Invalid package aliases in Rd file 'package-ptf.Rd':
  'package-ptf-package'
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.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.5Mb
'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
Invalid package aliases in Rd file 'PVAClone-package.Rd':
  'PVA-package' 'pva-package' 'Pva-package'
'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: \&
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
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.
'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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.3Mb
'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.
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
'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:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spDataLarge'
'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
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
Specified C++11: please drop specification unless essential
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
checkRd: (-1) NEWS.Rd:15: Escaped LaTeX specials: \&
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    4.4Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      2.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.0Mb
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.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  bounded_reg.cpp:33:25: warning: 'std::ostream& arma::arma_cerr_stream(std::ostream*) [with T = char; std::ostream = std::basic_ostream<char>]' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  elastic_net.cpp:35:25: warning: 'std::ostream& arma::arma_cerr_stream(std::ostream*) [with T = char; std::ostream = std::basic_ostream<char>]' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.4/quadrupen.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
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.
'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 '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'
'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  7.1Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    shiny_app   1.4Mb
Invalid package aliases in Rd file 'qut-package.Rd':
  'QUT-package'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   5.0Mb
Package suggested but not available for checking: 'RDCOMClient'
'library' or 'require' call to 'RDCOMClient' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'BRugs'
Documented arguments not in \usage in Rd file 'bugs.inits.Rd':
  'inits.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.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
'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
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
    libs          2.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
'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 10.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets  10.0Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   6.8Mb
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.
'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.
Invalid package aliases in Rd file 'randtests-package.Rd':
  'randomtests-package'
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: 'gurobi'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      1.4Mb
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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
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'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.5Mb
'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 '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.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   1.2Mb
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.
Specified C++11: please drop specification unless essential
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.
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  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
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
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.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    cont  24.2Mb
'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 '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.
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.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   4.5Mb
    po    2.4Mb
Package suggested but not available for checking: 'conics'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/Rcplex.Rcheck/00install.out' for details.
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
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
    libs      1.2Mb
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.
installed size is 46.7Mb
  sub-directories of 1Mb or more:
    include  46.4Mb
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
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
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.2Mb
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
'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
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.1Mb
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 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 long int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/Rcpp.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      1.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include        2.0Mb
    jsonexamples   3.8Mb
    libs           2.0Mb
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
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
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.
'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
Found the following significant warnings:
  libdieharder/bits.c:316:52: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
  libdieharder/countx.c:236:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  libdieharder/rngav.c:179:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  libdieharder/rng_file_input.c:165:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'off_t' {aka 'long long int'} [-Wformat=]
  libdieharder/rng_file_input.c:165:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'off_t' {aka 'long long int'} [-Wformat=]
  libdieharder/rng_file_input.c:165:41: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'off_t' {aka 'long long int'} [-Wformat=]
  libdieharder/rng_file_input.c:273:72: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'off_t' {aka 'long long int'} [-Wformat=]
  libdieharder/rng_file_input.c:325:56: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'off_t' {aka 'long long int'} [-Wformat=]
  libdieharder/sts_monobit.c:74:43: 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/RDieHarder.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.2Mb
'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
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
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.5Mb
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
'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
Found the following significant warnings:
  unicode_fopen.h:37:52: warning: conversion lacks type at end of format [-Wformat=]
  unicode_fopen.h:37:14: warning: too many arguments for format [-Wformat-extra-args]
  unicode_fopen.h:59:52: warning: conversion lacks type at end of format [-Wformat=]
  unicode_fopen.h:59:14: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.4/readr.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
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.
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
'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
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
--- finished re-building 'Introduction.Rmd'

--- re-building 'step00_prep.Rmd' using rmarkdown
--- finished re-building 'step00_prep.Rmd'

--- re-building 'step01_loading.Rmd' using rmarkdown
--- finished re-building 'step01_loading.Rmd'

--- re-building 'step02_initial_cluster.Rmd' using rmarkdown
--- finished re-building 'step02_initial_cluster.Rmd'

--- re-building 'step03_refinement.Rmd' using rmarkdown
--- finished re-building 'step03_refinement.Rmd'

--- re-building 'step04_manual_tweak.Rmd' using rmarkdown
--- re-building 'step05_visualization_export.Rmd' using rmarkdown
--- finished re-building 'step05_visualization_export.Rmd'

SUMMARY: processing the following file failed:
  'step04_manual_tweak.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
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
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.0Mb
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 ~~'
'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.
'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
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      1.3Mb
'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: 'Rcplex'
'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.
'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:
    doc    3.5Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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: \$
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.
'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
'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: \_ \_
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs      1.7Mb
    models    1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
Rd files without \alias:
  'retry-package.Rd'
'LazyData' is specified without a 'data' directory
checkRd: (-1) rec.Rd:23: 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
'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:
    libs   5.1Mb
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.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data  13.3Mb
'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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
'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
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 'd:/Rcompile/CRANpkg/local/4.4/Rglpk.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs    2.6Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'LazyData' is specified without a 'data' directory
'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.
'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
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    lib    3.3Mb
    libs   4.1Mb
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    '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.
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
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.
Found the following significant warnings:
  Rinit.c:170:24: warning: pointer targets in passing argument 2 of 'Re_ReadConsole' differ in signedness [-Wpointer-sign]
  Rinit.c:251:21: warning: assignment to 'int (*)(const char *, unsigned char *, int,  int)' from incompatible pointer type 'int (*)(const char *, char *, int,  int)' [-Wincompatible-pointer-types]
  init.c:197:49: warning: format '%d' expects argument of type 'int', but argument 2 has type 'jint' {aka 'long int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/rJava.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
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 for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.4/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'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:
    include   3.1Mb
    libs      2.3Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 50.2Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  45.7Mb
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    extdata  23.8Mb
Invalid package aliases in Rd file 'rkt-package.Rd':
  'tkt-package'
'LazyData' is specified without a 'data' directory
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: \$
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
GNU make is a SystemRequirements.
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    hdf5     16.0Mb
    include   6.5Mb
    lib       2.6Mb
    libs      8.2Mb
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
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
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
GNU make is a SystemRequirements.
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':
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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs       1.0Mb
    minizinc   2.3Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
Package suggested but not available for checking: 'rnaturalearthhires'
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
'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:
    extdata   2.0Mb
    libs      3.3Mb
'LazyData' is specified without a 'data' directory
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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.7Mb
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
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
Invalid package aliases in Rd file '0RobRDA-package.Rd':
  'RobRDA-package'
'LazyData' is specified without a 'data' directory
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RobLoxBioC.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\emmintrin.h:134:24: warning: array subscript '__m128d_u[0]' is partly outside array bounds of 'Eigen::internal::plain_matrix_type<Eigen::Product<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>, Eigen::Transpose<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false> >, 0>, Eigen::Dense>::type [1]' {aka 'Eigen::Matrix<double, 1, 1, 0, 1, 1> [1]'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.4/RobustGaSP.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              1.3Mb
    simulationStudy   1.6Mb
'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
'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
Found the following significant warnings:
  RODBC.c:294:31: warning: format '%d' expects argument of type 'int', but argument 3 has type 'SQLINTEGER' {aka 'long int'} [-Wformat=]
  RODBC.c:1078:59: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'SQLULEN' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/RODBC.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ROracle.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   1.5Mb
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'
'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  6.8Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs   1.5Mb
Package suggested but not available for checking: 'RandomFields'
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 'd:/Rcompile/CRANpkg/local/4.4/Rphylopars.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.4Mb
'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 'd:/Rcompile/CRANpkg/local/4.4/RPostgreSQL.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'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
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
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
'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'
'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   3.6Mb
'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.
'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:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
GNU make is a SystemRequirements.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.4/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_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. 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.
'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 'd:/Rcompile/CRANpkg/local/4.4/RSiena.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
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.
'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
'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: 'INLA'
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 18.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    4.7Mb
    libs  11.6Mb
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 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 long int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/rstan.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib    2.1Mb
    libs   1.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'SetHash.Rd':
  '\dots'
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
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.
Specified C++11: please drop specification unless essential
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    libs    1.1Mb
    swipl  40.2Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.4Mb
    help   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    rmarkdown   9.4Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
Specified C++11: please drop specification unless essential
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
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
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.
'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.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
'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.
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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RVA.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: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs      5.2Mb
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'
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
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.
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   2.6Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'unix'
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
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
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
Specified C++11: please drop specification unless essential
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
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
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: \#
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  13.5Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   1.3Mb
Package suggested but not available for checking: 'networkTomography'
'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: '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
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin   5.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.2Mb
'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
'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':
  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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
'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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R   5.3Mb
'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
checkRd: (-1) x.oreo.Rd:48: 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
Packages suggested but not available for checking:
  'sceasy', 'SeuratDisk', 'SeuratWrappers'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
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
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
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: 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
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
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 'd:/Rcompile/CRANpkg/local/4.4/sdcMicro.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
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
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
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.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
'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      1.5Mb
    libs   2.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spgrass6'
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    www  33.6Mb
'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) 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
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
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs     3.3Mb
    models   1.6Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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
Running 'testthat.R' [34s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(seqgendiff)
  > 
  > test_check("seqgendiff")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 63 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_theo.R:25:3'): seqgen_base works ───────────────────────────────
  Error in `FUN(newX[, i], ...)`: is.atomic(y) is not TRUE
  Backtrace:
      ▆
   1. └─base::apply(temp, 1, var) at test_theo.R:25:3
   2.   ├─BiocGenerics (local) FUN(newX[, i], ...)
   3.   └─stats (local) FUN(newX[, i], ...)
   4.     └─base::stopifnot(is.atomic(y))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 63 ]
  Error: Test failures
  Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'sequential.design.Rd':
  '\dots'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
'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', '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.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 106.4Mb
  sub-directories of 1Mb or more:
    doc      1.7Mb
    gdal     3.0Mb
    libs    88.8Mb
    proj     8.3Mb
    sqlite   1.5Mb
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 'd:/Rcompile/CRANpkg/local/4.4/SFSI.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
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
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
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.8Mb
'LazyData' is specified without a 'data' directory
'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'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   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
'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 '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
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'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
Problems with news in 'NEWS.md':
No news entries found.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    www   9.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
'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'
'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
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
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    help      1.7Mb
    libs      1.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SIGN.Rcheck/00install.out' for details.
'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
Argument items with no description in Rd file 'estThetaRow.Rd':
  'theta'
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      1.5Mb
'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:
  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 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 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 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 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 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 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 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 long int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/SimInf.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
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.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
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 'd:/Rcompile/CRANpkg/local/4.4/simPop.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
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'
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.
Package suggested but not available for checking: 'INLA'
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
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
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   1.6Mb
Specified C++11: please drop specification unless essential
'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
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'
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.
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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'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:
    doc   4.4Mb
checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
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
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Unknown package 'InformationValue' in Rd xrefs
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
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: \$
'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  6.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
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 'd:/Rcompile/CRANpkg/local/4.4/smog.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
'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 ~~'
'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: \&
Package suggested but not available for checking: 'doMC'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.3Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
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...'
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
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  5.2Mb
  sub-directories of 1Mb or more:
    R     3.3Mb
    doc   1.1Mb
checkRd: (-1) llwrPTF.Rd:7: 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:
  '.solveEnv'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.3Mb
    libs   1.7Mb
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: \_
'LazyData' is specified without a 'data' directory
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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.1Mb
'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'.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'NLMR'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R   4.9Mb
Package suggested but not available for checking: 'NLMR'
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    libs   1.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    java   3.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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 'd:/Rcompile/CRANpkg/local/4.4/SparseFactorAnalysis.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
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
'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 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.1Mb
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) NEWS.Rd:137: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'spDataLarge'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
    etc   1.4Mb
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.
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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
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
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:
    Feature Changes
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs      1.6Mb
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
Specified C++11: please drop specification unless essential
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
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.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
'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
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.3Mb
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
Running examples in 'SRTsim-Ex.R' failed
The error most likely occurred in:

