Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
File ‘optpart/libs/optpart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Package suggested but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘orca/libs/orca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘transformr’
  All declared Imports should be used.
Note: found 36 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Found the following significant warnings:
  /usr/include/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [176, 183] is out of the bounds [0, 176] of object ‘b’ with type ‘arma::vec’ {aka ‘arma::Col<double>’} [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/ordinalClust.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 263 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rcplex’
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
'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++11: please drop specification unless essential
Found the following files/directories:
  ‘result.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
Namespaces in Imports field not imported from:
  ‘flexsurv’ ‘nlme’ ‘tibble’ ‘tidyverse’ ‘tm’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘optparse’
  All declared Imports should be used.
'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
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 314 marked UTF-8 strings
Package which this enhances but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘dbplyr’ ‘downloadthis’ ‘ggExtra’ ‘htmlwidgets’ ‘methods’
  ‘rmarkdown’ ‘scales’
  All declared Imports should be used.
Note: found 34 marked UTF-8 strings
File ‘pamr/libs/pamr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) pan.bd.Rd:65: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘caret’ ‘gstat’ ‘pryr’
  All declared Imports should be used.
Specified C++14: 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
Note: found 16 marked UTF-8 strings
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_linearsolver.c:28:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_matrix.c:29:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_nonlinearsolver.c:26:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_nvector.c:28:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/arkode/arkode_adapt_impl.h:125:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/arkode/arkode_impl.h:825:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/arkode/arkode.c:58:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/arkode/arkode_adapt.c:42:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/paropt.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
Found the following files/directories:
  ‘Minimal-concordance.tex’ ‘Minimal.Rnw’ ‘Minimal.pdf’
  ‘Minimal.synctex.gz’ ‘Minimal.tex’ ‘figure’
Namespace in Imports field not imported from: ‘logger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 180 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘testthat’ ‘usethis’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘clusterProfiler’ ‘purrr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
---- unloading
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
File ‘pbdSLAP/libs/pbdSLAP.so’:
  Found ‘__vsprintf_chk’, possibly from ‘vsprintf’ (C)
    Object: ‘libslap.a’

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
File ‘pbivnorm/libs/pbivnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'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.
File ‘PCA4TS/libs/PCA4TS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Note: found 11 marked UTF-8 strings
File ‘pdc/libs/pdc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘PythonInR’
'LazyData' is specified without a 'data' directory
File ‘pdist/libs/pdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
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
Found the following significant warnings:
  PeakSegJoint_interface.c:113:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/PeakSegJoint.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘crrstep’
checkRd: (-1) pec.Rd:250: Escaped LaTeX specials: \&
checkRd: (-1) pec.Rd:251: Escaped LaTeX specials: \&
checkRd: (-1) pec.Rd:256: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘georob’
Note: found 7326 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) simulate.data.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) simulate.data.Rd:28: Escaped LaTeX specials: \_ \_
Specified C++11: please drop specification unless essential
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
Specified C++11: please drop specification unless essential
File ‘PenCoxFrail/libs/PenCoxFrail.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
File ‘penMSM/libs/penMSM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘fixest’
  All declared Imports should be used.
Found the following significant warnings:
  init.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/Peptides.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 4 marked UTF-8 strings
File ‘perccal/libs/perccal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 63777 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘pgee.mixed/libs/pgee.mixed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘rJava’ ‘shinyWidgets’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ph2bye/libs/ph2bye.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘animation.gif’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.pdf’
Note: found 114 marked UTF-8 strings
Running ‘testthat.R’ [271s/312s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PHEindicatormethods)
  > 
  > test_check("PHEindicatormethods")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 452 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('testLifeExpectancy.R:315'): LE - warnings are generated when invalid arguments are used ──
  wideci_warning\[2\] does not match "some life expectancy values have a 95% confidence interval > 20 years; these values have been suppressed to NAs".
  Actual value: "Each row in `x` is expected to match at most 1 row in `y`\.\\nℹ Row 1 of `x` matches multiple rows\.\\nℹ If multiple matches are expected, set `multiple = "all"` to silence this\\n  warning\."
  Backtrace:
      ▆
   1. └─testthat::expect_match(wideci_warning[2], "some life expectancy values have a 95% confidence interval > 20 years; these values have been suppressed to NAs") at testLifeExpectancy.R:315:2
   2.   └─testthat:::expect_match_(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 452 ]
  Error: Test failures
  Execution halted
'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: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
Note: found 13 marked UTF-8 strings
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘cowplot’ ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2048 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘pirate/libs/pirate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘ggsubplot’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sanitize_latex.Rd:49: 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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BH’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘plac/libs/plac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘RStoolbox’
Note: found 150 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
Packages suggested but not available for checking:
  'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
'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
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Note: found 12992 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) PLS_beta_wvc.Rd:5: Escaped LaTeX specials: \_
checkRd: (-1) plsRbeta.Rd:104: Escaped LaTeX specials: \^
Package suggested but not available for checking: ‘plsdepot’
checkRd: (-1) PLS_glm_wvc.Rd:5: Escaped LaTeX specials: \_
checkRd: (-1) PLS_lm_wvc.Rd:5: Escaped LaTeX specials: \_
Namespace in Imports field not imported from: ‘ssh’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘base’ ‘grDevices’
  All declared Imports should be used.
Note: found 62 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘abc’ ‘doParallel’ ‘gdistance’ ‘geosphere’ ‘lhs’ ‘metRology’ ‘raster’
  ‘trend’
  All declared Imports should be used.
Note: found 7256 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘argonDash’ ‘argonR’ ‘colourpicker’ ‘ggplot2’ ‘grid’ ‘hexSticker’
  ‘png’ ‘shinyWidgets’
  All declared Imports should be used.
'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: \&
Note: found 21 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘formula.tools’ ‘ggplot2’ ‘gplots’ ‘graphics’ ‘purrr’
  ‘rstatix’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Note: found 52 marked UTF-8 strings
Package suggested but not available for checking: ‘pollimetrydata’
Specified C++11: please drop specification unless essential
File ‘polyfreqs/libs/polyfreqs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
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’
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘RClone’
Found the following significant warnings:
  init.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  omp_test.c:7:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/poppr.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
checkRd: (-1) genetic_distance.Rd:106: Escaped LaTeX specials: \~
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘psych’ ‘zoo’
  All declared Imports should be used.
File ‘population/libs/population.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tradelist-class.Rd:91: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘StanHeaders’ ‘dplyr’ ‘ggplot2’ ‘gridExtra’ ‘rstan’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'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
Namespaces in Imports field not imported from:
  ‘rpart’ ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’ ‘numDeriv’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  sum.c:358:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  prod.c:27:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/PreciseSums.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘ffbase’
Unknown package ‘ffbase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'::' or ':::' imports not declared from:
  ‘rock’ ‘ufs’
Note: found 71 marked UTF-8 strings
Note: found 42966 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 165 marked UTF-8 strings
Specified C++11: please drop specification unless essential
File ‘PRIMAL/libs/PRIMAL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  init.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zhegv.c:232:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zhegv.c:3715:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/PRIMME.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gurobi', 'Rcplex'
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) prodlim.Rd:119: Escaped LaTeX specials: \&
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: 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: ‘ProFit’
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  pause.c:10:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/profvis.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cin’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
File ‘prototest/libs/prototest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 12717 marked UTF-8 strings
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
Specified C++11: please drop specification unless essential
File ‘pRSR/libs/pRSR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1 marked UTF-8 string
Found the following significant warnings:
  util.c:6:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/pscl.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Namespaces in Imports field not imported from:
  ‘LambertW’ ‘gtools’ ‘mstate’ ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 26 marked Latin-1 strings
File ‘pspearman/libs/pspearman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 140 marked UTF-8 strings
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
Specified C++11: please drop specification unless essential
checkRd: (-1) esa.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) meta_varcov.Rd:9: Escaped LaTeX specials: \&
checkRd: (-1) meta_varcov.Rd:120: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘lifecycle’ ‘patchwork’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 107 marked UTF-8 strings
'::' or ':::' import not declared from: ‘rock’
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
File ‘ptest/libs/ptest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 28898 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fulltext’
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘sjPlot’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
Note: found 35 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘data.table’ ‘itsadug’ ‘lazyeval’ ‘mgcv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
File ‘PWD/libs/PWD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) Ch0C-plot.cpd.PwrGSD.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘exampleplot_1_blockdist_1.png’ ‘exampleplot_1_blockdist_2.png’
  ‘exampleplot_1_blockdist_3.png’ ‘exampleplot_1_bootdist.png’
  ‘exampleplot_1_dist.png’ ‘exampleplot_1_histogramtest_EMD.png’
  ‘exampleplot_1_roc_dynamic.png’ ‘exampleplot_1_slidedist_1.png’
  ‘exampleplot_1_slidedist_2.png’ ‘exampleplot_1_slidedist_3.png’
  ‘exampleplot_1_trimmeddist.png’ ‘exampleplot_blockdist_1.png’
  ‘exampleplot_blockdist_2.png’ ‘exampleplot_blockdist_3.png’
  ‘exampleplot_bootdist.png’ ‘exampleplot_dist.png’
  ‘exampleplot_lim_dyn.png’ ‘exampleplot_lim_sig.png’
  ‘exampleplot_lim_sta.png’ ‘exampleplot_noc.png’
  ‘exampleplot_roc_dyn.png’ ‘exampleplot_roc_sta.png’
  ‘exampleplot_slidedist_1.png’ ‘exampleplot_slidedist_2.png’
  ‘exampleplot_slidedist_3.png’ ‘exampleplot_trimmeddist.png’
  ‘myworkflow_result.xml’ ‘test_2_roc_dynamic.png’ ‘test_4_dist.png’
  ‘test_5_blockdist_1.png’ ‘test_5_blockdist_2.png’
  ‘test_5_blockdist_3.png’ ‘test_6_slidedist_1.png’
  ‘test_6_slidedist_2.png’ ‘test_6_slidedist_3.png’
  ‘test_7_trimmeddist.png’ ‘test_8_bootdist.png’ ‘test_emd_1d.png’
  ‘test_emd_2d.png’ ‘test_jsd_1d.png’ ‘test_jsd_2d.png’
  ‘test_kld_1d.png’ ‘test_kld_2d.png’ ‘test_ms_1d.png’ ‘test_ms_2d.png’
  ‘test_rms_1d.png’ ‘test_rms_2d.png’
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Namespaces in Imports field not imported from:
  ‘rmarkdown’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: please drop specification unless essential
Note: found 76102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘missMethods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘readxl’ ‘reshape2’ ‘sjmisc’ ‘stringr’ ‘xlsx’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘lambda.pdf’ ‘qqplot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘qrencoder/libs/qrencoder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
Note: found 6 marked UTF-8 strings
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
'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
GNU make is a SystemRequirements.
checkRd: (-1) GRI.Rd:3: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 4 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 35707 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘SparseM’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  glmBias.c:84:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/QuasiSeq.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Note: found 8504 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘psych’ ‘psychTools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 12928 marked UTF-8 strings
Specified C++11: please drop specification unless essential
checkRd: (-1) qwraps2.Rd:73: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘pracma’ ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib/sundials/sundials_nonlinearsolver.c:26:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib/sundials/sundials_matrix.c:29:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib/sundials/sundials_nvector.c:28:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib/sundials/sundials_linearsolver.c:28:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/r2sundials.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
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
Namespaces in Imports field not imported from:
  ‘asd’ ‘cubature’ ‘data.table’ ‘ggplot2’ ‘multxpert’ ‘survival’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘comat’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘utf8’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘CGHbase’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
  ‘blcs.dot’ ‘blcs.pdf’ ‘ex1.dot’ ‘ex1.pdf’ ‘ex1bridge1.dot’
  ‘ex1bridge1.pdf’ ‘ex1bridge2.dot’ ‘ex1bridge2.pdf’ ‘ex1bridge3.dot’
  ‘ex1bridge3.pdf’ ‘ex1effect1.dot’ ‘ex1effect1.pdf’ ‘ex1effect2.dot’
  ‘ex1effect2.pdf’ ‘gcmlinear.dot’ ‘gcmlinear.pdf’ ‘latent.dot’
  ‘latent.pdf’ ‘lcs.dot’ ‘lcs.pdf’ ‘mimic.dot’ ‘mimic.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 7734 marked UTF-8 strings
Package suggested but not available for checking: ‘googlesheets’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dplyr’ ‘jsonlite’ ‘rgbif’ ‘rgdal’ ‘rgeos’ ‘sp’ ‘spThin’
  ‘spatstat’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘RANKS/libs/RANKS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  sketch.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sketch.c:38:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sketch.c:172:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sketch.c:206:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/RaProR.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘RaschSampler/libs/RaschSampler.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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++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
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: \_
Found the following significant warnings:
  /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:343:23: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_queue_impl.h:744:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_queue_impl.h:1003:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_unordered_impl.h:67:36: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/RMatrix.h:18:24: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/Ravages.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rex’
  All declared Imports should be used.
Found the following significant warnings:
  bedrock_leveldb.h:74:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.h:100:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.h:102:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.h:103:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  support.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.c:545:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.c:785:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.c:797:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.c:802:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:39:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:136:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:137:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:138:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nbt.c:35:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  random.c:44:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  random.c:56:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  random.c:90:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  subchunk.c:9:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  support.c:205:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rbedrock.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Note: found 8 marked UTF-8 strings
GNU make is a SystemRequirements.
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:343:23: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_queue_impl.h:744:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_queue_impl.h:1003:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_unordered_impl.h:67:36: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/RMatrix.h:18:24: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/rbiom.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) mn4joint1condi.Rd:39: Escaped LaTeX specials: \$
checkRd: (-1) mn4joint1condi.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) objets.Rd:66: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26334 marked UTF-8 strings
Found the following files/directories:
  ‘rcanvec.cache’
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’ ‘shinythemes’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘rlemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
Found the following significant warnings:
  nonred.c:99:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rcdd.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘data.csv’
Found the following significant warnings:
  RClickhouse_init.c:23:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/RClickhouse.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Specified C++11: please drop specification unless essential
'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.
Note: found 345 marked UTF-8 strings
Package suggested but not available for checking: ‘conics’
Note: found 1 marked UTF-8 string
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
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
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
File ‘RcppDL/libs/RcppDL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
‘configure’: /bin/bash is not portable
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
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
File ‘RcppNumerical/libs/RcppNumerical.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘Cuhre.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.
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘rredis’
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++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘PercentCodes’
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
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Found the following significant warnings:
  rDEA_init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rDEA.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'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
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  dsdp/include/dsdp5.h:206:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../../include/dsdp5.h:206:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dsdpcops.c:20:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dsdpsetoptions.c:280:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sdpalloc.c:4:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rdsdp.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) re2_syntax.Rd:539: Escaped LaTeX specials: \_
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without 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 ‘read.dbc/libs/read.dbc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following 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
'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
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Note: found 1036 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
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
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:
  ‘cur_plans’
Found the following significant warnings:
  redland.c:771:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redland.c:817:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redland.c:1846:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/redland.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘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
Namespaces in Imports field not imported from:
  ‘knitr’ ‘textshaping’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Found the following significant warnings:
  init.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/reglogit.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
checkRd: (-1) pima.Rd:24: Escaped LaTeX specials: \^
checkRd: (-1) reglogit.Rd:120: Escaped LaTeX specials: \&
checkRd: (-1) reglogit.Rd:124: Escaped LaTeX specials: \&
checkRd: (-1) reglogit.Rd:136: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) calc.relimp.Rd:41: Escaped LaTeX specials: \~
checkRd: (-1) classesmethods.relaimpo.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) classesmethods.relaimpo.Rd:104: Escaped LaTeX specials: \$
checkRd: (-1) mianalyze.relimp.Rd:69: Escaped LaTeX specials: \~
checkRd: (-1) mianalyze.relimp.Rd:73: Escaped LaTeX specials: \~
checkRd: (-1) relimplm-class.Rd:63: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbootMI-class.Rd:121: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbooteval-class.Rd:146: Escaped LaTeX specials: \$
Package which this enhances but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘remote/libs/remote.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘pbdRPC’
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.
Note: found 6034 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
File ‘repolr/libs/repolr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 25 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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: \_ \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) Burns.Rd:28: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘ccdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
Note: found 514 marked UTF-8 strings
File ‘RFCCA/libs/RFCCA.so’:
  Found ‘__vsprintf_chk’, possibly from ‘vsprintf’ (C)
    Object: ‘randomForestSRC.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
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
checkRd: (-1) CardioRiskFactors.Rd:35: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘RFpredInterval/libs/RFpredInterval.so’:
  Found ‘__vsprintf_chk’, possibly from ‘vsprintf’ (C)
    Object: ‘randomForestSRC.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
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'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
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  Rglpk_read_file.c:17:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:42:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rglpk.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
checkRd: (-1) Rglpk_read_file.Rd:6: 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
checkRd: (-1) columbus.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) columbus.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
Note: found 1473 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
File ‘RI2by2/libs/RI2by2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  convert.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  convert.c:79:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ring.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 169 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘Rip46/libs/Rip46.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 243 marked UTF-8 strings
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.h:19:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.h:26:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.h:30:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rjags.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Found the following significant warnings:
  rJava.h:123:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rJava.h:167:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Rglue.c:39:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Rglue.c:1214:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Rglue.c:1225:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:751:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:762:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loader.c:34:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  otables.c:11:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rJava.c:14:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rJava.c:142:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registration.c:6:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  tools.c:109:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  tools.c:131:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  tools.c:141:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
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 ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  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
Namespace in Imports field not imported from: ‘XLConnect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘rJPSGCS/libs/rJPSGCS.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘readPEDfile.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
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘rkvo/libs/rkvo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
File ‘rlang/libs/rlang.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘internal.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.
Specified C++14: please drop specification unless essential
Found the following significant warnings:
  RngWrap.c:12:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RngWrap.c:23:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RngWrap.c:304:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rlecuyer.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘Rlof/libs/Rlof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 31 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘RMKdiscrete/libs/RMKdiscrete.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 133 marked Latin-1 strings
Package suggested but not available for checking: ‘rnaturalearthhires’
Note: found 416 marked Latin-1 strings
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
File ‘rnetcarto/libs/rnetcarto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘attention’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) addLR.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) addLRinv.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) adtestWrapper.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) arcticLake.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cenLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) cenLRinv.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) expenditures.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) gemas.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) machineOperators.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) plot.imp.Rd:138: Escaped LaTeX specials: \&
checkRd: (-1) robCompositions-package.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) skyeLavas.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) variation.Rd:45: Escaped LaTeX specials: \&
Unknown package ‘StatDA’ in Rd xrefs
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘bridgesampling’ ‘extraDistr’ ‘psych’ ‘runjags’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘bridgesampling’ ‘runjags’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘graphics’ ‘methods’ ‘utils’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘methods’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 6 marked UTF-8 strings
Found the following significant warnings:
  monitor.c:15:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/robustbase.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
checkRd: (-1) aircraft.Rd:8: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
File ‘robustETM/libs/robustETM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  /usr/lib/gcc/x86_64-redhat-linux/12/include/emmintrin.h:131:24: 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 ‘/data/gannet/ripley/R/packages/tests-devel/RobustGaSP.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'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
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 261 marked UTF-8 strings
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
'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
'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
'::' or ':::' import not declared from: ‘RColorBrewer’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:

  Warning: 'rgl::rgl.texts' is deprecated.
  Warning: 'rgl::rgl.texts' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Found the following files/directories:
  ‘Rpdb.pdb’
Specified C++14: 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:
    IMPROVEMENTS AND ### BUG FIXES
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’ ‘timeDate’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  affine.cpp:33:53: warning: ‘QuantLib::CalibrationHelper’ is deprecated [-Wdeprecated-declarations]
  bermudan.cpp:33:53: warning: ‘QuantLib::CalibrationHelper’ is deprecated [-Wdeprecated-declarations]
  hullwhite.cpp:43:54: warning: ‘QuantLib::CalibrationHelper’ is deprecated [-Wdeprecated-declarations]
  hullwhite.cpp:111:54: warning: ‘QuantLib::CalibrationHelper’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/RQuantLib.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Specified C++14: please drop specification unless essential
File ‘RQuantLib/libs/RQuantLib.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘utils.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.
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
'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
Package suggested but not available for checking: ‘evolqg’
Unknown package ‘evolqg’ in Rd xrefs
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'loadNamespace' or 'requireNamespace' call not declared from: ‘dplyr’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gdalUtils’
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lubridate’ ‘reshape2’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  Stopwatch.h:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Stopwatch.c:4:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rscimark.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
File ‘rscimark/libs/rscimark.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘keys’ ‘shinyWidgets’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 467 marked UTF-8 strings
File ‘RSKC/libs/RSKC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Vdgraph’
Unknown package ‘Vdgraph’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MatrixExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [17s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rstpm2)
  Loading required package: survival
  Loading required package: splines
  
  Attaching package: 'rstpm2'
  
  The following object is masked from 'package:survival':
  
      colon
  
  > 
  > test_check("rstpm2")
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 92 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_base.R:21'): offset ──────────────────────────────────────────
  max(abs(expr - value)) is not strictly less than `eps`. Difference: 0.995
  Backtrace:
      ▆
   1. └─rstpm2 (local) expect_eps(coef(fit)[1], -6.6465454, 1e-05) at test_base.R:21:4
   2.   └─testthat::expect_lt(max(abs(expr - value)), eps) at test_base.R:8:14
  ── Failure ('test_base.R:22'): offset ──────────────────────────────────────────
  max(abs(expr - value)) is not strictly less than `eps`. Difference: 0.00167
  Backtrace:
      ▆
   1. └─rstpm2 (local) expect_eps(coef(fit)[2], -0.3601438, 1e-05) at test_base.R:22:4
   2.   └─testthat::expect_lt(max(abs(expr - value)), eps) at test_base.R:8:14
  
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 92 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘bitops’ ‘httpuv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  rsyslog.h:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rsyslog.c:50:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rsyslog.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘RTextTools/libs/RTextTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Note: found 40 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppProgress’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
Note: found 37 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 2023 marked Latin-1 strings
  Note: found 17 marked UTF-8 strings
Package suggested but not available for checking: ‘cmdstanr’
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘lubridate’ ‘rstantools’
  All declared Imports should be used.
Unknown package ‘cmdstanr’ in Rd xrefs
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘RQuantLib’
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
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) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘results’
checkRd: (-1) run.jags.study.Rd:67: 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
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘glmmADMB’
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘withr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘RVowpalWabbit/libs/RVowpalWabbit.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘parse_args.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
Package suggested but not available for checking: ‘rWCVPdata’
Note: found 16 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘rwfec/libs/rwfec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 4250 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 2016 marked UTF-8 strings
checkRd: (-1) mapBubbles.Rd:62: Escaped LaTeX specials: \$
Malformed Title field: should not end in a period.
Note: found 426306 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++14: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
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
Note: found 37 marked Latin-1 strings
  Note: found 172 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CARBayesdata’ ‘MASS’ ‘nimble’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 63 marked Latin-1 strings
Note: found 4 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Note: found 3 marked Latin-1 strings
Note: found 120 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  Gen_fun.h:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Gen_fun.c:121:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IFscratch.h:64:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  load_IFscratch.c:64:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/samon.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Found the following significant warnings:
  init.h:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.h:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/SamplerCompare.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘networkTomography’
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘sanitizers/libs/sanitizers.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘FitARMA’
Specified C++11: please drop specification unless essential
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
'library' or 'require' call to ‘progress’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘saturnin/libs/saturnin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Found the following significant warnings:
  error.h:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/scclust.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘SingleCellSignalR’
Namespaces in Imports field not imported from:
  ‘future’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DuoClustering2018’
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘cluster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mathjaxr’
  All declared Imports should be used.
File ‘SCEPtERbinary/libs/SCEPtERbinary.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 464 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'ssvd', 'conos', 'pagoda2'
Unexported object imported by a ':::' call: ‘simplifyEnrichment:::is_GO_id’
  See the note in ?`:::` about the use of this operator.
'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
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RhpcBLASctl’
  All declared Imports should be used.
File ‘scout/libs/scout.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘AUCell’
File ‘scquantum/libs/scquantum.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘crayon’ ‘knitr’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘untitled_consensus_cluster’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘Matrix’ ‘SingleCellExperiment’ ‘SummarizedExperiment’
  ‘ggsci’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘glmGamPoi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 51 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘MC p-value.ps’ ‘Output.csv’ ‘Rh.ps’ ‘Th.ps’ ‘dataratio .Rdata’
  ‘featuresRmax.csv’ ‘featuresT.csv’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Note: found 5 marked Latin-1 strings
  Note: found 51869 marked UTF-8 strings
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
Warning: elapsed-time limit of 30 minutes reached for sub-process
--- re-building ‘effect-of-climate-dependent-flux.Rmd’ using rmarkdown

Execution halted
--- re-building ‘introduction-to-sedproxy.Rmd’ using rmarkdown
--- finished re-building ‘introduction-to-sedproxy.Rmd’

SUMMARY: processing the following file failed:
  ‘effect-of-climate-dependent-flux.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘fansi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘Intro-to-seecolor-package.Rmd’ using rmarkdown
Quitting from lines 49-60 (Intro-to-seecolor-package.Rmd) 
Error: processing vignette 'Intro-to-seecolor-package.Rmd' failed with diagnostics:
[1m[22m[36mℹ[39m In index: 1.
[1mCaused by error in `dplyr::if_else()`:[22m
[33m![39m `condition` must be a vector with type <logical>.
Instead, it has type <logical[,1]>.
--- failed re-building ‘Intro-to-seecolor-package.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro-to-seecolor-package.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘ArrayExpress’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
File ‘segmag/libs/segmag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Package suggested but not available for checking: ‘spgrass6’
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘webp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘editData’ ‘miniUI’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grid’ ‘purrr’
  All declared Imports should be used.
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘semver/libs/semver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fahst.rd:39: Escaped LaTeX specials: \^
checkRd: (-1) fahst.rd:36: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:46: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:42: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:43: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:49: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:44: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:45: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:46: Escaped LaTeX specials: \^
checkRd: (-1) hsortplot.rd:24: Escaped LaTeX specials: \^
checkRd: (-1) nappesortplot.Rd:30: Escaped LaTeX specials: \^
checkRd: (-1) nappesortplot.Rd:28: Escaped LaTeX specials: \^
checkRd: (-1) plot.fahst.rd:45: Escaped LaTeX specials: \^
checkRd: (-1) plot.fasnt.Rd:47: Escaped LaTeX specials: \^
checkRd: (-1) plot.fast.Rd:45: Escaped LaTeX specials: \^
checkRd: (-1) print.fahst.rd:22: Escaped LaTeX specials: \^
checkRd: (-1) print.fasnt.Rd:22: Escaped LaTeX specials: \^
checkRd: (-1) print.fast.Rd:22: Escaped LaTeX specials: \^
Specified C++11: please drop specification unless essential
Note: found 836 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Note: found 3128 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 52 marked UTF-8 strings
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’
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.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘sequences/libs/sequences.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘copynumber’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘geometries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘sfheaders-Ex.R’ failed
The error most likely occurred in:

> ### Name: sf_cast
> ### Title: sf cast
> ### Aliases: sf_cast
> 
> ### ** Examples
> 
> 
> df <- data.frame(
+  id1 = c(1,1,1,1,1,1,1,1,2,2,2,2)
+  , id2 = c(1,1,1,1,2,2,2,2,1,1,1,1)
+  , x = c(0,0,1,1,1,1,2,2,3,4,4,3)
+  , y = c(0,1,1,0,1,2,2,1,3,3,4,4)
+ )
> 
> pt <- sf_point(obj = df, x = "x", y = "y", z = "id1")
> mpt <- sf_multipoint(obj = df, x = "x", y = "y", multipoint_id = "id1")
> ls <- sf_linestring(obj = df, x = "x", y = "y", linestring_id = "id1")
> mls <- sf_multilinestring(obj = df, x = "x", y = "y", multilinestring_id = "id1")
> p <- sf_polygon(
+   obj = df
+   , x = "x"
+   , y = "y"
+   , polygon_id = "id1"
+   , linestring_id = "id2"
+   , close = FALSE
+   )
> mp <- sf_multipolygon(
+   obj = df
+   , x = "x"
+   , y = "y"
+   , multipolygon_id = "id1"
+   , linestring_id = "id2"
+   , close = FALSE
+   )
> 
> sf_cast( pt, "LINESTRING" )
   geometry
1   0, 0, 1
2   0, 1, 1
3   1, 1, 1
4   1, 0, 1
5   1, 1, 1
6   1, 2, 1
7   2, 2, 1
8   2, 1, 1
9   3, 3, 2
10  4, 3, 2
11  4, 4, 2
12  3, 4, 2
> sf_cast( mpt, "POLYGON" )
Error: geometries - Expecting an integer vector for indexing
Execution halted
Unexported object imported by a ':::' call: ‘sf:::agr_levels’
  See the note in ?`:::` about the use of this operator.
Running ‘testthat.R’ [47s/79s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sfnetworks)
  > 
  > test_check("sfnetworks")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 277 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_paths.R:242'): ... is passed correcly onto igraph::distances ──
  isTRUE(all.equal(cost_dijkstra, cost_johnson)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 277 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘sgeostat/libs/sgeostat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) gPLS.Rd:72: Escaped LaTeX specials: \^
checkRd: (-1) gPLS.Rd:74: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:67: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:69: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:75: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:77: Escaped LaTeX specials: \^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Other ideas
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘huge’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘websocket’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  cairodev.h:86:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cairodev.c:11:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  outline.h:64:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.h:47:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  outline.c:169:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  register_routines.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  showtext.c:111:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.c:43:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.c:53:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/showtext.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
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
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 2397 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’
Specified C++11: please drop specification unless essential
Note: found 1231 marked UTF-8 strings
Note: found 28 marked UTF-8 strings
Package suggested but not available for checking: ‘copynumber’
Specified C++11: please drop specification unless essential
File ‘signal/libs/signal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘ExportFigtree1.tre’
Namespaces in Imports field not imported from:
  ‘car’ ‘ggplot2’ ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
checkRd: (-1) chol_s2Dp.Rd:147: Escaped LaTeX specials: \&
checkRd: (-1) chol_s2Dp.Rd:149: Escaped LaTeX specials: \&
checkRd: (-1) precision_builder.Rd:87: Escaped LaTeX specials: \&
checkRd: (-1) sim2D_RandSet_HPPP.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) sim2D_binarymap.Rd:157: Escaped LaTeX specials: \&
checkRd: (-1) sim_MVN_X.Rd:140: Escaped LaTeX specials: \&
checkRd: (-1) sim_Y_Binary_X.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) sim_Y_Binary_X.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) sim_Y_MVN_X.Rd:213: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pedtools’ ‘readr’
  All declared Imports should be used.
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:
  ‘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’
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Found the following files/directories:
  ‘simu.pheno’ ‘usedpars.txt’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘simplexreg/libs/simplexreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘SimRAD-exampleRefSeq-Fasta.fa’ ‘SimRAD-exampleRefSeq.fa’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘fg_step_tab_pp’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
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.
Found the following significant warnings:
  /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:343:23: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_queue_impl.h:744:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_queue_impl.h:1003:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/internal/_concurrent_unordered_impl.h:67:36: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/RMatrix.h:18:24: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/skm.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
GNU make is a SystemRequirements.
File ‘skm/libs/skm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘png’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
Note: found 23 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
File ‘SLHD/libs/SLHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘checkmate’ ‘glmnet’ ‘mice’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
File ‘slp/libs/slp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Unknown package ‘InformationValue’ in Rd xrefs
Note: found 1122 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rPython’
Found the following significant warnings:
  bbobStructures.h:126:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bbobStructures.h:128:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bbobStructures.h:130:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bbobStructures.h:131:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bbobStructures.h:133:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.h:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.h:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarks.h:27:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarks.h:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarks.c:1637:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarks.c:1671:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.c:192:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.c:204:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.c:304:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.c:314:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/smoof.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
File ‘smoof/libs/smoof.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘benchmarkshelper.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.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Scythe_Matrix_Iterator.h:73:31: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  Scythe_Matrix_Iterator.h:192:31: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/smoothSurv.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Specified C++11: please drop specification unless essential
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
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
'::' or ':::' import not declared from: ‘MASS’
Found the following significant warnings:
  SnowballC_init.c:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  stem.c:59:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/SnowballC.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘.R_Test’
Namespaces in Imports field not imported from:
  ‘iterators’ ‘itertools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘flextable’ ‘htmlTable’ ‘stringr’
  All declared Imports should be used.
Note: found 938 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘lgr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.solveEnv’
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.som.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) som.Rd:128: Escaped LaTeX specials: \_
File ‘som/libs/som.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘r2cytoscape’
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘SpaCCr/libs/SpaCCr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘sparcl/libs/sparcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'::' or ':::' import not declared from: ‘lifecycle’
'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:
  ‘fftw_available’
Namespaces in Imports field not imported from:
  ‘gtable’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Unknown package ‘sparsebn’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘SparseFactorAnalysis/libs/SparseFactorAnalysis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘sparseLTSEigen/libs/sparseLTSEigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘RStoolbox’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
checkRd: (-1) sarorderedprobit.Rd:84: Escaped LaTeX specials: \#
Note: found 283 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘pheatmap’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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.
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'

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.
Package unavailable to check Rd xrefs: ‘RandomFields’
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'
Package unavailable to check Rd xrefs: ‘RandomFields’
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
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘spDataLarge’
Note: found 56 marked UTF-8 strings
Note: found 34 marked UTF-8 strings
File ‘SPECIES/libs/SPECIES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 5 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘glue’ ‘httptest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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
Namespaces in Imports field not imported from:
  ‘sf’ ‘spData’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 189 marked UTF-8 strings
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
checkRd: (-1) PimaIndiansDiabetes_long.Rd:14: Escaped LaTeX specials: \^
checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Found the following significant warnings:
  timeObj.c:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  timeObj.c:63:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zoneObj.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zoneObj.c:52:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/splusTimeDate.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
File ‘splusTimeDate/libs/splusTimeDate.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Objects: ‘timeFormat.o’, ‘timeSpanFormat.o’
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘timeFormat.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.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘psy’ ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  spMC.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  spMC.c:303:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/spMC.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
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
Specified C++11: please drop specification unless essential
Note: found 7587 marked UTF-8 strings
Namespace in Imports field not imported from: ‘batchtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sampling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘rgeoda’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘progress’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 199 marked UTF-8 strings
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘RSQLite’ ‘dbplyr’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘arm’ ‘brms’ ‘lme4’ ‘plotly’ ‘shinyMatrix’
  All declared Imports should be used.
checkRd: (-1) B_sraAutoreg.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) C_sraMechanistic.Rd:68: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
checkRd: (-1) Snacks.Rd:6: Escaped LaTeX specials: \~
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Bug fixes
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 123 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘mice’ ‘sandwich’ ‘zoo’
  All declared Imports should be used.
Note: found 40748 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘reshape2’ ‘stats’
  All declared Imports should be used.
checkRd: (-1) katrina.Rd:36: Escaped LaTeX specials: \&
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘httr’ ‘latex2exp’ ‘rstantools’ ‘tibble’ ‘tidyverse’
  ‘utils’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘starma/libs/starma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pander’ ‘readr’ ‘tidyselect’
  All declared Imports should be used.
Running examples in ‘starschemar-Ex.R’ failed
The error most likely occurred in:

> ### Name: character_dimensions
> ### Title: Transform dimension numeric attributes to character
> ### Aliases: character_dimensions character_dimensions.star_schema
> 
> ### ** Examples
> 
> library(tidyr)
> 
> st <- star_schema(mrs_age_test, dm_mrs_age) %>%
+   role_playing_dimension(
+     dim_names = c("when", "when_available"),
+     name = "When Common",
+     attributes = c("date", "week", "year")
+   ) %>%
+   character_dimensions(length_integers = list(week = 2),
+                        NA_replacement_value = "Unknown")
Warning: The `.dots` argument of `group_by()` is deprecated as of dplyr 1.0.0.
ℹ The deprecated feature was likely used in the dplyr package.
  Please report the issue at <https://github.com/tidyverse/dplyr/issues>.
Error in `eval_select_impl()`:
! `x` must be a vector, not a <tbl_df/tbl/data.frame/dimension_table> object.
Backtrace:
     ▆
  1. ├─... %>% ...
  2. ├─starschemar::character_dimensions(...)
  3. ├─starschemar::role_playing_dimension(...)
  4. └─starschemar:::role_playing_dimension.star_schema(...)
  5.   └─starschemar:::union_of_dimensions(dl, name = name, type = "role_playing")
  6.     ├─base::unlist(dplyr::summarise_all(dimensions[[1]], class))
  7.     └─dplyr::summarise_all(dimensions[[1]], class)
  8.       ├─dplyr::summarise(.tbl, !!!funs)
  9.       └─dplyr:::summarise.data.frame(.tbl, !!!funs)
 10.         └─dplyr:::compute_by(...)
 11.           └─dplyr:::eval_select_by(by, data, error_call = error_call)
 12.             └─tidyselect::eval_select(...)
 13.               └─tidyselect:::eval_select_impl(...)
 14.                 └─vctrs::vec_assert(x)
 15.                   └─vctrs:::stop_scalar_type(x, arg, call = call)
 16.                     └─vctrs:::stop_vctrs(...)
 17.                       └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘starschemar.Rmd’ using rmarkdown
Quitting from lines 354-363 (starschemar.Rmd) 
Error: processing vignette 'starschemar.Rmd' failed with diagnostics:
`x` must be a vector, not a <tbl_df/tbl/data.frame/dimension_table> object.
--- failed re-building ‘starschemar.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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’
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 18 marked UTF-8 strings
Found the following files/directories:
  ‘testmat.sdml’ ‘testmat2.sdml’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
'LazyData' is specified without a 'data' directory
Note: found 56 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DDoutlier’ ‘car’ ‘corrplot’ ‘data.table’ ‘energy’ ‘ggplot2’
  ‘gridExtra’ ‘kableExtra’ ‘knitr’ ‘readr’ ‘reshape2’ ‘rmarkdown’
  ‘shinydisconnect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
File ‘steadyICA/libs/steadyICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘StepwiseTest/libs/StepwiseTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 370 marked UTF-8 strings
Note: found 240 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Found the following files/directories:
  ‘corrviz.html’
Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial TODO
Note: found 22806 marked UTF-8 strings
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Note: found 1725 marked UTF-8 strings
Package suggested but not available for checking: ‘isa2’
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Found the following files/directories:
  ‘myNewStrat.R’
Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
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
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Note: found 83 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘grDevices’ ‘graphics’ ‘jsonlite’
  ‘purrr’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘SummaryLasso/libs/SummaryLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 78 marked UTF-8 strings
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:106:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_linearsolver.c:28:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_matrix.c:29:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_nonlinearsolver.c:26:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_nvector.c:28:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/sundialr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) estweights.Rd:42: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
File ‘survivalROC/libs/survivalROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Note: found 25 marked UTF-8 strings
Unknown package ‘survJamda’ in Rd xrefs
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
checkRd: (-1) diabetes.Rd:18: Escaped LaTeX specials: \^
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘robets’
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Unknown package ‘robets’ in Rd xrefs
Running examples in ‘sweep-Ex.R’ failed
The error most likely occurred in:

> ### Name: tidiers_robets
> ### Title: Tidying methods for robets (Robust Error, Trend, Seasonal)
> ###   exponential smoothing modeling of time series
> ### Aliases: tidiers_robets sw_tidy.robets sw_glance.robets
> ###   sw_augment.robets sw_tidy_decomp.robets
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(robets)
Error in library(robets) : there is no package called ‘robets’
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sweep)
  > library(timetk)
  > library(forecast)
  > library(tidyverse)
  ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
  ✔ dplyr     1.1.0     ✔ readr     2.1.4
  ✔ forcats   1.0.0     ✔ stringr   1.5.0
  ✔ ggplot2   3.4.1     ✔ tibble    3.1.8
  ✔ lubridate 1.9.2     ✔ tidyr     1.3.0
  ✔ purrr     1.0.1     
  ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
  ✖ readr::edition_get()   masks testthat::edition_get()
  ✖ dplyr::filter()        masks stats::filter()
  ✖ purrr::is_null()       masks testthat::is_null()
  ✖ dplyr::lag()           masks stats::lag()
  ✖ readr::local_edition() masks testthat::local_edition()
  ✖ dplyr::matches()       masks tidyr::matches(), testthat::matches()
  ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
  > library(robets)
  Error in library(robets) : there is no package called 'robets'
  Execution halted
Package suggested but not available for checking: ‘swephRdata’
Found the following significant warnings:
  libswe/swephlib.h:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/swephlib.h:130:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/swepcalc.h:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/swepcalc.c:373:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/sweph.c:7099:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/swephlib.c:3033:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/swephR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘mapdata’ ‘utils’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    CRAN release
Running examples in ‘SwimmeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: name_reorder
> ### Title: Orders all names as "Firstname Lastname"
> ### Aliases: name_reorder
> 
> ### ** Examples
> 
> name_reorder(
+ data.frame(
+ Name = c("King, Lilly",
+  "Lilly King",
+  NA,
+  "Richards Ross, Sanya",
+  "Phelps, Michael F")),
+ verbose = TRUE
+ )
Error in `dplyr::na_if()`:
! Can't convert `y` <character> to match type of `x` <data.frame>.
Backtrace:
     ▆
  1. ├─SwimmeR::name_reorder(...)
  2. │ └─... %>% ...
  3. ├─dplyr::mutate(...)
  4. ├─dplyr::na_if(., "")
  5. │ └─vctrs::vec_cast(x = y, to = x, x_arg = "y", to_arg = "x")
  6. ├─dplyr::mutate(...)
  7. ├─dplyr::na_if(., "")
  8. │ └─vctrs::vec_cast(x = y, to = x, x_arg = "y", to_arg = "x")
  9. └─vctrs (local) `<fn>`()
 10.   └─vctrs::vec_default_cast(...)
 11.     ├─base::withRestarts(...)
 12.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
 13.     │   └─base (local) doWithOneRestart(return(expr), restart)
 14.     └─vctrs::stop_incompatible_cast(...)
 15.       └─vctrs::stop_incompatible_type(...)
 16.         └─vctrs:::stop_incompatible(...)
 17.           └─vctrs:::stop_vctrs(...)
 18.             └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘SwimmeR.Rmd’ using rmarkdown
Quitting from lines 60-66 (SwimmeR.Rmd) 
Error: processing vignette 'SwimmeR.Rmd' failed with diagnostics:
Can't convert `y` <character> to match type of `x` <data.frame>.
--- failed re-building ‘SwimmeR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R

See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R

All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: file:///data/gannet/ripley/R

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.
Running ‘winpath.R’
Running the tests in ‘tests/winpath.R’ failed.
Complete output:
  > library(switchr)
  > ## if(getOption("repos")["CRAN"] == "@CRAN@")
  > ##     chooseCRANmirror(ind=1L)
  > graceful_inet(TRUE)
  [1] TRUE
  > checkUrlRoundtrip = function(pth) {
  +     pth = switchr:::normalizePath2(pth)
  +     furl = switchr:::makeFileURL(pth)
  +     pth2 = switchr:::fileFromFileURL(furl)
  +     if(pth != pth2)
  +         stop("Round trip result (", pth2, ") does not match original (", pth, ") when creating file URLs")
  + }
  > 
  > ## regression test to ensure that the roundtrip
  > ## between path and file url is working properly
  > checkUrlRoundtrip(getwd())
  > checkUrlRoundtrip(tempdir())
  > if(switchr:::isWindows())
  +     checkUrlRoundtrip("\\\\localhost\\c$")
  > 
  > ## regreossion test to ensure that package dependencies
  > ## are added to the dontunload list when a package
  > ## is specified
  > bef = switchrDontUnload()
  > af = switchrDontUnload("knitr")
  'getOption("repos")' replaces Bioconductor standard repositories, see
  '?repositories' for details
  
  replacement repositories:
      CRAN: file:///data/gannet/ripley/R
  
  > stopifnot(all(c("stringr", "stringi", "magrittr") %in% af))
  Error: all(c("stringr", "stringi", "magrittr") %in% af) is not TRUE
  Execution halted
'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
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
possible bashism in configure line 12 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 22 (echo -n):
  echo -n "  checking for OS..."
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘StackImpute’ ‘arm’ ‘boot’ ‘broom’ ‘knitr’ ‘mvtnorm’
  ‘randomForest’
  All declared Imports should be used.
Suggests orphaned package: ‘udunits2’
Namespace in Imports field not imported from: ‘metR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.csv’
'LazyData' is specified without a 'data' directory
Note: found 38 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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:
  ‘.xls’ ‘attenu.xls’ ‘chick1.xls’ ‘chick2.xls’ ‘generic1.xls’
  ‘hands.xls’ ‘table1.xls’
Note: found 551 marked UTF-8 strings
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 81 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Note: found 301 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 137 marked UTF-8 strings
Note: found 30 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'::' or ':::' import not declared from: ‘scales’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘reshape2’ ‘truncnorm’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘psych’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'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: ‘R2wd’
checkRd: (-1) R2txt.Rd:164: Escaped LaTeX specials: \#
checkRd: (-1) bct.Rd:18: Escaped LaTeX specials: \^
checkRd: (-1) bct.Rd:19: Escaped LaTeX specials: \^
checkRd: (-1) ineq.Rd:10: Escaped LaTeX specials: \&
checkRd: (-1) put.points.demo.Rd:39: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:10: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:31: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
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
Found the following files/directories:
  ‘par-7269706c6579’
Package suggested but not available for checking: ‘gurobi’
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
Note: found 3 marked UTF-8 strings
Note: found 37 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘forecast’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 3 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Unknown package ‘textreadr’ in Rd xrefs
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
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
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘base’ ‘graphics’ ‘janitor’ ‘rlang’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 197527 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘readr’ ‘tidyverse’ ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘knitr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘badger’ ‘ggplot2’ ‘lubridate’ ‘scales’ ‘xgboost’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘autostats’ ‘badger’ ‘framecleaner’ ‘presenter’ ‘tidybins’ ‘validata’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
Note: found 4546 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘graphics’ ‘utils’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
Note: found 122 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘modeldata’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'::' or ':::' import not declared from: ‘pkgconfig’
Note: found 113 marked UTF-8 strings
Note: found 34206 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  common.c:36:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/tiff.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'::' or ':::' import not declared from: ‘pkgconfig’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘robets’
Note: found 2750 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
'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
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Note: found 134043 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pca3d’
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘corpus.JSS.papers’
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
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: ‘toscaData’
Namespace in Imports field not imported from: ‘hdi’
  All declared Imports should be used.
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'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
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘jpeg’ ‘pastecs’ ‘plyr’ ‘raster’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxidata’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 827 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Package suggested but not available for checking: ‘TreeDistData’
Specified C++11: please drop specification unless essential
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
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘treeplyr’
See ‘/data/gannet/ripley/R/packages/tests-devel/treeplyr.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following significant warnings:
  ../inst/include/radix/radix_tree_it.hpp:11:35: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/triebeard.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
File ‘triebeard/libs/triebeard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
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
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: information on .o files is not available
File ‘tseriesTARMA/libs/tseriesTARMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Running examples in ‘ts.extend-Ex.R’ failed
The error most likely occurred in:

> ### Name: intensity
> ### Title: Compute the spectral intensity of a time-series vector/matrix
> ### Aliases: intensity
> 
> ### ** Examples
> 
> 
> data(garma)
> intensity(SERIES1)
Error in class(INT) <- c("matrix", "intensity") : 
  invalid to set the class to matrix unless the dimension attribute is of length 2 (was 0)
Calls: intensity
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updates for the development version (0.1.0.9000) on Github
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘latticeExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
checkRd: (-1) lindner.Rd:44: 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
Note: found 34 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘sl3’
'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.
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: 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.
Found the following significant warnings:
  interface.c:114:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ucminf.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
File ‘ucminf/libs/ucminf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 2 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 548 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Note: found 3347 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 7872 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Note: found 488 marked UTF-8 strings
Package suggested but not available for checking: ‘USAboundariesData’
Package suggested but not available for checking: ‘USA.state.boundaries.data’
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
Note: found 1 marked UTF-8 string
Note: found 33 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'parallel' 'xml2'
  All declared Imports should be used.
Found the following significant warnings:
  rand.c:90:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rand.c:92:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rand.c:103:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rand.c:138:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/uuid.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘badger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) irf.Rd:111: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  computeCox.c:15:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/vdra.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 128 marked UTF-8 strings
Note: found 49 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) checkTS.VGAMextra.Rd:176: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘leaflet’ ‘mapview’
  All declared Imports should be used.
Note: found 60 marked UTF-8 strings
Note: found 468 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
File ‘VIFCP/libs/VIFCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘readr’ ‘uuid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 2754 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    NEW FEATURES
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Note: found 4954 marked UTF-8 strings
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
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
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
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘vctrs’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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
Note: found 3133 marked UTF-8 strings
Note: found 4413 marked UTF-8 strings
Running examples in ‘wcep-Ex.R’ failed
The error most likely occurred in:

> ### Name: wcep
> ### Title: Analysis of weighted composite endpoints
> ### Aliases: wcep
> 
> ### ** Examples
> 
> data(toyexample)
> #event weights
> EW <- data.frame(event = c('CHF','DTH','SHK','REMI'), weight = c(0.3,1,0.5,0.2))
> res1 <- wcep(toyexample, EW)
Error in `left_join()`:
! `...` must be empty.
✖ Problematic argument:
• stringsAsFactors = FALSE
Backtrace:
    ▆
 1. └─wcep::wcep(toyexample, EW)
 2.   └─wcep:::wcep_core(x[, 1:3], EW, alpha)
 3.     ├─dplyr::left_join(ew_h0, ew1, by = "event", stringsAsFactors = FALSE)
 4.     └─dplyr:::left_join.data.frame(ew_h0, ew1, by = "event", stringsAsFactors = FALSE)
 5.       └─rlang::check_dots_empty0(...)
 6.         └─rlang::check_dots_empty(call = call)
 7.           └─rlang:::action_dots(...)
 8.             ├─base (local) try_dots(...)
 9.             └─rlang (local) action(...)
Execution halted
'LazyData' is specified without a 'data' directory
Note: found 1668 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Package suggested but not available for checking: ‘prepr’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/WeightedCluster.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Specified C++11: please drop specification unless essential
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘ATE’
Unknown package ‘ATE’ in Rd xrefs
Specified C++14: 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:
    Major changes
    Minor changes
Note: found 4102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘plotly’ ‘shinythemes’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Note: found 1 marked UTF-8 string
File ‘wingui/libs/wingui.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘DescTools’ ‘HydeNet’ ‘RBGL’ ‘Rgraphviz’ ‘arules’ ‘bnlearn’
  ‘dplyr’ ‘graph’ ‘igraph’ ‘linkcomm’ ‘missRanger’ ‘parallel’ ‘psych’
  ‘rhandsontable’ ‘rintrojs’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinycssloaders’ ‘shinydashboard’ ‘tools’ ‘visNetwork’
  All declared Imports should be used.
'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
Note: found 3984 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  random_wrap.c:9:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/wnominate.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Note: found 933 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Note: found 6738 marked UTF-8 strings
Note: found 3 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Found the following files/directories:
  ‘aphiainfo.csv’ ‘tax.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
'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.
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RP2_data_1.txt’ ‘RP2_data_4.txt’ ‘RP2_qtl_1.txt’ ‘RP2_qtl_4.txt’
  ‘hp1_effect_qtl.txt’ ‘hp1_freq_mrk.txt’ ‘hp1_freq_qtl.txt’
  ‘hp1_genome.txt’ ‘hp1_last_hp_data.txt’ ‘hp1_lm_mrk.txt’
  ‘hp1_lm_qtl.txt’ ‘hp1_lm_qtl_mrk.txt’ ‘hp1_mrk.txt’ ‘hp1_qtl.txt’
  ‘hp2_effect_qtl.txt’ ‘hp2_freq_mrk.txt’ ‘hp2_freq_qtl.txt’
  ‘hp2_genome.txt’ ‘hp2_last_hp_data.txt’ ‘hp2_lm_mrk.txt’
  ‘hp2_lm_qtl.txt’ ‘hp2_lm_qtl_mrk.txt’ ‘hp2_mrk.txt’ ‘hp2_qtl.txt’
  ‘my_RP_data_1.txt’ ‘my_RP_data_4.txt’ ‘my_RP_mrk_1.txt’
  ‘my_RP_mrk_4.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘psychTools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'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 significant warnings:
  init.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:71:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:72:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/xml2.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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: \_
Running ‘testthat.R’ [113s/142s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xpose)
  Loading required package: ggplot2
  
  Attaching package: 'xpose'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("xpose")
  [ FAIL 1 | WARN 4 | SKIP 7 | PASS 521 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (7)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-xpose_save.R:33'): errors are returned for bad filename input ──
  `xpose_save(plot = plot, file = paths_1)` threw an error with unexpected message.
  Expected match: "device.+must be.+NULL.+string or a function"
  Actual message: "Unknown graphics device \"abcd\""
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-xpose_save.R:33:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─xpose::xpose_save(plot = plot, file = paths_1)
    7.   └─ggplot2::ggsave(...)
    8.     └─ggplot2:::plot_dev(device, filename, dpi = dpi)
    9.       └─cli::cli_abort("Unknown graphics device {.val {device}}", call = call)
   10.         └─rlang::abort(...)
  
  [ FAIL 1 | WARN 4 | SKIP 7 | PASS 521 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘XML’ ‘atom4R’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 47 marked UTF-8 strings
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 146804 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘zdat’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    NEW DEPENDENCIES
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: \_
Package suggested but not available for checking: ‘SDMTools’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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: 'INLA'
Specified C++11: please drop specification unless essential
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
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
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   2.9Mb
    libs   1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.3Mb
'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
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
'LazyData' is specified without a 'data' directory
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: 'INLA'
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
checkRd: (-1) BerryMielke.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) BlairLacy.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) Kvalseth.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) consensus.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) dsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) l.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) var.variance.Rd:12: Escaped LaTeX specials: \&
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
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       2.0Mb
'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
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: 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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/AlphaHull3D.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
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'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
'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
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: \_ \_
Specified C++14: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   1.2Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Error(s) in re-building vignettes:
--- re-building 'antaresEditObject.Rmd' using rmarkdown
--- finished re-building 'antaresEditObject.Rmd'

--- re-building 'api-variant-management.Rmd' using rmarkdown
--- finished re-building 'api-variant-management.Rmd'

--- re-building 'renewables-energy-sources.Rmd' using rmarkdown
--- finished re-building 'renewables-energy-sources.Rmd'

--- re-building 'scenario-builder.Rmd' using rmarkdown
Quitting from lines 26-55 (scenario-builder.Rmd) 
Error: processing vignette 'scenario-builder.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'scenario-builder.Rmd'

SUMMARY: processing the following file failed:
  'scenario-builder.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    test_v8    2.0Mb
    testdata   2.3Mb
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++14: 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
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++14: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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 which this enhances but not available for checking: 'ARTP'
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
'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
Package suggested but not available for checking: 'asteRiskData'
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running 'testthat.R' [100s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(attrib)
  attrib 2021.1.2 https://folkehelseinstituttet.github.io/attrib
  > 
  > test_check("attrib")
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%[ FAIL 2 | WARN 0 | SKIP 0 | PASS 6 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_fake.R:159'): simmulations ───────────────────────────────────
  round(as.numeric(median(dif_obs), 0)) not equal to c(0).
  1/1 mismatches
  [1] -1 - 0 == -1
  ── Failure ('test_fake.R:167'): simmulations ───────────────────────────────────
  round(as.numeric(median(dif), 0)) not equal to c(0).
  1/1 mismatches
  [1] -1 - 0 == -1
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
'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
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: 'lixoftConnectors'
Specified C++14: please drop specification unless essential
Specified C++14: please drop specification unless essential
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
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:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
Encountered the following conversion/validation errors:
'CreateProcess' failed to run 'd:\rtools43\x86_64-w64-mingw32.static.posix\bin\tidy.exe -language en -qe --drop-empty-elements no D:\temp\RtmpoXYIlp\filea83440102760'
'CreateProcess' failed to run 'd:\rtools43\x86_64-w64-mingw32.static.posix\bin\tidy.exe -language en -qe --drop-empty-elements no D:\temp\RtmpoXYIlp\filea83440102760'
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Specified C++14: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'ARIMA.Rmd' using rmarkdown
--- finished re-building 'ARIMA.Rmd'

--- re-building 'GARCH.Rmd' using rmarkdown
Quitting from lines 85-87 (GARCH.Rmd) 
Error: processing vignette 'GARCH.Rmd' failed with diagnostics:
cannot allocate vector of size 18.7 Mb
--- failed re-building 'GARCH.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Specified C++14: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
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
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.2Mb
'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:
    R     1.9Mb
    doc   3.9Mb
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++14: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Encountered the following conversion/validation errors:
'CreateProcess' failed to run 'd:\rtools43\x86_64-w64-mingw32.static.posix\bin\tidy.exe -language en -qe --drop-empty-elements no D:\temp\Rtmp0uJgkR\filefca83cf01376'
'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       1.2Mb
    extdata   3.3Mb
    libs      1.4Mb
Specified C++11: please drop specification unless essential
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
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.5Mb
Unexported object imported by a ':::' call: 'taxadb:::latest_version'
  See the note in ?`:::` about the use of this operator.
Running 'spelling.R' [0s]
  Running 'testthat.R' [68s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(beadplexr)
  > 
  > test_check("beadplexr")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 356 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_cluster_events.R:76'): bp_dbscan works ─────────────────────────
  Error: cannot allocate vector of size 14.8 Mb
  Backtrace:
      ▆
   1. ├─testthat::expect_is(...) at test_cluster_events.R:76:4
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─beadplexr::bp_dbscan(...)
   5.   ├─base::do.call(fpc::dbscan, .all_args)
   6.   └─fpc (local) `<fn>`(data = `<tibble[,2]>`, eps = 0.2, MinPts = 100, scale = TRUE)
   7.     └─fpc (local) distcomb(data[ap, , drop = FALSE], data[unclass, , drop = FALSE])
   8.       └─base::apply(...)
   9.         └─base::array(...)
  ── Error ('test_identify_assay_analyte.R:131'): dbscan works as expected ───────
  Error: cannot allocate vector of size 8.6 Mb
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test_identify_assay_analyte.R:131:4
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─beadplexr::identify_analyte(...)
    7.   └─beadplexr::bp_dbscan(...)
    8.     ├─base::do.call(fpc::dbscan, .all_args)
    9.     └─fpc (local) `<fn>`(data = `<tibble[,2]>`, eps = 0.2, MinPts = 50, scale = TRUE)
   10.       └─fpc (local) distcomb(data[ap, , drop = FALSE], data[unclass, , drop = FALSE])
   11.         └─base::apply(...)
   12.           └─base::array(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 356 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
GNU make is a SystemRequirements.
Running examples in 'bedr-Ex.R' failed
The error most likely occurred in:

> ### Name: read.vcf
> ### Title: Read a vcf into R
> ### Aliases: read.vcf
> ### Keywords: vcf
> 
> ### ** Examples
> 
> 
> clinVar.vcf.example      <- system.file("extdata/clinvar_dbSNP138_example.vcf.gz", package = "bedr")
> singleSample.vcf.example <- system.file("extdata/singleSampleOICR_example.vcf.gz", package = "bedr")
> multiSample.vcf.example  <- system.file("extdata/multiSampleOICR_example.vcf.gz", package = "bedr")
> 
> # read a subset of NCBI clinVar vcf.  Note this has no samples.
> vcf1.a <- read.vcf(clinVar.vcf.example)
READING VCF
 * checking if file exists... PASS
 * Reading vcf header...
Datei nicht gefunden
Warning in system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  :
  running command 'C:\Windows\system32\cmd.exe /c dir' had status 1
Datei nicht gefunden
Warning in system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  :
  running command 'C:\Windows\system32\cmd.exe /c dir' had status 1
Error in system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  : 
  'CreateProcess' failed to run 'C:\Windows\system32\cmd.exe /c dir'
Calls: read.vcf ... Sys.readlink2 -> sapply -> lapply -> FUN -> shell -> system
Execution halted
Specified C++14: please drop specification unless essential
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.8Mb
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++14: 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
Running examples in 'berryFunctions-Ex.R' failed
The error most likely occurred in:

> ### Name: normalizePathCP
> ### Title: normalizePath Cross Platform
> ### Aliases: normalizePathCP
> ### Keywords: file
> 
> ### ** Examples
> 
> 
> normalizePath  ("doesnotexist.file", mustWork=FALSE) # on unix not full path
[1] "doesnotexist.file"
> normalizePathCP("doesnotexist.file") # full path on all platforms
[1] "doesnotexist.file"
> 
> normalizePath  ("../doesnotexist.file", mustWork=FALSE)
[1] "../doesnotexist.file"
> normalizePathCP("../doesnotexist.file")
[1] "../doesnotexist.file"
>  
> checknp <- function(a,b=a,d=getwd())
+   {
+   aa <- normalizePathCP(a)
+   bb <- if(d=="") b else paste0(d,"/",b)
+   if(aa != bb) stop("'", a, "' -> '", aa, "', should be '",bb, "'.")
+   aa
+   }
> 
> checknp("notexist.file")
Error in checknp("notexist.file") : 
  'notexist.file' -> 'notexist.file', should be 'd:/Rcompile/CRANpkg/local/4.3/berryFunctions.Rcheck/notexist.file'.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    help   1.1Mb
    libs   1.6Mb
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is 151.7Mb
  sub-directories of 1Mb or more:
    include  150.6Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
Re-running with no redirection of stdout/stderr.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Encountered the following conversion/validation errors:
'CreateProcess' failed to run 'd:\rtools43\x86_64-w64-mingw32.static.posix\bin\tidy.exe -language en -qe --drop-empty-elements no D:\temp\RtmpiMJSGO\filee62875da5f60'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running examples in 'bigstatsr-Ex.R' failed
The error most likely occurred in:

> ### Name: big_prodMat
> ### Title: Product with a matrix
> ### Aliases: big_prodMat %*%,FBM,matrix-method %*%,matrix,FBM-method
> 
> ### ** Examples
> 
> X <- big_attachExtdata()
> n <- nrow(X)
> m <- ncol(X)
> A <- matrix(0, m, 10); A[] <- rnorm(length(A))
> 
> test <- big_prodMat(X, A)
> true <- X[] %*% A
> all.equal(test, true)
[1] TRUE
> 
> X2 <- big_copy(X, type = "double")
> all.equal(X2 %*% A, true)
[1] TRUE
> 
> # subsetting
> ind.row <- sample(n, n/2)
> ind.col <- sample(m, m/2)
> 
> tryCatch(test2 <- big_prodMat(X, A, ind.row, ind.col),
+          error = function(e) print(e))
<simpleError: Incompatibility between dimensions.
'ind.col' and 'rows_along(A.col)' should have the same length.>
> # returns an error. You need to use the subset of A:
> test2 <- big_prodMat(X, A[ind.col, ], ind.row, ind.col)
Error in { : task 1 failed - "std::bad_alloc"
Calls: big_prodMat ... big_parallelize -> <Anonymous> -> %dopar% -> <Anonymous>
Execution halted
Specified C++11: please drop specification unless essential
Running 'spelling.R' [0s]
  Running 'testthat.R' [314s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bigutilsr)
  > 
  > test_check("bigutilsr")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 53 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-knn.R:28'): knn_parallel() works ───────────────────────────────
  Error in `makePSOCKcluster(names = spec, ...)`: Cluster setup failed. 1 worker of 2 failed to connect.
  Backtrace:
       ▆
    1. ├─testthat::expect_failure(...) at test-knn.R:28:2
    2. │ └─testthat::capture_expectation(expr)
    3. │   └─base::tryCatch(...)
    4. │     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    5. │       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    6. │         └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    7. ├─testthat::expect_identical(...)
    8. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
    9. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   10. └─bigutilsr::knn_parallel(mat1, k = 8, ncores = 2)
   11.   └─bigparallelr::split_parapply(...)
   12.     ├─base::do.call(...)
   13.     └─bigparallelr (local) `<fn>`(ncores = 2)
   14.       └─parallel::makeCluster(ncores, ...)
   15.         └─parallel::makePSOCKcluster(names = spec, ...)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 53 ]
  Error: Test failures
  In addition: Warning message:
  In for (i in 1L:d2) { :
    closing unused connection 5 (<-CRANWIN2.fb05.statistik.uni-dortmund.de:11569)
  Execution halted
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
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
Warning in readLines(tf) :
  incomplete final line found on 'D:\temp\RtmpUz36tV\file1c958341b5086'
--- re-building 'comparisons.Rmd' using knitr
Mingw-w64 runtime failure:
  VirtualProtect failed with code 0x5af

SUMMARY: processing the following files failed:
  'comparisons.Rmd' 'cross-validation.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Encountered the following conversion/validation errors:
'CreateProcess' failed to run 'd:\rtools43\x86_64-w64-mingw32.static.posix\bin\tidy.exe -language en -qe --drop-empty-elements no D:\temp\RtmpYT8DqN\filea5c048704de7'
Error: package or namespace load failed for 'binspp':
 cannot allocate vector of size 1.3 Mb
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Specified C++14: please drop specification unless essential
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running massageExamples to create 'bioacoustics-Ex.R' failed

 NONE
Encountered the following conversion/validation errors:
'CreateProcess' failed to run 'd:\rtools43\x86_64-w64-mingw32.static.posix\bin\tidy.exe -language en -qe --drop-empty-elements no D:\temp\Rtmpqka1No\file3744c6a7db6'
'LazyData' is specified without a 'data' directory
Error: package or namespace load failed for 'biomartr':
 cannot allocate vector of size 657 Kb
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      1.2Mb
Fatal error: couldn't allocate memory for pointer stack
Running examples in 'bioseq-Ex.R' failed
The error occurred in:
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Error: package or namespace load failed for 'biostat3' in inDL(x, as.logical(local), as.logical(now), ...):
 unable to load shared object 'D:/RCompile/CRANpkg/lib/4.3/muhaz/libs/x64/muhaz.dll':
  LoadLibrary failure:  Die Auslagerungsdatei ist zu klein, um diesen Vorgang durchzuführen.

Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), do
Execution halted
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Error: package 'survival' could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)), 
       call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc, 
       .libPaths()))
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error in try(sys.source(codeFile, env, keep.source = keep.source, keep.parse.data = keep.parse.data)) : 
  lazy-load database 'D:/RCompile/recent/R/library/base/R/base.rdb' is corrupt
In addition: Warning messages:
1: In doTryCatch(return(expr), name, parentenv, handler) :
  internal error -4 in R_decompress1
2: In deparse(call, nlines = 1L) :
  restarting interrupted promise evaluation
During startup - Warning message:
package 'utils' in options("defaultPackages") was not found
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Loading this package had a fatal error status code 301
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Error: cannot allocate vector of size 20 Kb
Execution halted
Please remove or rename the files.
See section 'Package subdirectories' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Fatal error: couldn't allocate node stack
Mingw-w64 runtime failure:
  VirtualProtect failed with code 0x5af
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Error: package or namespace load failed for 'bkmrhat' in inDL(x, as.logical(local), as.logical(now), ...):
 unable to load shared object 'D:/RCompile/CRANpkg/lib/4.3/vctrs/libs/x64/vctrs.dll':
  LoadLibrary failure:  Die Auslagerungsdatei ist zu klein, um diesen Vorgang durchzuführen.
Execution halted
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
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
Package suggested but not available for checking: 'cmdstanr'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       3.7Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.2Mb
Loading this package had a fatal error status code 1
Loading log:
Loading required package: rtkore
Loading required package: Rcpp
Error: package or namespace load failed for 'Rcpp':
 cannot allocate vector of size 351 Kb
Error: package 'Rcpp' could not be loaded
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.9Mb
    libs      1.0Mb
Specified C++11: please drop specification unless essential
It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package.  All dependencies must be
declared in DESCRIPTION.
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
Specified C++14: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'INLA'
Specified C++14: please drop specification unless essential
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   4.2Mb
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
Problems with news in 'NEWS.md':
No news entries found.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/BonEV.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Boov.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) R2txtJG.Rd:90: 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: 'cmdstanr'
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   3.6Mb
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
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) kink_estimator.Rd:60: 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
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
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'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
Specified C++14: 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) belt.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) bipf.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) crime.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) da.cat.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) dabipf.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) ecm.cat.Rd:77: Escaped LaTeX specials: \&
checkRd: (-1) em.cat.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) ipf.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) logpost.cat.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) mda.cat.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) mi.inference.Rd:140: Escaped LaTeX specials: \&
checkRd: (-1) older.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) prelim.cat.Rd:67: Escaped LaTeX specials: \&
Specified C++14: please drop specification unless essential
'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
'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
Package which this enhances but not available for checking: 'CirceR'
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
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    include  38.4Mb
'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 significant warnings:
  checks.c:488:81: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  checks.c:492:81: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  checks.c:496:81: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.3/checkmate.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'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:
    data   1.1Mb
    doc    3.6Mb
    libs   1.0Mb
'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
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
'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
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
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: '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
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BrownBigrams.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BrownLOBPassives.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BrownPassives.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BrownStats.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) KrennPPV.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) KrennPPV.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) cosmoFns-package.Rd:34: 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
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.6Mb
    doc    1.2Mb
    libs   5.9Mb
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
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    help   1.0Mb
    libs   1.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
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:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
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:
> 
> ### Name: update_dev_pkg
> ### Title: Perform update of development version of a package
> ### Aliases: update_dev_pkg
> ### Keywords: data
> 
> ### ** Examples
> 
> ## Don't show: 
>  # using if(FALSE) because \dontrun could still be run by  --run-dontrun; #5421 
> ## End(Don't show)
>   if (FALSE) data.table::update_dev_pkg()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  7.64 0.16 10.07 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 ?) ========
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.1Mb
Package suggested but not available for checking: 'dblog'
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANWIN2.fb05.statistik.uni-dortmund.de:11491 (sockconn)
Execution halted
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'
Specified C++14: 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
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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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Package suggested but not available for checking: 'RDCOMClient'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.5Mb
    libs   1.2Mb
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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  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'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
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
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: \&
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
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Problems with news in 'NEWS.md':
No news entries found.
'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
'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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installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
Package suggested but not available for checking: 'dsBaseClient'
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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
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.0Mb
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installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.0Mb
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installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
'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':
  Cannot extract version info from the following section titles:
    20181118
'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  6.2Mb
  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
Specified C++11: please drop specification unless essential
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
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  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
checkRd: (-1) calibrate.Rd:151: Escaped LaTeX specials: \&
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installed size is  9.9Mb
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    help   1.5Mb
    libs   7.5Mb
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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    libs      1.0Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ExactData'
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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
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
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
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
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API call to R: 'match5'