> ### Name: compareSRT
> ### Title: Summarize metrics for reference data and synthetic data
> ### Aliases: compareSRT
> 
> ### ** Examples
> 
> 
> ## Create a simSRT object
> toySRT  <- createSRT(count_in=toyData$toyCount,loc_in = toyData$toyInfo)
> set.seed(1)
> ## Estimate model parameters for data generation
> toySRT <- srtsim_fit(toySRT,sim_schem="tissue")
> ## Generate synthetic data with estimated parameters
> toySRT <- srtsim_count(toySRT)
> ## Compute metrics 
> toySRT   <- compareSRT(toySRT)
Error in FUN(newX[, i], ...) : is.atomic(y) is not TRUE
Calls: compareSRT ... DataFrame -> get_stats_gene -> apply -> FUN -> FUN -> stopifnot
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SRTsim.Rmd' using rmarkdown

Quitting from lines 133-139 [tissue simulation metrics comparison] (SRTsim.Rmd)
Error: processing vignette 'SRTsim.Rmd' failed with diagnostics:
is.atomic(y) is not TRUE
--- failed re-building 'SRTsim.Rmd'

SUMMARY: processing the following file failed:
  'SRTsim.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  13.8Mb
'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  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
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.
'LazyData' is specified without a 'data' directory
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.
'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 '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.
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.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    include  11.3Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
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':
  Cannot extract version info from the following section titles:
    To do
Package suggested but not available for checking: 'starsdata'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    1.7Mb
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'statcheck-package.Rd':
  '{statcheck}-package'
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.4Mb
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'
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'
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'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:
    shiny-apps   6.1Mb
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
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
'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.
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Argument items with no description in Rd file 'd.sum.of.mixtures.EXPLN.Rd':
  'p.vector'
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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 ~~'
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: 'StrathE2E2examples'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'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   4.6Mb
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
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'STRaitRazoR'
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'
'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.
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:
Residual Deviance: 67.88 	AIC: 73.88

$p_value
[1] 0.117

$theta
(Intercept)          x1          x2 
  0.5782940  -0.3134291   0.7532186 

$prop
[1] 600

> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  0.66 0.34 1 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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.3Mb
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
surfaceSimulate : phytransform: no visible global function definition
  for 'rescale'
Undefined global functions or variables:
  rescale
'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'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.2Mb
    libs   1.1Mb
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', 'INLA'
Package suggested but not available for checking: 'distr6'
Unknown package 'distr6' in Rd xrefs
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.9Mb
Specified C++11: please drop specification unless essential
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
Unknown package 'survJamda' in Rd xrefs
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
'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
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'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
'LazyData' is specified without a 'data' directory
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'
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'syncrng-package.Rd':
  'syncrng-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
Package suggested but not available for checking: 'unix'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
'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.
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
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
'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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: 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
Package suggested but not available for checking: 'tashudata'
'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.
'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
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc  12.3Mb
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    7.3Mb
    libs   1.1Mb
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 'd:/Rcompile/CRANpkg/local/4.4/TDboost.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
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: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.7Mb
    libs      1.1Mb
    telemac   1.0Mb
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
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    4.5Mb
    help   2.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 106.4Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    gdal   3.0Mb
    libs  91.6Mb
    proj   8.3Mb
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       8.1Mb
    tessdata  14.0Mb
Package suggested but not available for checking: 'gurobi'
'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'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    data   3.0Mb
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
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
'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 '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
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes:
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.
'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.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   4.5Mb
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Found the following significant warnings:
  round.cpp:164:34: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  round.cpp:164:106: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  round.cpp:285:34: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  round.cpp:285:106: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/timechange.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
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.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'timeSeq_1.0.4-package.Rd':
  'timeSeq_1.0.4-package'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/tinyarray.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:131:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:334:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:453:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:471:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:496:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:497:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:509:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:522:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R/Tcl/include/X11/Xlib.h:1053:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:93:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:94:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:317:29: warning: format '%d' expects argument of type 'int', but argument 2 has type 'DWORD' {aka 'long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/tkrplot.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
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
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    examples  12.7Mb
    include    3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
'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 '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.
Specified C++11: please drop specification unless essential
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/TOmicsVis.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'corpus.JSS.papers'
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    R         5.5Mb
    help      1.6Mb
    include   3.4Mb
    libs     17.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'toscaData'
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.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    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'
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  13.3Mb
'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.
Packages which this enhances but not available for checking:
  'fwelnet', 'doMC'
'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.
Package suggested but not available for checking: 'TreeDistData'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.2Mb
Specified C++11: please drop specification unless essential
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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    doc       1.3Mb
    extdata  14.8Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.4Mb
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
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'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
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'
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
'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.
'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
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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.2Mb
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
'LazyData' is specified without a 'data' directory
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
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
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.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc     6.6Mb
    ubinc   2.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.0Mb
    libs   4.4Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.6Mb
'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:
> ### Aliases: variantQC
> 
> ### ** Examples
> 
> ## Not run: 
> ##D variantQC(snpQcFile=covid_example("sim_ukb_snp_qc.txt.gz"), 
> ##D mfiDir=covid_example("alleleFreqs"), 
> ##D mafFilt=0.001, 
> ##D infoFilt=0.5, 
> ##D outDir=covid_example("results"))
> ## End(Not run)
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.69 0.42 2.16 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
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
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
'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
'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 18.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.4Mb
    libs  14.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: 'USA.state.boundaries.data'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'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 '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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
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  6.6Mb
  sub-directories of 1Mb or more:
    extdata   6.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
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.
Found the following significant warnings:
  randutils.c:60:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/uuid.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  22.0Mb
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   8.8Mb
'LazyData' is specified without a 'data' directory
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
installed size is 103.4Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    gdal      3.0Mb
    libs     88.0Mb
    proj      8.3Mb
'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.
'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: \&
'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
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs     10.5Mb
GNU make is a SystemRequirements.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
'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 '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.
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.
'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
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  7.9Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    help   3.0Mb
'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'
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.
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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     19.9Mb
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.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.5Mb
'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  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'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
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    6.3Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
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 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
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'
'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  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
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
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
'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
Problems with news in 'NEWS.md':
No news entries found.
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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.
'LazyData' is specified without a 'data' directory
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.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
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 'd:/Rcompile/CRANpkg/local/4.4/wrassp.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Malformed Title field: should not end in a period.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
'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
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
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
Argument items with no description in Rd file 'getCondition.Rd':
  'object'
Argument items with no description in Rd file 'screen.Rd':
  'fac' 'condition' 'position'
'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
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'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
Malformed Description field: should contain one or more complete sentences.
Auto-generated content requiring editing in Rd file 'ZIBseq-package.Rd':
  \seealso: '~~ Optional links to other man pages, e.g. ~~ ~~ \code{\link...'
'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) 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘acceldata2.RData’
'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
Problems with news in ‘NEWS.md’:
No news entries found.
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 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
Specified C++11: please drop specification unless essential
Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                 old_size new_size compress
  estrogen.RData    339Kb    241Kb       xz
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
'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
'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:
  ‘table_AeRobiology’
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 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
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
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: \&
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Running examples in ‘algaeClassify-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genus_search_itis
> ### Title: Wrapper function for several functions in ritis:: Searches ITIS
> ###   database for matches to a genus name
> ### Aliases: genus_search_itis
> 
> ### ** Examples
> 
> genus='Anabaena'
> genus_search_itis(genus,higher=TRUE)
Error:
! The `x` argument of `as_tibble()` can't be missing as of tibble 3.0.0.
Backtrace:
    ▆
 1. └─algaeClassify::genus_search_itis(genus, higher = TRUE)
 2.   └─ritis::accepted_names(tsn = tsn)
 3.     └─ritis:::parse_raw(out)
 4.       ├─tibble::as_tibble()
 5.       └─tibble:::as_tibble.NULL()
 6.         └─lifecycle::deprecate_stop("3.0.0", "as_tibble(x = 'can\\'t be missing')")
 7.           └─lifecycle:::deprecate_stop0(msg)
 8.             └─rlang::cnd_signal(...)
Execution halted
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
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
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
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: \~
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
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
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
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
Found the following calls to attach():
File ‘apollo/R/apollo_attach.R’:
  attach(as.list(apollo_beta), warn.conflicts = FALSE)
  attach(database, warn.conflicts = FALSE)
  attach(draws, warn.conflicts = FALSE)
  attach(randcoeff, warn.conflicts = FALSE)
  attach(lcpars, warn.conflicts = FALSE)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
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’
'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
'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.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'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
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
'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
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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
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
'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’
'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
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
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
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Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rgdal’
'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
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
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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: \$
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: ‘INLA’
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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
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.
'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.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
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.
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 documentation object 'export.bce':
  ‘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
'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
Found the following files/directories:
  ‘dump.txt’
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:
  ‘beast_plot_toy.pdf’
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
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Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘lavaan.survey’
Unknown package ‘lavaan.survey’ in Rd xrefs
Package suggested but not available for checking: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
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
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
'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 documentation object 'select.cfs':
  ‘select.cfs’

S3 methods shown with full name in documentation object 'select.fast.filter':
  ‘select.fast.filter’

S3 methods shown with full name in documentation object 'select.forward.Corr':
  ‘select.forward.Corr’

S3 methods shown with full name in documentation object 'select.forward.wrapper':
  ‘select.forward.wrapper’

S3 methods shown with full name in documentation object 'select.inf.chi2':
  ‘select.inf.chi2’

S3 methods shown with full name in documentation object 'select.inf.gain':
  ‘select.inf.gain’

S3 methods shown with full name in documentation object 'select.inf.symm':
  ‘select.inf.symm’

S3 methods shown with full name in documentation object 'select.process':
  ‘select.process’

S3 methods shown with full name in documentation object 'select.relief':
  ‘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’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: 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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bistablehistory.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: ‘cmdstanr’
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
'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.
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
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
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
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'
'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.
S3 methods shown with full name in documentation object 'subset.int':
  ‘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
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:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
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
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
checkRd: (-1) kink_estimator.Rd:60: 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
'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: \& \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'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: ‘rgdal’
Found the following files/directories:
  ‘MDA231_tree.pdf’
'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
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
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
'LazyData' is specified without a 'data' directory
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
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: \&
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'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
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
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
'LazyData' is specified without a 'data' directory
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
'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’:
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
'LazyData' is specified without a 'data' directory
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 documentation object 'select.cglasso':
  ‘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
S3 methods shown with full name in documentation object 'internals':
  ‘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
'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’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
'LazyData' is specified without a 'data' directory
'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.
'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
'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: ‘userfriendlyscience’
'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
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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘clusterhap_reports’
Specified C++11: please drop specification unless essential
'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
'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.
Package suggested but not available for checking: ‘PopGenome’
Package suggested but not available for checking: ‘disttree’
'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’
Package which this enhances but not available for checking: ‘rkward’
Package suggested but not available for checking: ‘userfriendlyscience’
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Package suggested but not available for checking: ‘bvpSolve’
'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
'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
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
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
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’
'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) 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
'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:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
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
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
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
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
Package required but not available: ‘ctsem’

See section ‘The DESCRIPTION file’ 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
Found the following files/directories:
  ‘covfefe_inauguration.txt’
'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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘BEST’
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
'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
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
'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
Package suggested but not available for checking: ‘rgeos’
'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
S3 methods shown with full name in documentation object 'internals':
  ‘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.
Package required but not available: ‘ctsem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ctsem.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
Found the following files/directories:
  ‘Hello.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘curephEM-vignette.Rmd’ using rmarkdown

Quitting from lines 41-42 [unnamed-chunk-5] (curephEM-vignette.Rmd)
Error: processing vignette 'curephEM-vignette.Rmd' failed with diagnostics:
invalid 'times' argument
--- failed re-building ‘curephEM-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘curephEM-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
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
'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: \_ \_ \_
Package which this enhances but not available for checking: ‘RGtk2’
'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:
  'gurobi', 'rcbc'
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
'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.
'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:
  ‘my new data set.rds’
'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
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 documentation object 'dbglm-inl':
  ‘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
Problems with news in ‘NEWS.md’:
No news entries found.
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
'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
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
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
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'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
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
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.
'LazyData' is specified without a 'data' directory
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’
Package which this enhances but not available for checking: ‘gurobi’
'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
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
'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
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
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
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’
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
'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: \&
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.
'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: ‘BOLTSSIRR’
Package suggested but not available for checking: ‘rgdal’
'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:
    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: \&
'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
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
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 documentation object 'add.joint.mean.many':
  ‘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.
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
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
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
Found the following calls to attach():
File ‘doSNOW/R/doSNOW.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'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
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
'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: ‘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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [4s/4s]
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(duke)
  > 
  > test_check("duke")
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 25 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-scale_duke_color_discrete.R:42:3'): appropriate fill for factors over 8-levels ──
  `ggplot2::ggplot_build(p4)` did not throw the expected warning.
  ── Failure ('test-scale_duke_fill_discrete.R:47:3'): appropriate fill for factors over 8-levels ──
  `ggplot2::ggplot_build(p4)` did not throw the expected warning.
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 25 ]
  Error: Test failures
  Execution halted
'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: ‘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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
'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
'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’
'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
'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.
'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
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
Package suggested but not available for checking: ‘lavaan.survey’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
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
'LazyData' is specified without a 'data' directory
'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
GNU make is a SystemRequirements.
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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/emdist.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 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
Specified C++11: please drop specification unless essential
checkRd: (-1) encode.character.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
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Server error: (500) Internal Server Error

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Error(s) in re-building vignettes:
  ...
--- re-building ‘enrichR.Rmd’ using rmarkdown

Quitting from lines 96-99 [unnamed-chunk-11] (enrichR.Rmd)
Error: processing vignette 'enrichR.Rmd' failed with diagnostics:
arguments imply differing number of rows: 2, 0
--- failed re-building ‘enrichR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RStoolbox’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘epidict’
GNU make is a SystemRequirements.
S3 methods shown with full name in documentation object 'addDrug.Lexis':
  ‘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’
'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
Found the following significant warnings:
  Rd warning: no hsearch.rds meta data for package ergm
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ergm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
S3 methods shown with full name in documentation object 'summary.error_interval':
  ‘summary.error_interval’

S3 methods shown with full name in documentation object 'summary.measure':
  ‘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
'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 documentation object 'ETAS-internal':
  ‘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.
'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
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’
'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
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
Unknown package ‘iptools’ in Rd xrefs
Package suggested but not available for checking: ‘INLA’
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: ‘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: \&
'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
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
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: \#
'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
'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
'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
'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
'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
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
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: \&
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: \&
.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
'LazyData' is specified without a 'data' directory
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.
'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
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.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
'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
'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
Package suggested but not available for checking: ‘MicrobeDS’
'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
'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: \&
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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/finity.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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:
  'nCDunnett', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
'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.
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'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
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘flux.CH4.txt’
'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
'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.
'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
'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:
    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
'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
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
'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: 'dggrids', 'INLA'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
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
'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.
S3 methods shown with full name in documentation object 'plot.funData':
  ‘plot.funData’

S3 methods shown with full name in documentation object 'plot.irregFunData':
  ‘plot.irregFunData’

S3 methods shown with full name in documentation object 'plot.multiFunData':
  ‘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
'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’
'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) 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: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
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: \&
Package suggested but not available for checking: ‘gputools’
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
Found the following calls to attach():
File ‘g.data/R/g.data.attach.R’:
  attach(NULL, pos, basename(dir))
See section ‘Good practice’ in ‘?attach’.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gdxrrw’
'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: ‘genderdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘maptools’
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’:
No news entries found.
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++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
'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
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘geomarocdata’
'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.
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.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
Package suggested but not available for checking: ‘rgdal’
'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: ‘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
'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
Found the following assignments to the global environment:
File ‘ggExtra/R/ggMarginalGadget.R’:
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
'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
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.
'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: ‘lixoftConnectors’
'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:
    * Changes all data options to .data to decrease possibility of column naming overlap
'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:
    Win CRAN check results - R Windows
'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
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
'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: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mlr3proba’
'LazyData' is specified without a 'data' directory
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.
'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
'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
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
Package suggested but not available for checking: ‘ganalytics’
'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.
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’
'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: \_
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
Package suggested but not available for checking: ‘monocle’
Package unavailable to check Rd xrefs: ‘monocle’
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'groc.fit':
  ‘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
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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’
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’
'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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RRprof.out’
'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
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
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
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: \&
Found the following significant warnings:
  HARDataCreationC.cpp:43:31: 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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/HARModel.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
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
'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.
'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
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
'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
'LazyData' is specified without a 'data' directory
Running examples in ‘hexfont-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: unifont
> ### Title: Load Unifont font
> ### Aliases: unifont
> 
> ### ** Examples
> 
> # Much faster to load only the subset of GNU Unifont one needs
> # Mandarin Chinese
> if (require("bittermelon")) {
+   s <- "\uff32\u5f88\u68d2\uff01"
+   font <- unifont(ucp = str2ucp(s))
+   bm <- as_bm_bitmap(s, font = font)
+   print(bm, px = px_ascii)
+ }
Loading required package: bittermelon

Attaching package: ‘bittermelon’

The following object is masked from ‘package:base’:

    which

Error in vector("list", n_orig - n_combining) : vector size cannot be NA
Calls: as_bm_bitmap -> as_bm_bitmap.character -> lapply -> FUN
Execution halted
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'defunct':
  ‘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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘INLA’
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
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
html_describe_con: multiple local function definitions for ‘g’ with
  different formal arguments
'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: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
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) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
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’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgeos’
checkRd: (-1) palettes.Rd:25: 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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SparkR’
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
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: \$
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
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object 'internals':
  ‘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
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
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
'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
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’
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
'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’
'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
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
'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
Specified C++11: please drop specification unless essential
'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
'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
File ‘iotools/libs/iotools.so’:
  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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
S3 methods shown with full name in documentation object 'print.Item':
  ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
GNU make is a SystemRequirements.
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’
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
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
GNU make is a SystemRequirements.
'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'.
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.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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
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
'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’
'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
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)
Dependence on R version ‘4.1.2’ not with patchlevel 0
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
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
'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
S3 methods shown with full name in documentation object 'bw.abram.temp':
  ‘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.
'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 documentation object 'unlist.constr':
  ‘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’
'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
'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:
  '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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
'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
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: ‘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
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
'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:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
'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
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
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
GNU make is a SystemRequirements.
'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
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
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S3 methods shown with full name in documentation object 'BIC.threshold':
  ‘BIC.threshold’