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
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
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checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Found the following significant warnings:
  Rconnection.cc:282:52: warning: format '%p' expects argument of type 'void*', but argument 3 has type 'Rexp*' [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.3/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    Rcgi      3.0Mb
    cgi-bin   2.8Mb
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Undefined global functions or variables:
  init run
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'NNLM'
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
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) 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: \#
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Found the following significant warnings:
  fgsg.h:96:75: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:202:48: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:347:48: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:460:48: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:516:75: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:636:48: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:717:48: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:852:48: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:996:48: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.3/FGSG.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R         4.3Mb
    doc       1.9Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
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'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    lib    3.0Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fk_regression.Rd:32: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
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installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
GNU make is a SystemRequirements.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.6Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
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checkRd: (-1) block.Rd:150: Escaped LaTeX specials: \^ \^
checkRd: (-1) blockpick.Rd:114: Escaped LaTeX specials: \^ \^
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.7Mb
    libs  12.9Mb
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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
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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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installed size is 46.1Mb
  sub-directories of 1Mb or more:
    doc   44.3Mb
    libs   1.2Mb
':::' call which should be '::': 'graphics:::grid'
  See the note in ?`:::` about the use of this operator.
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(GauPro)
  > 
  > test_check("GauPro")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3064 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_kernel_model_and_kernels.R:1209'): EI minimize is right ──────
  `ei1` not equal to `eiinv`.
  17/101 mismatches (average diff: 0.0033)
  [71] 0.0519 - 0.0530 == -0.00105
  [72] 0.0549 - 0.0561 == -0.00120
  [73] 0.0574 - 0.0587 == -0.00137
  [74] 0.0590 - 0.0605 == -0.00156
  [75] 0.0595 - 0.0613 == -0.00177
  [76] 0.0587 - 0.0608 == -0.00202
  [77] 0.0563 - 0.0587 == -0.00232
  [78] 0.0519 - 0.0546 == -0.00270
  [79] 0.0452 - 0.0484 == -0.00324
  ...
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3064 ]
  Error: Test failures
  Execution halted
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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.
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installed size is 97.8Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    gdal     2.9Mb
    libs    83.4Mb
    proj     8.1Mb
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++14: please drop specification unless essential
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) estGF.Rd:106: Escaped LaTeX specials: \&
checkRd: (-1) estGF.Rd:107: Escaped LaTeX specials: \&
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installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
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checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.3Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
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installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs            4.3Mb
    test_data       2.2Mb
    vignette_data   1.1Mb
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
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
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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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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
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Malformed Description field: should contain one or more complete sentences.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
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checkRd: (-1) GUTS-package.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:201: Escaped LaTeX specials: \&
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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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installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs    1.0Mb
    shiny   4.3Mb
installed size is  8.1Mb
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    HaDeX   4.0Mb
    doc     4.0Mb
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installed size is  6.0Mb
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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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installed size is  5.0Mb
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    data   3.5Mb
    libs   1.3Mb
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Package suggested but not available for checking: 'ROI.plugin.mosek'
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    doc    2.1Mb
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installed size is  6.1Mb
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    data   6.1Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gurobi'
Package suggested but not available for checking: 'INLA'
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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'.
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installed size is  6.7Mb
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    libs      1.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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    data   5.5Mb
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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installed size is  5.6Mb
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    libs      1.0Mb
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GNU make is a SystemRequirements.
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installed size is  5.5Mb
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    R      1.5Mb
    data   2.3Mb
    libs   1.3Mb
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checkRd: (-1) maxControl.Rd:83: Escaped LaTeX specials: \&
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:
gradient close to zero (gradtol) 
5  iterations
estimate: 1.940473 
Function value: -33.70681 
> vcov(a)
           [,1]
[1,] 0.03764041
> ## Estimate with analytic gradient and hessian
> a <- maxLik(loglik, gradlik, hesslik, start=1)
> vcov(a)
           [,1]
[1,] 0.03765436
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  6.45 0.19 6.67 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 ?) ========
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    libs   1.5Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/MeshesTools.Rcheck/00install.out' for details.
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'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
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GNU make is a SystemRequirements.
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    mev v.1.9x
    mev v.1.8x
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/MinkowskiSum.Rcheck/00install.out' for details.
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installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
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installed size is 13.6Mb
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Problems with news in 'NEWS.md':
No news entries found.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
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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
Packages suggested but not available for checking:
  'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene'
'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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installed size is  5.2Mb
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    data   2.0Mb
    libs   1.5Mb
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installed size is  8.4Mb
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    R      1.9Mb
    data   4.5Mb
    libs   1.2Mb
installed size is  5.1Mb
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    libs   4.7Mb
checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
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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
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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  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
Problems with news in 'NEWS.md':
No news entries found.
Specified C++14: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
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installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'jpndistrict'
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Other ideas
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GNU make is a SystemRequirements.
checkRd: (-1) simulatePop.Rd:43: Escaped LaTeX specials: \&
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installed size is  7.2Mb
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    libs   1.6Mb
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Package suggested but not available for checking: 'cmdstanr'
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'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/OpenCL.Rcheck/00install.out' for details.
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installed size is  5.1Mb
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    libs   1.6Mb
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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
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    java     1.2Mb
    models   6.0Mb
Package suggested but not available for checking: 'openNLPmodels.en'
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Malformed Title field: should not end in a period.
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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'LazyData' is specified without a 'data' directory
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installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
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'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:
    lib    2.8Mb
    libs   2.4Mb
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'LazyData' is specified without a 'data' directory
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installed size is  7.6Mb
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    R      4.4Mb
    data   3.1Mb
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'LazyData' is specified without a 'data' directory
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   1.3Mb
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installed size is  5.9Mb
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    doc       1.5Mb
    extdata   3.1Mb
    libs      1.0Mb
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checkRd: (-1) GarlandJanis.varcov.Rd:7: 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
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'monocle3', 'ProjecTILs', 'SeuratWrappers'
'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: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/PolygonSoup.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
Problems with news in 'NEWS.md':
No news entries found.
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
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
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
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata  11.6Mb
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
Specified C++14: 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  5.1Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      1.2Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    doc        4.0Mb
    examples   2.5Mb
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: \#
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
'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
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.0Mb
'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
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.
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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.6Mb
    libs   1.1Mb
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
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.4Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.3/RcppParallel/include/RcppParallel/RMatrix.h:18:24: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.3/Ravages.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'g++.exe (GCC) 12.2.0'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'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 24.3Mb
  sub-directories of 1Mb or more:
    cont  24.2Mb
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Encountered the following conversion/validation errors:
'CreateProcess' failed to run 'd:\rtools43\x86_64-w64-mingw32.static.posix\bin\tidy.exe -language en -qe --drop-empty-elements no D:\temp\Rtmp8gQUJT\file1d678484c27d'
Specified C++11: please drop specification unless essential
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
Package suggested but not available for checking: 'ROpenOffice'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.2Mb
    po    2.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rcplex.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    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
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    include  45.3Mb
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.5Mb
  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
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
'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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      1.3Mb
Specified C++11: please drop specification unless essential
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++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
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'PercentCodes'
GNU make is a SystemRequirements.
'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'
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
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
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
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
'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
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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
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:
39 8  1    g
40 1  2    j
41 1  1    r
42 4  3    t
43 2  7    g
44 1  6    s
45 6 10    f
46 6  2    a
47 2  4    e
48 7 24    c
49 8  1    g
50 1  2    j
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  10.28 0.48 11.04 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 ?) ========
Specified C++11: please drop specification unless essential
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) Rglpk_read_file.Rd:6: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
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
installed size is  7.8Mb
  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
'LazyData' is specified without a 'data' directory
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]
See 'd:/Rcompile/CRANpkg/local/4.3/rJava.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
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)
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/4.3/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
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    include   2.9Mb
    libs      2.2Mb
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
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: \$
Specified C++14: please drop specification unless essential
Specified C++14: 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
Specified C++11: please drop specification unless essential
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: \_
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.3Mb
Specified C++11: please drop specification unless essential
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) addLR.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) addLRinv.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) adtestWrapper.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) arcticLake.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cenLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) cenLRinv.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) expenditures.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) gemas.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) machineOperators.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) plot.imp.Rd:138: Escaped LaTeX specials: \&
checkRd: (-1) robCompositions-package.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) skyeLavas.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) variation.Rd:45: Escaped LaTeX specials: \&
Specified C++14: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
Found the following significant warnings:
  d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\emmintrin.h:131:24: 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/4.3/RobustGaSP.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'g++.exe (GCC) 12.2.0'
'LazyData' is specified without 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: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/ROracle.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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
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 significant warnings:
  standalone.c:160:301: warning: format '%ld' expects argument of type 'long int', but argument 16 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:3788:97: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4133:62: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4435:118: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4804:106: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4824:147: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4836:114: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4864:121: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4870:139: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  qap_encode.c:142:17: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'rlen_t' {aka 'long long int'} [-Wformat=]
  websockets.c:513:119: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.3/Rserve.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
GNU make is a SystemRequirements.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/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
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++14: please drop specification unless essential
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.8Mb
    libs   8.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rstpm2)
  Loading required package: survival
  Loading required package: splines
  
  Attaching package: 'rstpm2'
  
  The following object is masked from 'package:survival':
  
      colon
  
  > 
  > test_check("rstpm2")
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 92 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_base.R:21'): offset ──────────────────────────────────────────
  max(abs(expr - value)) is not strictly less than `eps`. Difference: 0.995
  Backtrace:
      ▆
   1. └─rstpm2 (local) expect_eps(coef(fit)[1], -6.6465454, 1e-05) at test_base.R:21:4
   2.   └─testthat::expect_lt(max(abs(expr - value)), eps) at test_base.R:8:14
  ── Failure ('test_base.R:22'): offset ──────────────────────────────────────────
  max(abs(expr - value)) is not strictly less than `eps`. Difference: 0.00167
  Backtrace:
      ▆
   1. └─rstpm2 (local) expect_eps(coef(fit)[2], -0.3601438, 1e-05) at test_base.R:22:4
   2.   └─testthat::expect_lt(max(abs(expr - value)), eps) at test_base.R:8:14
  
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 92 ]
  Error: Test failures
  Execution halted
installed size is 38.8Mb
  sub-directories of 1Mb or more:
    libs    1.1Mb
    swipl  37.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) run.jags.study.Rd:67: Escaped LaTeX specials: \$
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:
> nameEx("writeBinFragments")
> ### * writeBinFragments
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: writeBinFragments
> ### Title: Writes binary data to disjoint sections of a connection or a
> ###   file
> ### Aliases: writeBinFragments.default writeBinFragments
> ### Keywords: IO
> 
> ### ** Examples
> ## Not run: # See example(readBinFragments.connection)
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  232.93 783.83 1045.9 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 ?) ========
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
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'.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'unix'
Specified C++14: please drop specification unless essential
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   3.3Mb
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
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
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
'LazyData' is specified without a 'data' directory
'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
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++14: please drop specification unless essential
Package suggested but not available for checking: 'doMC'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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:
> ### Aliases: contrast-theory Intensity Luminance
> 
> ### ** Examples
> 
> Intensity(color = c('black', 'white', '#E76BF3'))
  black   white #E76BF3 
   0.00  255.00  159.58 
> 
> Luminance(color = c('black', 'white', '#E76BF3'))
    black     white   #E76BF3 
0.0000000 1.0000000 0.3397538 
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  81.87 1.72 83.86 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 ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/sf.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
checkRd: (-1) gPLS.Rd:72: Escaped LaTeX specials: \^
checkRd: (-1) gPLS.Rd:74: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:67: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:69: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:75: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:77: Escaped LaTeX specials: \^
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.0Mb
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: 'cmdstanr'
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
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.
'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'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Specified C++14: please drop specification unless essential
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 significant warnings:
  D:/RCompile/CRANpkg/lib/4.3/RcppParallel/include/tbb/concurrent_hash_map.h:343:23: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  D:/RCompile/CRANpkg/lib/4.3/RcppParallel/include/tbb/internal/_concurrent_queue_impl.h:744:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  D:/RCompile/CRANpkg/lib/4.3/RcppParallel/include/tbb/internal/_concurrent_queue_impl.h:1003:21: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  D:/RCompile/CRANpkg/lib/4.3/RcppParallel/include/tbb/internal/_concurrent_unordered_impl.h:67:36: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  D:/RCompile/CRANpkg/lib/4.3/RcppParallel/include/RcppParallel/RMatrix.h:18:24: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.3/skm.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.2.0'
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
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.
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
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: 'doMC'
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.3Mb
    libs   1.7Mb
'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
Error(s) in re-building vignettes:
Error in readRDS(mapfile) : error reading from connection
Error: unable to load R code in package 'tools'
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    2.1Mb
    libs   1.7Mb
checkRd: (-1) plot.som.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) som.Rd:128: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.1Mb
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:
> pkgname <- "sparkhail"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('sparkhail')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
> nameEx("hail_context")
> ### * hail_context
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: hail_context
> ### Title: Create Hail Context
> ### Aliases: hail_context
> 
> ### ** Examples
> 
> library(sparklyr)

Attaching package: 'sparklyr'

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

    filter

> 
> sc <- spark_connect(master = "spark://HOST:PORT", config = hail_config())
======== End of example output (where/before crash/hang up occured ?) ========
Specified C++11: please drop specification unless essential
Warning in grep("^[ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789]",  :
  TRE pattern compilation error 'Out of memory'
Error in grep("^[ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789]",  : 
  invalid regular expression '^[ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789]', reason 'Out of memory'
Calls: <Anonymous> ... .find_calls_in_package_code -> list_files_with_type -> grep
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Loading this package had a fatal error status code 301
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
    etc   1.4Mb
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'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
checkRd: (-1) B_sraAutoreg.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) C_sraMechanistic.Rd:68: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
--- re-building 'classification.Rmd' using rmarkdown
--- finished re-building 'classification.Rmd'

--- re-building 'clustering.Rmd' using rmarkdown
Warning in strsplit(generic, "::") :
  TRE pattern compilation error 'Out of memory'
Error: processing vignette 'clustering.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'rlang', details:
  call: strsplit(generic, "::")
  error: invalid regular expression '::', reason 'Out of memory'
--- failed re-building 'clustering.Rmd'

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
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 changes
    Bug fixes
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    include   9.4Mb
Specified C++14: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    To do
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    1.7Mb
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
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'
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.1Mb
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
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
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'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
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
'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:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'winpath.R' [2s]
Running the tests in 'tests/winpath.R' failed.
Complete output:
  > library(switchr)
  > ## if(getOption("repos")["CRAN"] == "@CRAN@")
  > ##     chooseCRANmirror(ind=1L)
  > graceful_inet(TRUE)
  [1] TRUE
  > checkUrlRoundtrip = function(pth) {
  +     pth = switchr:::normalizePath2(pth)
  +     furl = switchr:::makeFileURL(pth)
  +     pth2 = switchr:::fileFromFileURL(furl)
  +     if(pth != pth2)
  +         stop("Round trip result (", pth2, ") does not match original (", pth, ") when creating file URLs")
  + }
  > 
  > ## regression test to ensure that the roundtrip
  > ## between path and file url is working properly
  > checkUrlRoundtrip(getwd())
  > checkUrlRoundtrip(tempdir())
  > if(switchr:::isWindows())
  +     checkUrlRoundtrip("\\\\localhost\\c$")
  > 
  > ## regreossion test to ensure that package dependencies
  > ## are added to the dontunload list when a package
  > ## is specified
  > bef = switchrDontUnload()
  > af = switchrDontUnload("knitr")
  Switchr needs a default CRAN mirror set via R options. Using the cloud mirror. This happens only when no CRAN mirror is selected *and* the BiocInstaller package is not installed.
  > stopifnot(all(c("stringr", "stringi", "magrittr") %in% af))
  Error: all(c("stringr", "stringi", "magrittr") %in% af) is not TRUE
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.4Mb
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
'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.
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Specified C++11: please drop specification unless essential
installed size is 99.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    gdal   2.9Mb
    libs  85.6Mb
    proj   8.1Mb
Package suggested but not available for checking: 'gurobi'
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
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
'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: \&
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    examples  12.6Mb
    include    3.6Mb
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'taxidata'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'TreeDistData'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes
Running examples in 'TrustVDJ-Ex.R' failed
The error most likely occurred in:

> ### Name: .Read10x_consensus
> ### Title: Read 10x consensus file
> ### Aliases: .Read10x_consensus
> 
> ### ** Examples
> 
> consensus_file = system.file('extdata', '10x_consensus_annotations.csv.gz', package = 'TrustVDJ')
> consensus = .Read10x_consensus(consensus_file = consensus_file, verbose = FALSE)
Datei nicht gefunden
Warning in system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  :
  running command 'C:\Windows\system32\cmd.exe /c dir' had status 1
Error in system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  : 
  'CreateProcess' failed to run 'C:\Windows\system32\cmd.exe /c dir'
Calls: .Read10x_consensus ... Sys.readlink2 -> sapply -> lapply -> FUN -> shell -> system
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Updates for the development version (0.1.0.9000) on Github
Codoc mismatches from documentation object 'ttdo_boolean_and_message_tests':
expect_warning_xl
  Code: function(current, pattern = ".*", class = "warning", info =
                 NA_character_, strict = FALSE, ...)
  Docs: function(current, pattern = ".*", class = "warning", info =
                 NA_character_, ...)
  Argument names in code not in docs:
    strict
  Mismatches in argument names:
    Position: 5 Code: strict Docs: ...
expect_message_xl
  Code: function(current, pattern = ".*", class = "message", info =
                 NA_character_, strict = FALSE, ...)
  Docs: function(current, pattern = ".*", class = "message", info =
                 NA_character_, ...)
  Argument names in code not in docs:
    strict
  Mismatches in argument names:
    Position: 5 Code: strict Docs: ...
checkRd: (-1) lindner.Rd:44: Escaped LaTeX specials: \_
'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
GNU make is a SystemRequirements.
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:  5.5 0.62 6.14 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 ?) ========
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
Package suggested but not available for checking: 'USAboundariesData'
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
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: \&
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  15.3Mb
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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.0Mb
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.2Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    NEW FEATURES
'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:
    vortexRdata pre-1.0.3
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: 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
'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
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
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.
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    java  24.5Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.2Mb
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
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
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
'LazyData' is specified without 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:
  'RGtk2', 'gWidgets2RGtk2'
'LazyData' is specified without 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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown packages ‘HI’, ‘MHadaptive’ 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
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
Found the following files/directories:
  ‘table_AeRobiology’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package which this enhances but not available for checking: ‘asreml’
'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
'LazyData' is specified without 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
Encountered the following conversion/validation errors:
as.data.frame.feem.Rd:11: condition must be plain text
cmf.Rd:16: condition must be plain text
feem.Rd:19: condition must be plain text
feemflame.Rd:55: condition must be plain text
feemife.Rd:78: condition must be plain text
feemindex.Rd:83: condition must be plain text
feemjackknife.Rd:78: condition must be plain text
feemparafac.Rd:82: condition must be plain text
feemscatter.Rd:36: condition must be plain text
feemsplithalf.Rd:43: condition must be plain text
marine.colours.Rd:46: condition must be plain text
whittaker2.Rd:45: condition must be plain text
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
'LazyData' is specified without 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:
  ‘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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘ARTP’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
GNU make is a SystemRequirements.
'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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘exemplary_input1.txt’ ‘exemplary_input2.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
Package which this enhances but not available for checking: ‘rPython’
'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
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
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
GNU make is a SystemRequirements.
'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
'LazyData' is specified without a 'data' directory
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’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘dump.txt’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘alist.txt’ ‘rpkg’
'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
'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: ‘SoDA’
'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: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
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’.
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’
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
'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
'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
'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
'LazyData' is specified without 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
Package suggested but not available for checking: ‘INLA’
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'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: 'RGtk2', 'cairoDevice'
'LazyData' is specified without 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: ‘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
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: ‘gvcm.cat’
Unknown package ‘gvcm.cat’ 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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RxODE’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tmp.txt’
Found the following files/directories:
  ‘MDA231_tree.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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘GAMBoost’
'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’
'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
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
Found the following files/directories:
  ‘hotcold.csv’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CirceR’
Found the following files/directories:
  ‘out.png’ ‘out1.txt’ ‘out2.txt’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Found the following files/directories:
  ‘stepres00.txt’
'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’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘clusterhap_reports’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘tobit1’
'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: ‘PopGenome’
'LazyData' is specified without a 'data' directory
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickdemo.Rmd’ using rmarkdown
Quitting from lines 38-46 (quickdemo.Rmd) 
Error: processing vignette ‘quickdemo.Rmd’ failed with diagnostics:
ℹ In argument: `his.lag = if_else(...)`.
ℹ In group 1: `ID = 1`.
Caused by error in `nth()`:
! Can't convert `default` <character> to match type of `x` <double>.
--- failed re-building ‘quickdemo.Rmd’