S3 methods shown with full name in documentation object 'BIC.threshold.ggm':
  ‘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
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checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
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    Author
    Maintainer
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Found the following files/directories:
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Malformed Description field: should contain one or more complete sentences.
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
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Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
checkRd: (-1) Interpolation-class.Rd:41: Escaped LaTeX specials: \#
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘gurobi’
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checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
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checkRd: (-1) maxControl.Rd:83: Escaped LaTeX specials: \&
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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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘cmdstanr’
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'LazyData' is specified without a 'data' directory
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    Initial version.
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
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checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
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Package suggested but not available for checking: ‘INLA’
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Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Problems with news in ‘NEWS.md’:
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Unknown packages ‘Rcgmin’, ‘Rvmmin’ 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
GNU make is a SystemRequirements.
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checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
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Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Package suggested but not available for checking: ‘INLA’
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'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++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
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.
S3 methods shown with full name in documentation object 'complete.miceadds':
  ‘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
'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: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘midfielddata’
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Package suggested but not available for checking: ‘gurobi’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/minimaxdesign.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
':::' call which should be '::': ‘parallel:::detectCores’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
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checkRd: (-1) AKMCS.Rd:215: Escaped LaTeX specials: \&
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checkRd: (-1) oscillator_d6.Rd:14: Escaped LaTeX specials: \&
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checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
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  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
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checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
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Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
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'LazyData' is specified without a 'data' directory
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Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
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'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
No news entries found.
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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'
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checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
'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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.txt’
'LazyData' is specified without a 'data' directory
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Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
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checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
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'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
S3 methods shown with full name in documentation object 'pca.plot.wrap':
  ‘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: \&
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'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
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
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
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
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'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
Package suggested but not available for checking: ‘re2r’
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Package suggested but not available for checking: ‘spatialClust’
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
Package suggested but not available for checking: ‘gurobi’
Packages suggested but not available for checking:
  'rgeos', 'rgdal', 'maptools'
'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
'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.
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
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
':::' call which should be '::': ‘lhs:::maximinLHS’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_
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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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
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
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
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Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘mail’
'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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'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
'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
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Specified C++11: please drop specification unless essential
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
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checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
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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’:
No news entries found.
'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
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                   old_size new_size compress
  numerical_experiments_data.RData    1.3Mb    1.2Mb       xz
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'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
Running examples in ‘oldbailey-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
'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’
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'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
Package suggested but not available for checking: ‘rgdal’
'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.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'unary_ops':
  ‘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.
'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: ‘openNLPmodels.en’
Packages suggested but not available for checking: 'maptools', 'rgeos'
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
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Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
'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: ‘rrelaxiv’
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
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
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
'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
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
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
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'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:
  Rd warning: pkg_deps.Rd:40: missing link ‘parse_pkg_refs’
  Rd warning: pkg_download.Rd:53: missing link ‘parse_pkg_refs’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pak.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
Package which this enhances but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'pamr-internal':
  ‘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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
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checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
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'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.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rgdal’
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
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’
S3 methods shown with full name in documentation object 'vec_cast.partial_time':
  ‘vec_cast.partial_time’

S3 methods shown with full name in documentation object 'vec_cast.timespan':
  ‘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: \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
S3 methods shown with full name in documentation object 'ped':
  ‘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.
'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.
'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
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
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
Package suggested but not available for checking: ‘PythonInR’
'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
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object 'format.relation':
  ‘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’
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
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checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
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checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
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Specified C++11: please drop specification unless essential
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
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checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘dendextendRcpp’
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: 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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: \&
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
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checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
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checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'qr.solve_exact':
  ‘qr.solve_exact’

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) 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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'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
'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: ‘pinnacle.API’
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.
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
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
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
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pmartRdata’
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
'LazyData' is specified without a 'data' directory
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
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’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Rd warning: pop.predict.Rd:64: missing link ‘rrBLUP’
  Rd warning: pop.predict.Rd:99: missing link ‘rrBLUP’
  Rd warning: pop.predict.Rd:103: missing link ‘rrBLUP’
  Rd warning: x.val.Rd:45: missing link ‘rrBLUP’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopVar.Rcheck/00install.out’ for details.
Missing link or links in documentation object 'pop.predict.Rd':
  ‘rrBLUP’

Missing link or links in documentation object '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
'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: \&
Unknown package ‘advclust’ in Rd xrefs
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
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
'LazyData' is specified without a 'data' directory
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
'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.
'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
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
Packages suggested but not available for checking: 'gurobi', '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
'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) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cin’
Specified C++11: please drop specification unless essential
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’
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
'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
'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: \&
'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
S3 methods shown with full name in documentation object 'internals':
  ‘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’
'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
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object 'internals':
  ‘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.
S3 methods shown with full name in documentation object 'internals':
  ‘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
Specified C++11: please drop specification unless essential
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  bounded_reg.cpp:33:25: warning: ‘std::ostream& arma::arma_cerr_stream(std::ostream*) [with T = char; std::ostream = std::basic_ostream<char>]’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  elastic_net.cpp:35:25: warning: ‘std::ostream& arma::arma_cerr_stream(std::ostream*) [with T = char; std::ostream = std::basic_ostream<char>]’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/quadrupen.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
'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.
Package suggested but not available for checking: ‘fastshp’
'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
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
'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.
'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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'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
'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: \_
'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.
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
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 documentation object 'export.default':
  ‘export.default’

S3 methods shown with full name in documentation object 'export.listpoly':
  ‘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.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘data.csv’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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
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.
Package suggested but not available for checking: ‘conics’
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
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
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
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.
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.
'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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘devAll’
'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
Package suggested but not available for checking: ‘DIDmultiplegt’
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'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
'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
'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
'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
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
'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 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
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
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
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: \$
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.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PackageCites.bib’
'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
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: \_ \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) rec.Rd:23: 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
'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
'LazyData' is specified without a 'data' directory
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’
'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:
  ‘mydata.rda’ ‘thedata.rda’
'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:
  '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.
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
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
'LazyData' is specified without a 'data' directory
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)
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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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
'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
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
'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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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’:
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
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
'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
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rnaturalearthhires’
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: 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: ‘rgdal’
'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
'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
'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
'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
GNU make is a SystemRequirements.
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
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
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
'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’
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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rphylopars.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
'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
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'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
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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’

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.
'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: ‘gurobi’
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: ‘INLA’
Specified C++11: please drop specification unless essential
Running ‘tinytest.R’ [0s/1s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > tmp_user_dir <- tempdir()
  > Sys.setenv(RSPM_USER_DIR=tmp_user_dir)
  > 
  > if (requireNamespace("tinytest", quietly=TRUE)) {
  +   home <- identical(Sys.getenv("CI"), "true")
  +   tinytest::test_package("rspm", at_home=home)
  + }
   You are using 'tinytest::' to express test expectations.
   The results from these tests are not collected. Found the following occurrences:
   > test_integration.R#002: tinytest::expect_match 
   Remove the 'tinytest::' prefix to register the test results.FALSE
  
  test_integration.R............    0 tests    
  test_integration.R............    1 tests [0;32mOK[0m 
  test_integration.R............    2 tests [0;32mOK[0m 
  test_integration.R............    2 tests [0;32mOK[0m 
  test_integration.R............    3 tests [0;32mOK[0m Error: please, install the following required utilities: apt-file
  Execution halted
'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.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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.
Found the following files/directories:
  ‘Tsttwalk.dat’
'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
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object 'printHTML.trackInfo':
  ‘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’
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
S3 methods shown with full name in documentation object 'matmult':
  ‘%*%.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’
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
Malformed Title field: should not end in a period.
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
matrixOps:
  function(x, y)
matrixOps.S7_object:
  function(e1, e2)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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
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
'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
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’
'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: ‘FitARMA’
Specified C++11: please drop specification unless essential
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
'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
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.
Package suggested but not available for checking: ‘rgdal’
'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
Specified C++11: please drop specification unless essential
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
Packages which this enhances but not available for checking:
  'gurobi', 'pogs'
'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
checkRd: (-1) x.oreo.Rd:48: 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
Packages suggested but not available for checking:
  'sceasy', 'SeuratDisk', 'SeuratWrappers'
'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
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 documentation object 'plot':
  ‘plot.discretization’

S3 methods shown with full name in documentation object 'predict':
  ‘predict.discretization’ ‘predict.reject_infered’

S3 methods shown with full name in documentation object 'summary':
  ‘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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'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.
'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
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'rgdal', 'rgeos'
Packages suggested but not available for checking: 'maptools', 'rgdal'
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
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: 'spgrass6', 'rgdal'
'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.
'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.
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ctsemOMX’

See section ‘The DESCRIPTION file’ 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.
'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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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.
'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
'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
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'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: ‘uchardet’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
'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
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
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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'ggseqlogo', 'qlcMatrix'
Unknown package ‘ggseqlogo’ in Rd xrefs
'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.
Found the following files/directories:
  ‘ExportFigtree1.tre’
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
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Packages suggested but not available for checking: 'Rcgmin', 'Rvmmin'
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]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rgdal', 'rgeos'
Specified C++11: please drop specification unless essential
'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:
  ‘fg_step_tab_pp’
Package suggested but not available for checking: ‘INLA’
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
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
'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
Specified C++11: please drop specification unless essential
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.
Package suggested but not available for checking: ‘texPreview’
Unknown package ‘texPreview’ 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
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’
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
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rgdal’
'LazyData' is specified without a 'data' directory
Unknown package ‘InformationValue’ in Rd xrefs
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
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: \$
'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
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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/smog.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
'LazyData' is specified without a 'data' directory
'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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Found the following files/directories:
  ‘my_new_social_media_plot.png’
'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
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘.R_Test’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) llwrPTF.Rd:7: 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:
  ‘.solveEnv’
S3 methods shown with full name in documentation object 'plot.predictions':
  ‘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: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'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: ‘NLMR’
Package suggested but not available for checking: ‘NLMR’
'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
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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/SparseFactorAnalysis.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
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
Package suggested but not available for checking: ‘spDataLarge’
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
checkRd: (-1) image.plot.Rd:78: 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
Found the following files/directories:
  ‘.neig’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
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
'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
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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
'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
'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.
'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.
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’:
  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: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Running examples in ‘statGraph-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘imputeMissings’
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myNewStrat.R’
Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgeos’
Specified C++11: please drop specification unless essential
Malformed Title field: should not end in a period.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
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: \&
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S3 methods shown with full name in documentation object 'size.penalize':
  ‘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.
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Unknown package ‘extraTrees’ in Rd xrefs
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surfaceSimulate : phytransform: no visible global function definition
  for ‘rescale’
Undefined global functions or variables:
  rescale
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
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Unknown package ‘survJamda’ in Rd xrefs
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘swephRdata’
Problems with news in ‘NEWS.md’:
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    Additional functions and data sets
    Amendments to functions
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Problems with news in ‘NEWS.md’:
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Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
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Found the following files/directories:
  ‘test.csv’
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checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
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S3 methods shown with full name in documentation object 'designMatrices':
  ‘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.
'LazyData' is specified without a 'data' directory
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Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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Packages which this enhances but not available for checking:
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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.
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
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    Minor changes:
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checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
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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
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'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
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
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Package suggested but not available for checking: ‘corpus.JSS.papers’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
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Package suggested but not available for checking: ‘toscaData’
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No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘moveVis’
Unknown package ‘moveVis’ in Rd xrefs
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
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Package which this enhances but not available for checking: ‘fwelnet’
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  'Eunomia', 'CohortGenerator', 'CirceR', 'Capr'
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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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.
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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’
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checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
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S3 methods shown with full name in documentation object 'tsibble-vctrs':
  ‘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.
'LazyData' is specified without a 'data' directory
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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
Problems with news in ‘NEWS.md’:
No news entries found.
'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
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Package which this enhances but not available for checking: ‘sl3’
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Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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'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.
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'LazyData' is specified without a 'data' directory
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Running examples in ‘uniswappeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘USA.state.boundaries.data’
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No news entries found.
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Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
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Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'syntab':
  ‘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.
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'LazyData' is specified without a 'data' directory
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
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Missing link or links in documentation object 'profilevglm.Rd':
  ‘[stats]{plot.profile}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
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    vortexRdata pre-1.0.3
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'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.
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
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
'LazyData' is specified without a 'data' directory
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
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'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
S3 methods shown with full name in documentation object 'QIC.gee':
  ‘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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
'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
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
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'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.
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
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
Found the following files/directories:
  ‘xgb.txt’
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
'LazyData' is specified without a 'data' directory
'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: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
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
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.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'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
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
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘acceldata2.RData’
'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
Problems with news in ‘NEWS.md’:
No news entries found.
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 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
Specified C++11: please drop specification unless essential
Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                 old_size new_size compress
  estrogen.RData    339Kb    241Kb       xz
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
'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
'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:
  ‘table_AeRobiology’
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 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
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
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
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
'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.
'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
'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
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
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: \~
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
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
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
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
Found the following calls to attach():
File ‘apollo/R/apollo_attach.R’:
  attach(as.list(apollo_beta), warn.conflicts = FALSE)
  attach(database, warn.conflicts = FALSE)
  attach(draws, warn.conflicts = FALSE)
  attach(randcoeff, warn.conflicts = FALSE)
  attach(lcpars, warn.conflicts = FALSE)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
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’
'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
'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.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'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
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
'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
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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
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
'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’
'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
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
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rgdal’
'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
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
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: \$
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bayesdfa.Rcheck/00install.out’ for details.
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: ‘INLA’
GNU make is a SystemRequirements.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bayesGAM.Rcheck/00install.out’ for details.
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
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.
'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.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
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.
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 documentation object 'export.bce':
  ‘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
'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
Found the following files/directories:
  ‘dump.txt’
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:
  ‘beast_plot_toy.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bellreg.Rcheck/00install.out’ for details.
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
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
'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
Package suggested but not available for checking: ‘lavaan.survey’
Unknown package ‘lavaan.survey’ in Rd xrefs
Package suggested but not available for checking: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
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
Found the following files/directories:
  ‘outputs’
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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/BINtools.Rcheck/00install.out’ for details.
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 documentation object 'select.cfs':
  ‘select.cfs’

S3 methods shown with full name in documentation object 'select.fast.filter':
  ‘select.fast.filter’

S3 methods shown with full name in documentation object 'select.forward.Corr':
  ‘select.forward.Corr’

S3 methods shown with full name in documentation object 'select.forward.wrapper':
  ‘select.forward.wrapper’

S3 methods shown with full name in documentation object 'select.inf.chi2':
  ‘select.inf.chi2’

S3 methods shown with full name in documentation object 'select.inf.gain':
  ‘select.inf.gain’

S3 methods shown with full name in documentation object 'select.inf.symm':
  ‘select.inf.symm’

S3 methods shown with full name in documentation object 'select.process':
  ‘select.process’

S3 methods shown with full name in documentation object 'select.relief':
  ‘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’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: 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
Package suggested but not available for checking: ‘cmdstanr’
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
'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.
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
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
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
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'
'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.
S3 methods shown with full name in documentation object 'subset.int':
  ‘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
Package required but not available: ‘trialr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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'.
'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
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
'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) kink_estimator.Rd:60: 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
'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: \& \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'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: ‘rgdal’
Found the following files/directories:
  ‘MDA231_tree.pdf’
'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
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
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
'LazyData' is specified without a 'data' directory
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
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: \&
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/cbq.Rcheck/00install.out’ for details.
Found the following significant warnings:
  RPP.cpp:23:17: 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]
  RPP.cpp:24:17: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/cccp.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
'LazyData' is specified without a 'data' directory
'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
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
'LazyData' is specified without a 'data' directory
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
'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’:
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
'LazyData' is specified without a 'data' directory
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 documentation object 'select.cglasso':
  ‘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
S3 methods shown with full name in documentation object 'internals':
  ‘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
'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’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
'LazyData' is specified without a 'data' directory
'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.
'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
'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: ‘userfriendlyscience’
'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
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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘clusterhap_reports’
Specified C++11: please drop specification unless essential
'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
'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.
Package suggested but not available for checking: ‘PopGenome’
Package suggested but not available for checking: ‘disttree’
'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’
Package which this enhances but not available for checking: ‘rkward’
Package suggested but not available for checking: ‘userfriendlyscience’
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Package suggested but not available for checking: ‘bvpSolve’
'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
'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
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
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
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’
'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) 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
'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:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/conStruct.Rcheck/00install.out’ for details.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
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
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
Package required but not available: ‘ctsem’

See section ‘The DESCRIPTION file’ 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
Found the following files/directories:
  ‘covfefe_inauguration.txt’
'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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘BEST’
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
'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
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
'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
Package suggested but not available for checking: ‘rgeos’
'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
S3 methods shown with full name in documentation object 'internals':
  ‘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.
Package required but not available: ‘ctsem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ctsem.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
Found the following files/directories:
  ‘Hello.csv’
'LazyData' is specified without a 'data' directory
'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
'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: \_ \_ \_
Package which this enhances but not available for checking: ‘RGtk2’
'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:
  'gurobi', 'rcbc'
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
'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.
'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:
  ‘my new data set.rds’
'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
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 documentation object 'dbglm-inl':
  ‘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
Problems with news in ‘NEWS.md’:
No news entries found.
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DCPO.Rcheck/00install.out’ for details.
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
'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
'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
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.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'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
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
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.
'LazyData' is specified without a 'data' directory
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’
Package which this enhances but not available for checking: ‘gurobi’
'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
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
'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
Error(s) in re-building vignettes:
  ...
--- re-building ‘dhis2r.Rmd’ using rmarkdown

Quitting from lines 35-37 [unnamed-chunk-3] (dhis2r.Rmd)
Error: processing vignette 'dhis2r.Rmd' failed with diagnostics:
Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached: [play.dhis2.org] Failed to connect to play.dhis2.org port 443 after 10002 ms: Timeout was reached
--- failed re-building ‘dhis2r.Rmd’

SUMMARY: processing the following file failed:
  ‘dhis2r.Rmd’

Error: Vignette re-building failed.
Execution halted
'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
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
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’
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
'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: \&
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.
'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: ‘BOLTSSIRR’
Package suggested but not available for checking: ‘rgdal’
'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:
    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: \&
'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
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
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 documentation object 'add.joint.mean.many':
  ‘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.
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
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
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
Found the following calls to attach():
File ‘doSNOW/R/doSNOW.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'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
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘tmbstan’
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [4s/5s]
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(duke)
  > 
  > test_check("duke")
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 25 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-scale_duke_color_discrete.R:42:3'): appropriate fill for factors over 8-levels ──
  `ggplot2::ggplot_build(p4)` did not throw the expected warning.
  ── Failure ('test-scale_duke_fill_discrete.R:47:3'): appropriate fill for factors over 8-levels ──
  `ggplot2::ggplot_build(p4)` did not throw the expected warning.
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 25 ]
  Error: Test failures
  Execution halted
'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: ‘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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
'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
'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’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/EcoEnsemble.Rcheck/00install.out’ for details.
'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
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
Package suggested but not available for checking: ‘lavaan.survey’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/eggCounts.Rcheck/00install.out’ for details.
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
'LazyData' is specified without a 'data' directory
'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
GNU make is a SystemRequirements.
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 ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/emdist.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 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
Specified C++11: please drop specification unless essential
checkRd: (-1) encode.character.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
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RStoolbox’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘epidict’
GNU make is a SystemRequirements.
S3 methods shown with full name in documentation object 'addDrug.Lexis':
  ‘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’
'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
S3 methods shown with full name in documentation object 'summary.error_interval':
  ‘summary.error_interval’

S3 methods shown with full name in documentation object 'summary.measure':
  ‘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
Package required but not available: ‘trialr’

See section ‘The DESCRIPTION file’ 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
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 documentation object 'ETAS-internal':
  ‘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.
'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
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’
'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
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
Unknown package ‘iptools’ in Rd xrefs
Package suggested but not available for checking: ‘INLA’
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: ‘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: \&
'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
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
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: \#
'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
'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
'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
'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
'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
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
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: \&
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: \&
.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
'LazyData' is specified without a 'data' directory
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.
'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
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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/fdaPDE.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
'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
'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
Package suggested but not available for checking: ‘MicrobeDS’
'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
'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
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: \&
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 ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/finity.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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:
  'nCDunnett', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
'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.
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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘FPCEnv’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'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
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘flux.CH4.txt’
'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
'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.
'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
'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:
    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
'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
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
'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: 'dggrids', 'INLA'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
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
'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.
S3 methods shown with full name in documentation object 'plot.funData':
  ‘plot.funData’

S3 methods shown with full name in documentation object 'plot.irregFunData':
  ‘plot.irregFunData’