--- re-building ‘selectionbias.Rmd’ using rmarkdown
Quitting from lines 154-164 (selectionbias.Rmd) 
Error: processing vignette ‘selectionbias.Rmd’ failed with diagnostics:
ℹ In argument: `his.lag = if_else(...)`.
ℹ In group 1: `ID = 1001`.
Caused by error in `nth()`:
! Can't convert `default` <character> to match type of `x` <double>.
--- failed re-building ‘selectionbias.Rmd’

SUMMARY: processing the following files failed:
  ‘quickdemo.Rmd’ ‘selectionbias.Rmd’

Error: Vignette re-building failed.
Execution halted
'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’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
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
Found the following significant warnings:
  Warning: replacing previous import ‘geiger::rescale’ by ‘phytools::rescale’ when loading ‘convevol’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/convevol.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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘covfefe_inauguration.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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [37s/49s]
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(dail)
  > 
  > test_check("dail")
  No internet connection or data source broken.
  Downloading 2015 dataset.
  trying URL 'https://dadosabertos-download.cgu.gov.br/FalaBR/Arquivos_FalaBR_Filtrado/Arquivos_csv_2015.zip'
  Content type 'application/x-zip-compressed' length 45584203 bytes (43.5 MB)
  ==================================================
  downloaded 43.5 MB
  
  ℹ Using "','" as decimal and "'.'" as grouping mark. Use `read_delim()` for more control.
  Downloading 2016 dataset.
  trying URL 'https://dadosabertos-download.cgu.gov.br/FalaBR/Arquivos_FalaBR_Filtrado/Arquivos_csv_2016.zip'
  Content type 'application/x-zip-compressed' length 52095795 bytes (49.7 MB)
  ==================================================
  downloaded 49.7 MB
  
  ℹ Using "','" as decimal and "'.'" as grouping mark. Use `read_delim()` for more control.
  Ended query.
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-appeals.R:61'): test the arguments agency, year, answer and search ──
  nrow(df10) (`actual`) not equal to 5 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (5)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1 ]
  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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pca3d’
Package suggested but not available for checking: ‘dash’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dash’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dash’
Package suggested but not available for checking: ‘dash’
'LazyData' is specified without 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:
  ‘my new data set.rds’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘stubthat’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [112s/127s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dbplyr)
  > 
  > test_check("dbplyr")
  Registering testing src: sqlite OK
  [ FAIL 1 | WARN 0 | SKIP 294 | PASS 1312 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Need at least two srcs to compare (6)
  • No MariaDB (4)
  • No mssql (13)
  • No postgres (7)
  • On CRAN (258)
  • `grouped_df()` needs a `name_repair` argument (1)
  • identical(Sys.getenv("GITHUB_POSTGRES"), "true") is not TRUE (1)
  • not clear whether test makes sense (2)
  • not yet correctly supported (1)
  • tidyselect issue #221 (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-rows.R:767'): `rows_upsert()` works with `in_place = TRUE` and `returning` ──
  get_returned_rows(df_upserted) (`actual`) not equal to tibble(x = 4, y = 24) (`expected`).
  
    `attr(actual, 'row.names')`: 1 2 3
  `attr(expected, 'row.names')`: 1    
  
  actual vs expected
                  x  y
  - actual[1, ]   2 22
  - actual[2, ]   3 23
    actual[3, ]   4 24
  
    `actual$x`: 2 3 4
  `expected$x`:     4
  
    `actual$y`: 22 23 24
  `expected$y`:       24
  
  [ FAIL 1 | WARN 0 | SKIP 294 | PASS 1312 ]
  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
'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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-portable flags in variable ‘PKG_FFLAGS’:
  -std=f2008
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'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:
  ‘smd_table.docx’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Documentation.Rmd’ using rmarkdown
Quitting from lines 82-83 (Documentation.Rmd) 
Error: processing vignette ‘Documentation.Rmd’ failed with diagnostics:
Cannot load glue from the private library
--- failed re-building ‘Documentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
'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: ‘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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Package suggested but not available for checking: ‘rrelaxiv’
'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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘discreteMTP’
Unknown package ‘discreteMTP’ 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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
'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’.
Found the following calls to attach():
File ‘doSNOW/R/doSNOW.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Package suggested but not available for checking: ‘OpenMPController’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
'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
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [18s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dtplyr)
  > 
  > test_check("dtplyr")
  [ FAIL 1 | WARN 1 | SKIP 25 | PASS 603 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (24)
  • transmuting grouping vars with nesting is not supported (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-step-subset-slice.R:122'): slice_*() checks for empty ... ──────
  Error in `slice_head(dt, 5)`: `n` must be explicitly named.
  i Did you mean `slice_head(n = 5)`?
  Backtrace:
      ▆
   1. ├─testthat::expect_error(slice_head(dt, 5), class = "rlib_error_dots_nonempty") at test-step-subset-slice.R:122:2
   2. │ └─testthat:::expect_condition_matching(...)
   3. │   └─testthat:::quasi_capture(...)
   4. │     ├─testthat (local) .capture(...)
   5. │     │ └─base::withCallingHandlers(...)
   6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   7. └─dplyr::slice_head(dt, 5)
   8.   └─dplyr:::check_slice_unnamed_n_prop(..., n = n, prop = prop)
   9.     └─rlang::abort(bullets, call = error_call)
  
  [ FAIL 1 | WARN 1 | SKIP 25 | PASS 603 ]
  Error: Test failures
  Execution halted
'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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
'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
'LazyData' is specified without a 'data' directory
Codoc mismatches from documentation object ‘IQLearnFS_VHet-methods’:
\S4method{qqplot}{IQLearnFS_VHet}
  Code: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ...)
  Docs: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ..., conf.level =
                 NULL, conf.args = list(exact = NULL, simulate.p.value
                 = FALSE, B = 2000, col = NA, border = NULL))
  Argument names in docs not in code:
    conf.level conf.args
'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
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
'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
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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Package suggested but not available for checking: ‘osmar’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘file.path(temp_dir, gp2.csv)’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RStoolbox’
Found the following files/directories:
  ‘Environmental variables.csv’ ‘Inf.txt’ ‘List of species.csv’ ‘Mean
  overlap among taxa.csv’ ‘Overlap among taxa.csv’ ‘Pointsize.dat’
  ‘Polar coordinates.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
Package suggested but not available for checking: ‘epidict’
GNU make is a SystemRequirements.
'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
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  Warning: replacing previous import ‘geiger::rescale’ by ‘phytools::rescale’ when loading ‘evobiR’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/evobiR.Rcheck/00install.out’ for details.
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
Package suggested but not available for checking: ‘ExactData’
'LazyData' is specified without a 'data' directory
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cec2013’
'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
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: ‘exuberdata’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘Bogota.tex’ ‘DogBreeds1.tex’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in ‘?.onAttach’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘default5.eps’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘coxKM’
'LazyData' is specified without 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 ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

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
.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
Package suggested but not available for checking: ‘NNLM’
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
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
Unexported objects imported by ‘:::’ calls:
  ‘fdapace:::GCVLwls1D1’ ‘fdapace:::GetSmoothedMeanCurve’
  ‘fdapace:::HandleNumericsAndNAN’ ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.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
'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: ‘MicrobeDS’
Package suggested but not available for checking: ‘RStoolbox’
Running examples in ‘fieldRS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rankPlots
> ### Title: rankPlots
> ### Aliases: rankPlots
> 
> ### ** Examples
> 
> {
+ 
+ require(raster)
+ require(RStoolbox)
+ require(ggplot2)
+ 
+ # read raster data
+ r <- brick(system.file("extdata", "ndvi.tif", package="fieldRS"))
+ 
+ # read road information
+ data(roads)
+ 
+ # unsupervised classification with kmeans
+ uc <- unsuperClass(r, nSamples=5000, nClasses=5)$map
+ 
+ # derive potential sampling plots
+ pp <- derivePlots(uc, 1000)
+ 
+ # plot ranking
+ pp@data <- rankPlots(uc, pp, roads)
+ 
+ # plot output
+ gp <- fortify(pp, region="ranking")
+ ggplot(gp, aes(x=long, y=lat, group=group, fill=as.numeric(id))) + 
+ geom_polygon() + scale_fill_continuous(name="Ranking")
+ 
+ }
Loading required package: raster
Loading required package: sp
Loading required package: RStoolbox
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘RStoolbox’
Loading required package: ggplot2
Error in unsuperClass(r, nSamples = 5000, nClasses = 5) : 
  could not find function "unsuperClass"
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fieldRS.Rmd’ using rmarkdown
Quitting from lines 21-28 (fieldRS.Rmd) 
Error: processing vignette ‘fieldRS.Rmd’ failed with diagnostics:
there is no package called 'RStoolbox'
--- failed re-building ‘fieldRS.Rmd’

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

Error: Vignette re-building failed.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
'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
Packages suggested but not available for checking:
  'benchden', '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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘flux.CH4.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
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
Running examples in ‘forceR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_strongest_peaks
> ### Title: Find Peaks
> ### Aliases: find_strongest_peaks
> 
> ### ** Examples
> 
> require(dplyr)
Loading required package: dplyr

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> # Using the forceR::df.all.200.tax dataset:
> 
> # reduce dataset
> df.all.200.tax_filtered <- forceR::df.all.200.tax %>%
+   filter(species == "species_A")
> 
> # find strongest peaks
> peaks.df <- find_strongest_peaks(df = df.all.200.tax_filtered,
+                                  no.of.peaks = 5)
Error in `slice()`:
! Arguments in `...` must be passed by position, not name.
✖ Problematic argument:
• n = 1
Backtrace:
    ▆
 1. ├─forceR::find_strongest_peaks(df = df.all.200.tax_filtered, no.of.peaks = 5)
 2. │ └─curr.plot.window %>% slice(n = 1) %>% pull(specimen)
 3. ├─dplyr::pull(., specimen)
 4. ├─dplyr::slice(., n = 1)
 5. └─dplyr:::slice.data.frame(., n = 1)
 6.   └─rlang::check_dots_unnamed()
 7.     └─rlang:::action_dots(...)
 8.       ├─base (local) try_dots(...)
 9.       └─rlang (local) action(...)
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘forceR.Rmd’ using rmarkdown
Quitting from lines 518-523 (forceR.Rmd) 
Error: processing vignette ‘forceR.Rmd’ failed with diagnostics:
Arguments in `...` must be passed by position, not name.
✖ Problematic argument:
• n = 1
--- failed re-building ‘forceR.Rmd’