S3 methods shown with full name in documentation object 'plot.multiFunData':
  ‘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
'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’
'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) 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: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
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: \&
Package suggested but not available for checking: ‘gputools’
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
Found the following calls to attach():
File ‘g.data/R/g.data.attach.R’:
  attach(NULL, pos, basename(dir))
See section ‘Good practice’ in ‘?attach’.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gdxrrw’
'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 required but not available: ‘ggseqlogo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘genderdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘maptools’
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’:
No news entries found.
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++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
'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
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/geostan.Rcheck/00install.out’ for details.
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.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
Package suggested but not available for checking: ‘rgdal’
'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: ‘argon2’
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
'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
Found the following assignments to the global environment:
File ‘ggExtra/R/ggMarginalGadget.R’:
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
'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
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.
'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: ‘lixoftConnectors’
'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:
    * Changes all data options to .data to decrease possibility of column naming overlap
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaBMA’
'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
'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
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
'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: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mlr3proba’
'LazyData' is specified without a 'data' directory
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.
'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: \&
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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
'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
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
Package suggested but not available for checking: ‘ganalytics’
'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.
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’
'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: \_
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
Package suggested but not available for checking: ‘monocle’
Package unavailable to check Rd xrefs: ‘monocle’
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/greencrab.toolkit.Rcheck/00install.out’ for details.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'groc.fit':
  ‘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
Found the following significant warnings:
  hmg.cpp:202:25: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  hmg.cpp:203:40: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  hmg.cpp:453:33: 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 ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/grove.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
Found the following significant warnings:
  gpdpmix_moves.cpp:1014:48: warning: ‘void arma::Col<eT>::insert_rows(arma::uword, arma::uword, bool) [with eT = unsigned int; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
  gpdpmix_moves.cpp:1015:36: warning: ‘void arma::Col<eT>::insert_rows(arma::uword, arma::uword, bool) [with eT = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
  sppmcarmix_moves.cpp:134:22: warning: ‘void arma::Col<eT>::insert_rows(arma::uword, arma::uword, bool) [with eT = unsigned int; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
  sppmcarmix_moves.cpp:135:22: warning: ‘void arma::Col<eT>::insert_rows(arma::uword, arma::uword, bool) [with eT = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/growfunctions.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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’
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’
'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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RRprof.out’
'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
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
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
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: \&
Found the following significant warnings:
  HARDataCreationC.cpp:43:31: 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 ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/HARModel.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hbamr.Rcheck/00install.out’ for details.
Specified C++14: 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
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
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
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘hexfont-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: unifont
> ### Title: Load Unifont font
> ### Aliases: unifont
> 
> ### ** Examples
> 
> # Much faster to load only the subset of GNU Unifont one needs
> # Mandarin Chinese
> if (require("bittermelon")) {
+   s <- "\uff32\u5f88\u68d2\uff01"
+   font <- unifont(ucp = str2ucp(s))
+   bm <- as_bm_bitmap(s, font = font)
+   print(bm, px = px_ascii)
+ }
Loading required package: bittermelon

Attaching package: ‘bittermelon’

The following object is masked from ‘package:base’:

    which

Error in vector("list", n_orig - n_combining) : vector size cannot be NA
Calls: as_bm_bitmap -> as_bm_bitmap.character -> lapply -> FUN
Execution halted
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'defunct':
  ‘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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘INLA’
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
Package required but not available: ‘trialr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
html_describe_con: multiple local function definitions for ‘g’ with
  different formal arguments
'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: \&
Package required but not available: ‘tmbstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
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) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
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’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgeos’
checkRd: (-1) palettes.Rd:25: 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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SparkR’
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
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: \$
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
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object 'internals':
  ‘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
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
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
'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
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’
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaBMA’
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
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
'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
Specified C++11: please drop specification unless essential
'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
'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
File ‘iotools/libs/iotools.so’:
  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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
S3 methods shown with full name in documentation object 'print.Item':
  ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
GNU make is a SystemRequirements.
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’
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
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
GNU make is a SystemRequirements.
'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'.
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.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Package which this enhances but not available for checking: ‘remMap’
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'LazyData' is specified without a 'data' directory
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'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)
Dependence on R version ‘4.1.2’ not with patchlevel 0
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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S3 methods shown with full name in documentation object 'bw.abram.temp':
  ‘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.
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
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Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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S3 methods shown with full name in documentation object 'unlist.constr':
  ‘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.
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘maptools’
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Found the following files/directories:
  ‘Killed after ’
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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
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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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’
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Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
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checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
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checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
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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
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checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
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Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
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Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
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  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
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘maptools’
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
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S3 methods shown with full name in documentation object 'BIC.threshold':
  ‘BIC.threshold’

S3 methods shown with full name in documentation object 'BIC.threshold.ggm':
  ‘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.
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Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/LMMELSM.Rcheck/00install.out’ for details.
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Found the following files/directories:
  ‘tTestTable.rda’
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    Author
    Maintainer
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Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
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Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
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checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
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Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/MADPop.Rcheck/00install.out’ for details.
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Running examples in ‘mapping-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loadCoordEU
> ### Title: Get European coordinates
> ### Aliases: loadCoordEU
> 
> ### ** Examples
> 
> 
> EU_coords = loadCoordEU(unit = "nuts0")
> str(EU_coords)
Classes ‘sf’, ‘EU’ and 'data.frame':	37 obs. of  8 variables:
 $ id          : chr  "FR" "HR" "HU" "AL" ...
 $ iso2        : chr  "FR" "HR" "HU" "AL" ...
 $ name        : chr  "France" "Hrvatska" "Magyarország" "Shqipëria" ...
 $ nuts0_id    : chr  "FR" "HR" "HU" "AL" ...
 $ country     : chr  "France" "Croatia" "Hungary" "Albania" ...
 $ iso3        : chr  "FRA" "HRV" "HUN" "ALB" ...
 $ country_code: int  250 191 348 8 40 56 100 756 196 203 ...
 $ geometry    :sfc_MULTIPOLYGON of length 37; first list element: List of 6
  ..$ :List of 1
  .. ..$ : num [1:21, 1:2] 8.59 8.67 8.85 8.8 8.83 ...
  ..$ :List of 1
  .. ..$ : num [1:312, 1:2] 2.55 2.3 2.09 1.61 1.57 ...
  ..$ :List of 1
  .. ..$ : num [1:6, 1:2] -1.46 -1.43 -1.41 -1.41 -1.44 ...
  ..$ :List of 1
  .. ..$ : num [1:7, 1:2] -1.46 -1.46 -1.51 -1.57 -1.54 ...
  ..$ :List of 1
  .. ..$ : num [1:6, 1:2] -2.33 -2.33 -2.27 -2.23 -2.24 ...
  ..$ :List of 1
  .. ..$ : num [1:6, 1:2] -3.26 -3.22 -3.11 -3.16 -3.25 ...
  ..- attr(*, "class")= chr [1:3] "XY" "MULTIPOLYGON" "sfg"
 - attr(*, "sf_column")= chr "geometry"
 - attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA NA NA NA NA NA NA
  ..- attr(*, "names")= chr [1:7] "id" "iso2" "name" "nuts0_id" ...
 - attr(*, "unit")= chr "nuts0"
 - attr(*, "colID")= chr "nuts0"
> 
> coords_eu_it_de <- loadCoordEU(unit = "nuts0", unit_subset = c("italy", "germany"))
Error in `[.data.frame`(x, i, j, drop = drop) : 
  undefined columns selected
Calls: loadCoordEU -> tolower -> [ -> [.sf -> [ -> [.data.frame
Execution halted
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GNU make is a SystemRequirements.
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Found the following files/directories:
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Found the following files/directories:
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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
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checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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'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: ‘MethylCapSig’
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Package suggested but not available for checking: ‘cmdstanr’
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
'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
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘INLA’
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Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/metaBMA.Rcheck/00install.out’ for details.
'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’:
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'Rcgmin', 'Rvmmin'
Unknown packages ‘Rcgmin’, ‘Rvmmin’ in Rd xrefs
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'LazyData' is specified without a 'data' directory
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'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
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
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Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Package suggested but not available for checking: ‘INLA’
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'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++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
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.
S3 methods shown with full name in documentation object 'complete.miceadds':
  ‘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
'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: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘midfielddata’
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘gurobi’
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
'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 ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/minimaxdesign.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
':::' call which should be '::': ‘parallel:::detectCores’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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
checkRd: (-1) AKMCS.Rd:215: Escaped LaTeX specials: \&
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checkRd: (-1) IRW.Rd:144: Escaped LaTeX specials: \&
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checkRd: (-1) oscillator_d6.Rd:14: Escaped LaTeX specials: \&
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checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
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  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
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checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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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
'LazyData' is specified without a 'data' directory
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'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
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'LazyData' is specified without a 'data' directory
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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'
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checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
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checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rgdal', 'rgeos'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  main.cpp:41:34: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  recursion.cpp:645:13: 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 ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/MRS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
'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
Found the following files/directories:
  ‘test.txt’
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Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
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checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
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'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
S3 methods shown with full name in documentation object 'pca.plot.wrap':
  ‘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: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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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
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: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
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
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
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checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'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
Package suggested but not available for checking: ‘re2r’
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
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
Package suggested but not available for checking: ‘gurobi’
Packages suggested but not available for checking:
  'rgeos', 'rgdal', 'maptools'
'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
'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.
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
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
':::' 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: \_
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checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
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checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
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'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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/networkscaleup.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
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
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
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Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
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'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
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Packages suggested but not available for checking: 'Rvmmin', 'Rcgmin'
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checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘mail’
'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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'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
'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
Specified C++11: please drop specification unless essential
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
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'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
Problems with news in ‘NEWS.md’:
No news entries found.
'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
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                   old_size new_size compress
  numerical_experiments_data.RData    1.3Mb    1.2Mb       xz
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
'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
'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’
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'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
Package suggested but not available for checking: ‘rgdal’
'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.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'unary_ops':
  ‘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.
'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: ‘openNLPmodels.en’
Packages suggested but not available for checking: 'maptools', 'rgeos'
Problems with news in ‘NEWS.md’:
No news entries found.
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Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
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Package suggested but not available for checking: ‘rrelaxiv’
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
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'LazyData' is specified without a 'data' directory
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Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
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checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
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Package which this enhances but not available for checking: ‘CorShrink’
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S3 methods shown with full name in documentation object 'pamr-internal':
  ‘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.
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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’
S3 methods shown with full name in documentation object 'vec_cast.partial_time':
  ‘vec_cast.partial_time’

S3 methods shown with full name in documentation object 'vec_cast.timespan':
  ‘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.
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checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
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Running ‘testthat.R’ [60s/79s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(patientProfilesVis)
  > 
  > test_check("patientProfilesVis")
  [ FAIL 2 | WARN 2 | SKIP 20 | PASS 365 ]
  
  == Skipped tests (20) ==================================================================================================================================================================================
  * On CRAN (20): 'test_createSubjectProfileReport.R:46:2', 'test_createSubjectProfileReport.R:82:2', 'test_createSubjectProfileReport.R:124:2', 'test_createSubjectProfileReport.R:154:2',
    'test_createSubjectProfileReport.R:197:2', 'test_createSubjectProfileReport.R:252:2', 'test_createSubjectProfileReport.R:316:2', 'test_createSubjectProfileReport.R:381:2',
    'test_createSubjectProfileReport.R:420:2', 'test_createSubjectProfileReport.R:475:2', 'test_createSubjectProfileReport.R:531:2', 'test_createSubjectProfileReport.R:570:2',
    'test_createSubjectProfileReport.R:622:2', 'test_createSubjectProfileReport.R:671:2', 'test_createSubjectProfileReport.R:723:2', 'test_createSubjectProfileReport.R:775:2',
    'test_createSubjectProfileReport.R:820:2', 'test_createSubjectProfileReport.R:878:2', 'test_createSubjectProfileReport.R:908:2', 'test_createSubjectProfileReport.R:939:2'
  
  == Failed tests ========================================================================================================================================================================================
  -- Failure ('test_timeTransformations.R:6:2'): A hyperbolic arc-sin transformation is correctly extracted --
  `timeTrans` inherits from `'transform'` not `'character'`.
  -- Failure ('test_timeTransformations.R:19:2'): A hyperbolic arc-sin transformation handling negative values is correctly extracted --
  `timeTrans` inherits from `'transform'` not `'character'`.
  
  [ FAIL 2 | WARN 2 | SKIP 20 | PASS 365 ]
  Error: Test failures
  Execution halted
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GNU make is a SystemRequirements.
S3 methods shown with full name in documentation object 'ped':
  ‘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.
'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.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/pcFactorStan.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
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No news entries found.
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Package suggested but not available for checking: ‘PythonInR’
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
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S3 methods shown with full name in documentation object 'format.relation':
  ‘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’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/pema.Rcheck/00install.out’ for details.
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
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Unknown packages ‘maptools’, ‘rgdal’ in Rd xrefs
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  ‘animation.gif’
'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
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  ‘test.pdf’
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S3 methods shown with full name in documentation object 'qr.solve_exact':
  ‘qr.solve_exact’

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.
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'LazyData' is specified without a 'data' directory
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No news entries found.
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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No news entries found.
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'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
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Specified C++11: please drop specification unless essential
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'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
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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No news entries found.
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'LazyData' is specified without a 'data' directory
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Package unavailable to check Rd xrefs: ‘INLA’
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checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
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checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
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  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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Unknown package ‘advclust’ in Rd xrefs
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Unknown package ‘ffbase’ in Rd xrefs
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
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Packages suggested but not available for checking: 'gurobi', '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
'LazyData' is specified without a 'data' directory
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'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 documentation object 'internals':
  ‘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
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No news entries found.
'LazyData' is specified without a 'data' directory
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S3 methods shown with full name in documentation object 'internals':
  ‘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.
S3 methods shown with full name in documentation object 'internals':
  ‘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
Specified C++11: please drop specification unless essential
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  bounded_reg.cpp:33:25: warning: ‘std::ostream& arma::arma_cerr_stream(std::ostream*) [with T = char; std::ostream = std::basic_ostream<char>]’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  elastic_net.cpp:35:25: warning: ‘std::ostream& arma::arma_cerr_stream(std::ostream*) [with T = char; std::ostream = std::basic_ostream<char>]’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/quadrupen.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
'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.
Package suggested but not available for checking: ‘fastshp’
'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
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
'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.
'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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'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
'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: \_
'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.
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
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 documentation object 'export.default':
  ‘export.default’

S3 methods shown with full name in documentation object 'export.listpoly':
  ‘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.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rcbayes.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rrelaxiv’
'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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘data.csv’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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
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.
Package suggested but not available for checking: ‘conics’
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
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
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
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.
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.
'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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘devAll’
'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
Package suggested but not available for checking: ‘DIDmultiplegt’
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'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
'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
'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
'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
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
'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
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
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
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
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: \$
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.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PackageCites.bib’
'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
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: \_ \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) rec.Rd:23: 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
'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
'LazyData' is specified without a 'data' directory
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’
'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:
  ‘mydata.rda’ ‘thedata.rda’
'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:
  '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.
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
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
'LazyData' is specified without a 'data' directory
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)
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 ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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
'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
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
'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
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rmBayes.Rcheck/00install.out’ for details.
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’:
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
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
'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
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rnaturalearthhires’
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: 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: ‘rgdal’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘metaBMA’
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
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) 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
'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
GNU make is a SystemRequirements.
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
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
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
'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’
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 ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rphylopars.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
'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
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'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
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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’

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.
'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: ‘gurobi’
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: ‘INLA’
Specified C++11: please drop specification unless essential
Running ‘tinytest.R’ [0s/1s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > tmp_user_dir <- tempdir()
  > Sys.setenv(RSPM_USER_DIR=tmp_user_dir)
  > 
  > if (requireNamespace("tinytest", quietly=TRUE)) {
  +   home <- identical(Sys.getenv("CI"), "true")
  +   tinytest::test_package("rspm", at_home=home)
  + }
   You are using 'tinytest::' to express test expectations.
   The results from these tests are not collected. Found the following occurrences:
   > test_integration.R#002: tinytest::expect_match 
   Remove the 'tinytest::' prefix to register the test results.FALSE
  
  test_integration.R............    0 tests    
  test_integration.R............    1 tests [0;32mOK[0m 
  test_integration.R............    2 tests [0;32mOK[0m 
  test_integration.R............    2 tests [0;32mOK[0m 
  test_integration.R............    3 tests [0;32mOK[0m Error: please, install the following required utilities: apt-file
  Execution halted
'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.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RTMB.Rcheck/00install.out’ for details.
'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.
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.
Found the following files/directories:
  ‘Tsttwalk.dat’
'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
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object 'printHTML.trackInfo':
  ‘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’
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
S3 methods shown with full name in documentation object 'matmult':
  ‘%*%.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’
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
Malformed Title field: should not end in a period.
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
matrixOps:
  function(x, y)
matrixOps.S7_object:
  function(e1, e2)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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
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
'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
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: \#
Package suggested but not available for checking: ‘tmbstan’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘networkTomography’
'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: ‘FitARMA’
Specified C++11: please drop specification unless essential
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
'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
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.
Package suggested but not available for checking: ‘rgdal’
'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
Specified C++11: please drop specification unless essential
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
Packages which this enhances but not available for checking:
  'gurobi', 'pogs'
'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
checkRd: (-1) x.oreo.Rd:48: 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
Packages suggested but not available for checking:
  'sceasy', 'SeuratDisk', 'SeuratWrappers'
'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
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 documentation object 'plot':
  ‘plot.discretization’

S3 methods shown with full name in documentation object 'predict':
  ‘predict.discretization’ ‘predict.reject_infered’

S3 methods shown with full name in documentation object 'summary':
  ‘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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'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.
'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
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'rgdal', 'rgeos'
Packages suggested but not available for checking: 'maptools', 'rgdal'
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
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: 'spgrass6', 'rgdal'
'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.
'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.
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ctsemOMX’

See section ‘The DESCRIPTION file’ 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.
'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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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.
'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
'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
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'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: ‘uchardet’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
'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
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
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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'ggseqlogo', 'qlcMatrix'
Unknown package ‘ggseqlogo’ in Rd xrefs
'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.
Found the following files/directories:
  ‘ExportFigtree1.tre’
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
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Packages suggested but not available for checking: 'Rcgmin', 'Rvmmin'
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]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rgdal', 'rgeos'
Specified C++11: please drop specification unless essential
'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:
  ‘fg_step_tab_pp’
Package suggested but not available for checking: ‘INLA’
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
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
'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
Specified C++11: please drop specification unless essential
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.
Package suggested but not available for checking: ‘texPreview’
Unknown package ‘texPreview’ 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
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’
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
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rgdal’
'LazyData' is specified without a 'data' directory
Unknown package ‘InformationValue’ in Rd xrefs
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
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: \$
'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
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 ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/smog.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
'LazyData' is specified without a 'data' directory
'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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Found the following files/directories:
  ‘my_new_social_media_plot.png’
'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
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘.R_Test’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) llwrPTF.Rd:7: 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:
  ‘.solveEnv’
S3 methods shown with full name in documentation object 'plot.predictions':
  ‘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: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
Package suggested but not available for checking: ‘NLMR’
'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
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 ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SparseFactorAnalysis.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
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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
Package suggested but not available for checking: ‘spDataLarge’
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
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.neig’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
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
'LazyData' is specified without a 'data' directory
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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
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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/spsurv.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
'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.
'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.
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’:
  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: \&
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Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
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'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’
There are updates for the following statnet packages on CRAN:
               Installed ReposVer Built  
networkDynamic "0.11.3"  "0.11.4" "4.3.2"
Restart R and use "statnet::update_statnet()" to get the updates.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaBMA’
Package suggested but not available for checking: ‘imputeMissings’
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myNewStrat.R’
Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgeos’
Specified C++11: please drop specification unless essential
Malformed Title field: should not end in a period.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
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: \&
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'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'size.penalize':
  ‘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’
'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’
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’
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Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [68s/78s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Superpower)
  > 
  > 
  > test_check("Superpower")
  [ FAIL 2 | WARN 18 | SKIP 13 | PASS 397 ]
  
  ══ Skipped tests (13) ══════════════════════════════════════════════════════════
  • On CRAN (13): 'test-ANOVA_compromise.R:45:3', 'test-anova_exact.R:152:3',
    'test-anova_power.R:93:3', 'test-anova_power.R:119:3',
    'test-anova_power.R:160:3', 'test-anova_power.R:193:3',
    'test-anova_power.R:232:3', 'test-emmeans_power.R:44:3',
    'test-justifieR.R:29:3', 'test-plot_power.R:43:3', 'test-plot_power.R:102:3',
    'test-plot_power.R:148:3', 'test-plot_power.R:169:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_sim_cor.R:37:3'): simulated correlations fit expected values ──
  `res4` not equal to 0.
  1/1 mismatches
  [1] 0.00305 - 0 == 0.00305
  ── Failure ('test_sim_cor.R:38:3'): simulated correlations fit expected values ──
  `res5` not equal to 0.
  1/1 mismatches
  [1] 0.0034 - 0 == 0.0034
  
  [ FAIL 2 | WARN 18 | SKIP 13 | PASS 397 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
surfaceSimulate : phytransform: no visible global function definition
  for ‘rescale’
Undefined global functions or variables:
  rescale
'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’
GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘gurobi’
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Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
Specified C++11: please drop specification unless essential
Unknown package ‘survJamda’ in Rd xrefs
'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
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
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'
'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
Found the following files/directories:
  ‘test.csv’
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
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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
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
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'designMatrices':
  ‘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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: 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
Package suggested but not available for checking: ‘tashudata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'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
Malformed Description field: should contain one or more complete sentences.
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
Packages suggested but not available for checking: 'maptools', 'R2wd'
checkRd: (-1) R2txt.Rd:164: Escaped LaTeX specials: \#
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Package suggested but not available for checking: ‘rgdal’
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
'LazyData' is specified without a 'data' directory
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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.
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Unknown package ‘textreadr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'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
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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'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
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
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) compare.Rd:46: 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
Specified C++14: please drop specification unless essential
'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
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/tmbstan.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'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
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘corpus.JSS.papers’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
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Package suggested but not available for checking: ‘toscaData’
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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: ‘moveVis’
Unknown package ‘moveVis’ in Rd xrefs
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
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Package suggested but not available for checking: ‘taxidata’
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Package which this enhances but not available for checking: ‘fwelnet’
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Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR'
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
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Problems with news in ‘NEWS.md’:
No news entries found.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/trialr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
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'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
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.
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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’
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checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
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S3 methods shown with full name in documentation object 'tsibble-vctrs':
  ‘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.
'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
'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
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Package which this enhances but not available for checking: ‘sl3’
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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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.
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Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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Running examples in ‘uniswappeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘USA.state.boundaries.data’
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checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
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Malformed Title field: should not end in a period.
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Problems with news in ‘NEWS.md’:
No news entries found.
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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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
'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
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No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'syntab':
  ‘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.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
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checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
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checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Missing link or links in documentation object 'profilevglm.Rd':
  ‘[stats]{plot.profile}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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No news entries found.
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
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
GNU make is a SystemRequirements.
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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
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checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘prepr’
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Packages suggested but not available for checking: 'iptools', 'rgeolocate'
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'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
S3 methods shown with full name in documentation object 'QIC.gee':
  ‘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
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Package suggested but not available for checking: ‘pageviews’
Package suggested but not available for checking: ‘pageviews’
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'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
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.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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'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:
  ‘xgb.txt’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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No news entries found.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) read.npc.vpc.results.Rd:16: Escaped LaTeX specials: \_
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checkRd: (-1) read.npc.vpc.results.Rd:22: Escaped LaTeX specials: \_
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Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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Packages suggested but not available for checking: 'RNRCS', 'metScanR'
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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installed size is 31.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.4Mb
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    libs   2.5Mb
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installed size is 88.8Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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    libs   4.7Mb
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installed size is 11.4Mb
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    libs   8.0Mb
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installed size is 13.4Mb
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installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
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installed size is  7.8Mb
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    doc    1.7Mb
    libs   5.8Mb
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'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R  14.1Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
Packages suggested but not available for checking: 'DeconRNASeq', 'WGCNA'
installed size is  7.6Mb
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checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
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installed size is  9.2Mb
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    R      2.0Mb
    data   3.0Mb
    libs   2.6Mb
installed size is  5.8Mb
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    data    1.3Mb
    files   1.7Mb
installed size is  5.3Mb
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    R     2.0Mb
    doc   2.7Mb
installed size is 10.2Mb
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    data  10.1Mb
installed size is  5.1Mb
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    doc   4.7Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
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    doc   3.7Mb
Packages suggested but not available for checking: 'HiTC', 'snpStats'
installed size is  5.5Mb
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    libs   2.5Mb
Package unavailable to check Rd xrefs: ‘snpStats’
installed size is  6.4Mb
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'library' or 'require' call to ‘network’ in package code.
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Bad \usage lines found in documentation object 'annmatrix':
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Functions with \usage entries need to have the appropriate \alias
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The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Unknown package ‘snpar’ in Rd xrefs
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GNU make is a SystemRequirements.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Error(s) in re-building vignettes:
--- re-building ‘article.Rnw’ using Sweave
Setting levels: control = No, case = Yes
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-7
Setting levels: control = No, case = Yes
Setting levels: control = No, case = Yes
Loading required package: Biostrings
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,
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    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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Error: processing vignette 'article.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'article.Rnw'

SUMMARY: processing the following file failed:
  'article.Rnw'

Error: Vignette re-building failed.
Execution halted
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Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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S3 methods shown with full name in documentation object 'export.bce':
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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.
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Running ‘testthat.R’ [23s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test-formattedCombiner.R:61:1'): (code run outside of `test_that()`) ──
  Error in `xml2::read_xml(.)`: `x` must be a single string, not a character vector.
  Backtrace:
      ▆
   1. ├─BeeBDC::formattedCombiner(...) at test-formattedCombiner.R:61:1
   2. │ └─... %>% xml2::read_xml()
   3. ├─xml2::read_xml(.)
   4. └─xml2:::read_xml.character(x = .)
   5.   └─xml2:::check_string(x)
   6.     └─xml2:::stop_input_type(...)
   7.       └─rlang::abort(message, ..., call = call, arg = arg)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 228 ]
  Error: Test failures
  Execution halted
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Malformed Title field: should not end in a period.
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checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
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Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package suggested but not available for checking: ‘rrelaxiv’
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Package suggested but not available for checking: ‘msa’
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S3 methods shown with full name in documentation object 'select.cfs':
  ‘select.cfs’

S3 methods shown with full name in documentation object 'select.fast.filter':
  ‘select.fast.filter’

S3 methods shown with full name in documentation object 'select.forward.Corr':
  ‘select.forward.Corr’

S3 methods shown with full name in documentation object 'select.forward.wrapper':
  ‘select.forward.wrapper’

S3 methods shown with full name in documentation object 'select.inf.chi2':
  ‘select.inf.chi2’

S3 methods shown with full name in documentation object 'select.inf.gain':
  ‘select.inf.gain’

S3 methods shown with full name in documentation object 'select.inf.symm':
  ‘select.inf.symm’

S3 methods shown with full name in documentation object 'select.process':
  ‘select.process’

S3 methods shown with full name in documentation object 'select.relief':
  ‘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.
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Package which this enhances but not available for checking: ‘asreml’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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S3 methods shown with full name in documentation object 'subset.int':
  ‘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.
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Unknown package ‘gvcm.cat’ in Rd xrefs
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Error(s) in re-building vignettes:
--- re-building ‘bunching_examples.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_examples.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/bunching.Rcheck/vign_test/bunching/vignettes/bunching_examples.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_examples.log for more info.
--- failed re-building ‘bunching_examples.Rmd’

--- re-building ‘bunching_theory.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_theory.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/bunching.Rcheck/vign_test/bunching/vignettes/bunching_theory.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_theory.log for more info.
--- failed re-building ‘bunching_theory.Rmd’

SUMMARY: processing the following files failed:
  ‘bunching_examples.Rmd’ ‘bunching_theory.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
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Malformed Description field: should contain one or more complete sentences.
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GNU make is a SystemRequirements.
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  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
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GNU make is a SystemRequirements.
Running examples in ‘cbsodataR-Ex.R’ failed
The error most likely occurred in:

> ### Name: cbs_get_catalogs
> ### Title: Retrieves the possible catalog values that can be used for
> ###   retrieving data
> ### Aliases: cbs_get_catalogs
> 
> ### ** Examples
> 
> catalogs <- cbs_get_catalogs()
Warning in readBin(3L, raw(0), 32768L) :
  URL 'https://opendata.cbs.nl/ODataCatalog/Tables?$format=json': Timeout of 60 seconds was reached
Warning: Failing: http://opendata.cbs.nl/ODataCatalog/Tables?$format=json
Retrying...
Warning in readBin(3L, raw(0), 32768L) :
  URL 'https://opendata.cbs.nl/ODataCatalog/Tables?$format=json': Timeout of 60 seconds was reached
Error in readBin(3L, raw(0), 32768L) : cannot read from connection
Calls: cbs_get_catalogs ... parse_and_simplify -> parseJSON -> parse_con -> readBin
Execution halted
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No news entries found.
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
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Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
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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
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Malformed Title field: should not end in a period.
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S3 methods shown with full name in documentation object 'select.cglasso':
  ‘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
installed size is  6.3Mb
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S3 methods shown with full name in documentation object 'internals':
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The \usage entries for S3 methods should use the \method markup and not
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See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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Package suggested but not available for checking: ‘pbdMPI’
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Package suggested but not available for checking: ‘darts’
Package required but not available: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking:
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Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Packages required but not available:
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
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installed size is  5.5Mb
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checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
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Problems with news in ‘NEWS.md’:
No news entries found.
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘moe430a.db’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
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Package suggested but not available for checking: ‘tobit1’
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installed size is 35.6Mb
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GNU make is a SystemRequirements.
Package required but not available: ‘GenomicInteractions’

Packages suggested but not available for checking:
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Package suggested but not available for checking: ‘PopGenome’
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Package suggested but not available for checking: ‘disttree’
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checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
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Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'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
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Unexported object imported by a ':::' call: ‘crayon:::mypaste’
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Problems with news in ‘NEWS.md’:
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Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'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
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'LazyData' is specified without a 'data' directory
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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
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  5.1Mb
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checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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'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
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installed size is  6.9Mb
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'LazyData' is specified without a 'data' directory
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installed size is  5.5Mb
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Error(s) in re-building vignettes:
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--- re-building ‘cplm.Rnw’ using Sweave
Loading required package: coda
Loading required package: Matrix
Loading required package: splines
Error: processing vignette 'cplm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cplm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cplm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Specified C++14: please drop specification unless essential
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Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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installed size is  6.3Mb
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installed size is 42.9Mb
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'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: ‘BSgenome.Scerevisiae.UCSC.sacCer3’
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Package suggested but not available for checking: ‘rhdf5’
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Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’
'LazyData' is specified without a 'data' directory
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installed size is  6.2Mb
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Package suggested but not available for checking: ‘INLA’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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installed size is  8.1Mb
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'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 documentation object 'internals':
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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 required but not available: ‘ctsem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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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 required and available but unsuitable version: ‘IRanges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
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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
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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:
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checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: ‘RGtk2’
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installed size is  5.3Mb
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Packages listed in more than one of Depends, Imports, Suggests, Enhances:
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A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
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Problems with news in ‘NEWS.md’:
No news entries found.
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Error(s) in re-building vignettes:
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--- re-building ‘CytoSimplex.Rmd’ using rmarkdown
File rotating_tetra.gif not found in resource path
Error: processing vignette 'CytoSimplex.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘CytoSimplex.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 29.3Mb
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'LazyData' is specified without a 'data' directory