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

Error: Vignette re-building failed.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: 'dggrids', 'INLA'
Unknown package ‘frm’ in Rd xrefs
Unknown package ‘frm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
'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
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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘checkdata.csv’ ‘gbmforest.sas’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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.
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
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’.
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
Malformed Description field: should contain one or more complete sentences.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘RGtk2’
Package suggested but not available for checking: ‘condSURV’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 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
'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: ‘ggOceanMapsData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  'nlmixr', '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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Unknown package ‘IC2’ 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
Package suggested but not available for checking: ‘mlr3proba’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 objects imported by ‘:::’ calls:
  ‘gargle:::secret_can_decrypt’ ‘gargle:::secret_read’
  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
Unexported objects imported by ‘:::’ calls:
  ‘gargle:::secret_can_decrypt’ ‘gargle:::secret_read’
  See the note in ?`:::` about the use of this operator.
'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’
Unknown package ‘gvcm.cat’ 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
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
'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:
  'taxstats', 'taxstats1516'
'LazyData' is specified without a 'data' directory
Running examples in ‘GREMLINS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotMBM
> ### Title: Plot the mesoscopic view of the estimated MBM
> ### Aliases: plotMBM
> 
> ### ** Examples
> 
> namesFG <- c('A','B')
> list_pi <- list(c(0.5,0.5),c(0.3,0.7)) # prop of blocks in each FG
> E  <-  rbind(c(1,2),c(2,2)) # architecture of the multipartite net.
> typeInter <- c( "inc","diradj")
> v_distrib <- c('gaussian','bernoulli')
> list_theta <- list()
> list_theta[[1]] <- list()
> list_theta[[1]]$mean  <- matrix(c(6.1, 8.9, 6.6, 3), 2, 2)
> list_theta[[1]]$var  <-  matrix(c(1.6, 1.6, 1.8, 1.5),2, 2)
> list_theta[[2]] <- matrix(c(0.7,1.0, 0.4, 0.6),2, 2)
> list_Net <- rMBM(v_NQ = c(30,30),E , typeInter, v_distrib, list_pi,
+                 list_theta, namesFG = namesFG, seed = 2)$list_Net
> res_MBMsimu <- multipartiteBM(list_Net, v_distrib,
+                               namesFG = c('A','B'), v_Kinit = c(2,2),
+                               nbCores = 2,initBM = FALSE)
[1] "------------Nb of entities in each functional group--------------"
 A  B 
30 30 
[1] "------------Probability distributions on each network--------------"
[1] "gaussian"  "bernoulli"
[1] "-------------------------------------------------------------------"
[1] " ------ Searching the numbers of blocks starting from [ 2 2 ] blocks"
[1] "ICL : -2028.78 . Nb of blocks: [ 2 2 ]"
[1] "Best model------ ICL : -2028.78 . Nb of clusters: [ 2 2 ] for [ A , B ] respectively"
> plotMBM(res_MBMsimu)
Error in i_set_edge_attr(graph = graph, name = name, value = value, check = FALSE) : 
  Length of new attribute value must be 1 or 0, the number of target edges, not 8
Calls: plotMBM -> %>% -> set_edge_attr -> i_set_edge_attr
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EcologicalNetwork.Rmd’ using rmarkdown
Quitting from lines 130-131 (EcologicalNetwork.Rmd) 
Error: processing vignette ‘EcologicalNetwork.Rmd’ failed with diagnostics:
Length of new attribute value must be 1 or 0, the number of target edges, not 14
--- failed re-building ‘EcologicalNetwork.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
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.
'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
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’
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
'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
Found the following problems:
GWASinlps.Rd:187:1: Warning: trimming empty <h4>
'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:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [9s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hablar)
  > test_check("hablar")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 418 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test.ifs.R:53'): if_else_ ─────────────────────────────────────────
  `if_else_(c(T, F, NA), 1, 1L)` did not throw an error.
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 418 ]
  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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘helda-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kmeans_procedure
> ### Title: K-means procedure
> ### Aliases: kmeans_procedure
> ### Keywords: cluster kmeans sizes
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> data <- iris %>% select(Sepal.Length, Sepal.Width, Petal.Length, Petal.Width)
> features <- colnames(data)
> result <- kmeans_procedure(data = data, columns = features, threshold_min = 2, threshold = 10,
+ verbose=FALSE, seed=10)
Error in `between()`:
! Can't combine `x` <table[1d]> and `left` <double>.
Backtrace:
     ▆
  1. ├─helda::kmeans_procedure(...)
  2. │ └─dplyr::between(...)
  3. │   └─vctrs::vec_cast_common(!!!args)
  4. └─vctrs (local) `<fn>`()
  5.   └─vctrs::vec_default_ptype2(...)
  6.     ├─base::withRestarts(...)
  7.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
  8.     │   └─base (local) doWithOneRestart(return(expr), restart)
  9.     └─vctrs::stop_incompatible_type(...)
 10.       └─vctrs:::stop_incompatible(...)
 11.         └─vctrs:::stop_vctrs(...)
 12.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘synbreed’
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
‘:::’ call which should be ‘::’: ‘ggplot2:::guide_axis’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ‘:::’ calls:
  ‘ggplot2:::build_guides’ ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘colorfulVennPlot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 suggested but not available for checking: ‘trackr’
Package which this enhances but not available for checking: ‘HadoopStreaming’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘glmmADMB’
Package suggested but not available for checking: ‘ROI.plugin.mosek’
'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: 'RGtk2', 'cairoDevice'
'LazyData' is specified without 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
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
'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:
  ‘AIC.txt’ ‘AICc.txt’ ‘IAS.pdf’ ‘IAS2.pdf’ ‘IAS3.pdf’
  ‘P.microlepis-AIC.txt’ ‘P.microlepis-AICc.txt’ ‘P.microlepis-IAS.pdf’
  ‘P.microlepis-IAS2.pdf’ ‘P.microlepis-IAS3.pdf’
'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: ‘SparkR’
'LazyData' is specified without 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: ‘icd’
Package suggested but not available for checking: ‘ICBayes’
'LazyData' is specified without 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 suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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
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’
'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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘surveyspec’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
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'
'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
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
'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: ‘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
'LazyData' is specified without 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:
  ‘song.wav’ ‘song4karaoke.wav’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘Killed after ’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘VARSEDIG’
Unknown package ‘VARSEDIG’ in Rd xrefs
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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:
  Warning: replacing previous import ‘dplyr::where’ by ‘imager::where’ when loading ‘LARGB’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/LARGB.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘example.llo’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ergm.userterms’
Unknown package ‘ergm.userterms’ in Rd xrefs
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 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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:
  'gWidgets', 'gWidgetsRGtk2', '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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘tTestTable.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Dependence on R version ‘4.0.3’ not with patchlevel 0
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kerdiest’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘test’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
'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: ‘RGtk2’
'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: ‘scrubr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘flashier’
'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’
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without 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
Found the following files/directories:
  ‘utilities.R’
'LazyData' is specified without 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:
  ‘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
'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: ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MethylCapSig’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘genuMet’
'LazyData' is specified without a 'data' directory
Running examples in ‘metacore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check_inconsistent_labels
> ### Title: Optional checks to consistency of metadata
> ### Aliases: check_inconsistent_labels check_inconsistent_types
> ###   check_inconsistent_formats
> 
> ### ** Examples
> 
> ## EXAMPLE WITH DUPLICATES
> # Loads in a metacore obj called metacore
> load(metacore_example("pilot_ADaM.rda"))
> check_inconsistent_labels(metacore)
Error in `mutate()`:
ℹ In argument: `across(...)`.
ℹ In group 3: `var1 = "CHG"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
     ▆
  1. ├─metacore::check_inconsistent_labels(metacore)
  2. │ └─metacore:::basic_check(label, metacore)
  3. │   └─... %>% select(variable = var1, everything())
  4. ├─dplyr::select(., variable = var1, everything())
  5. ├─dplyr::summarise(...)
  6. ├─dplyr::group_by(...)
  7. ├─dplyr::mutate(...)
  8. ├─dplyr:::mutate.data.frame(...)
  9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
 10. │   ├─base::withCallingHandlers(...)
 11. │   └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 12. │     ├─base::withCallingHandlers(...)
 13. │     └─mask$eval_all_mutate(quo)
 14. │       └─dplyr (local) eval()
 15. └─dplyr:::dplyr_internal_error("dplyr:::mutate_incompatible_size", `<named list>`)
 16.   └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
Execution halted
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Running ‘testthat.R’ [28s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(meteR)
  > 
  > test_check("meteR")
  1    0.00146    0.00146   [1] TRUE
  2    0.000162    0.000162   [1] TRUE
  3    0.000155    0.000155   [1] TRUE
  4    0.00464    0.00464   [1] TRUE
  5    0.007085    0.007085   [1] TRUE
  6    0.00511    0.00511   [1] TRUE
  7    0.00261    0.00261   [1] TRUE
  8    0.00279    0.00279   [1] TRUE
  9    0.021    0.021   [1] TRUE
  10    0.00823    0.00823   [1] TRUE
  11    0.0168    0.0168   [1] TRUE
  12    0.0135    0.0135   [1] TRUE
  13    0.0228    0.0228   [1] TRUE
  14    0.000174    0.000174   [1] TRUE
  15    0.000254    0.000254   [1] TRUE
  16    0.00042    0.00042   [1] TRUE
  17    0.000244    0.000244   [1] TRUE
  18    0.000488    0.000488   [1] TRUE
  19    0.000342    0.000341   [1] TRUE
  20    0.00168    0.00168   [1] TRUE
  21    5.9e-05    5.92e-05   [1] TRUE
  22    4.3e-05    4.27e-05   [1] TRUE
  23    0.000117    0.000117   [1] TRUE
  24    0.061    0.061   [1] TRUE
  25    0.003175    0.003175   [1] TRUE
  26    0.003872    0.003872   [1] TRUE
  27    0.134    0.134   [1] TRUE
  28    0.0189    0.0189   [1] TRUE
  29    0.00109    0.00109   [1] TRUE
  simulating data that conform to state variables: 
  attempt 1 
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_zScore.R:11'): z score for logLik is approx chi-squared ──────
  ... < 0.05 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.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
'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
Package unavailable to check Rd xrefs: ‘DAPAR’
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without 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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘AnalyzeFMRI’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mixRasch’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
Found the following significant warnings:
  ./mlpack/core/data/save_impl.hpp:107:40: warning: ‘bool arma::Mat<eT>::quiet_save(std::ostream&, arma::file_type) const [with eT = long unsigned int; std::ostream = std::basic_ostream<char>]’ is deprecated [-Wdeprecated-declarations]
  ./mlpack/core/data/save_impl.hpp:128:43: warning: ‘bool arma::Mat<eT>::quiet_save(std::ostream&, arma::file_type) const [with eT = long unsigned int; std::ostream = std::basic_ostream<char>]’ is deprecated [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mlpack.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘Flury’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alstructure’

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Package suggested but not available for checking: ‘ArchR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘MortalityLaws’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
'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
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
'LazyData' is specified without 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:
  ‘test.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [409s/452s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(multicolor)
  Colors cannot be applied in this environment. Please use another application, such as RStudio or a color-enabled terminal.
  Colors cannot be applied in this environment. Please use another application, such as RStudio or a color-enabled terminal.
  > 
  > test_check("multicolor")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 29 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • use_color() is not TRUE (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-multicolor.R:103'): colors(), including grays, rainbow, and rbg work ──
  `suppressMessages(...)` produced warnings.
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 29 ]
  Error: Test failures
  Execution halted
'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: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘asreml’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
'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
'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: ‘re2r’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Running examples in ‘netmeta-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: netcontrib
> ### Title: Contribution matrix in network meta-analysis
> ### Aliases: netcontrib print.netcontrib
> ### Keywords: contribution
> 
> ### ** Examples
> 
> # Use the Woods dataset
> #
> data("Woods2010")
> p1 <- pairwise(treatment, event = r, n = N,
+   studlab = author, data = Woods2010, sm = "OR")
> 
> net1 <- netmeta(p1)
> cm <- netcontrib(net1)
Error: node stack overflow
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
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'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘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
'LazyData' is specified without 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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without 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:
  'originr', 'parallelsugar'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘openNLPmodels.en’
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘result.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘CorShrink’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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’
'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
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
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: ‘PythonInR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘crrstep’
Package suggested but not available for checking: ‘georob’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
'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
Found the following files/directories:
  ‘animation.gif’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.pdf’
Running ‘testthat.R’ [219s/244s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PHEindicatormethods)
  > 
  > test_check("PHEindicatormethods")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 452 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('testLifeExpectancy.R:315'): LE - warnings are generated when invalid arguments are used ──
  wideci_warning\[2\] does not match "some life expectancy values have a 95% confidence interval > 20 years; these values have been suppressed to NAs".
  Actual value: "Each row in `x` is expected to match at most 1 row in `y`\.\\nℹ Row 1 of `x` matches multiple rows\.\\nℹ If multiple matches are expected, set `multiple = "all"` to silence this\\n  warning\."
  Backtrace:
      ▆
   1. └─testthat::expect_match(wideci_warning[2], "some life expectancy values have a 95% confidence interval > 20 years; these values have been suppressed to NAs") at testLifeExpectancy.R:315:2
   2.   └─testthat:::expect_match_(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 452 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘ggsubplot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘RStoolbox’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
Packages suggested but not available for checking:
  'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘plsdepot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
Package unavailable to check Rd xrefs: ‘INLA’
'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: ‘pollimetrydata’
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: ‘RClone’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘advclust’ 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
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
'LazyData' is specified without 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:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: ‘gurobi’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProFit’
'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
'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: ‘cin’
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’
'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
Package suggested but not available for checking: ‘fulltext’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘exampleplot_1_blockdist_1.png’ ‘exampleplot_1_blockdist_2.png’
  ‘exampleplot_1_blockdist_3.png’ ‘exampleplot_1_bootdist.png’
  ‘exampleplot_1_dist.png’ ‘exampleplot_1_histogramtest_EMD.png’
  ‘exampleplot_1_roc_dynamic.png’ ‘exampleplot_1_slidedist_1.png’
  ‘exampleplot_1_slidedist_2.png’ ‘exampleplot_1_slidedist_3.png’
  ‘exampleplot_1_trimmeddist.png’ ‘exampleplot_blockdist_1.png’
  ‘exampleplot_blockdist_2.png’ ‘exampleplot_blockdist_3.png’
  ‘exampleplot_bootdist.png’ ‘exampleplot_dist.png’
  ‘exampleplot_lim_dyn.png’ ‘exampleplot_lim_sig.png’
  ‘exampleplot_lim_sta.png’ ‘exampleplot_noc.png’
  ‘exampleplot_roc_dyn.png’ ‘exampleplot_roc_sta.png’
  ‘exampleplot_slidedist_1.png’ ‘exampleplot_slidedist_2.png’
  ‘exampleplot_slidedist_3.png’ ‘exampleplot_trimmeddist.png’
  ‘myworkflow_result.xml’ ‘test_2_roc_dynamic.png’ ‘test_4_dist.png’
  ‘test_5_blockdist_1.png’ ‘test_5_blockdist_2.png’
  ‘test_5_blockdist_3.png’ ‘test_6_slidedist_1.png’
  ‘test_6_slidedist_2.png’ ‘test_6_slidedist_3.png’
  ‘test_7_trimmeddist.png’ ‘test_8_bootdist.png’ ‘test_emd_1d.png’
  ‘test_emd_2d.png’ ‘test_jsd_1d.png’ ‘test_jsd_2d.png’
  ‘test_kld_1d.png’ ‘test_kld_2d.png’ ‘test_ms_1d.png’ ‘test_ms_2d.png’
  ‘test_rms_1d.png’ ‘test_rms_2d.png’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘lambda.pdf’ ‘qqplot.pdf’
'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
GNU make is a SystemRequirements.
'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
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'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
'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
Found the following files/directories:
  ‘blcs.dot’ ‘ex1.dot’ ‘ex1bridge1.dot’ ‘ex1bridge2.dot’
  ‘ex1bridge3.dot’ ‘ex1effect1.dot’ ‘ex1effect2.dot’ ‘gcmlinear.dot’
  ‘latent.dot’ ‘lcs.dot’ ‘mimic.dot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘googlesheets’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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'
'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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘rcanvec.cache’
'LazyData' is specified without a 'data' directory
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
'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’
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rredis’
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
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
'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:
  ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘pbdRPC’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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'
'LazyData' is specified without 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.
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:
  /tmp/RtmpDoVnSa/R.INSTALL3cfca67df2c9f6/riot/src/vtk-src/Common/DataModel/vtkCellTreeLocator.cxx:312:7: warning: ‘detail::CellTreeBuilder<long long int>::Bucket::Cnt’ will be initialized after [-Wreorder]
  /tmp/RtmpDoVnSa/R.INSTALL3cfca67df2c9f6/riot/src/vtk-src/Common/DataModel/vtkCellTreeLocator.cxx:310:12: warning:   ‘double detail::CellTreeBuilder<long long int>::Bucket::Min’ [-Wreorder]
  /tmp/RtmpDoVnSa/R.INSTALL3cfca67df2c9f6/riot/src/vtk-src/Common/DataModel/vtkCellTreeLocator.cxx:314:5: warning:   when initialized here [-Wreorder]
  /tmp/RtmpDoVnSa/R.INSTALL3cfca67df2c9f6/riot/src/vtk-src/Common/DataModel/vtkCellTreeLocator.cxx:312:7: warning: ‘detail::CellTreeBuilder<int>::Bucket::Cnt’ will be initialized after [-Wreorder]
  /tmp/RtmpDoVnSa/R.INSTALL3cfca67df2c9f6/riot/src/vtk-src/Common/DataModel/vtkCellTreeLocator.cxx:310:12: warning:   ‘double detail::CellTreeBuilder<int>::Bucket::Min’ [-Wreorder]
  /tmp/RtmpDoVnSa/R.INSTALL3cfca67df2c9f6/riot/src/vtk-src/Common/DataModel/vtkPolyhedron.cxx:1501:23: warning: array subscript 2 is outside array bounds of ‘long long int [2]’ [-Warray-bounds]
  /tmp/RtmpDoVnSa/R.INSTALL3cfca67df2c9f6/riot/src/vtk-src/Common/DataModel/vtkPolyhedron.cxx:1491:23: warning: array subscript 2 is outside array bounds of ‘long long int [2]’ [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/riot.Rcheck/00install.out’ for details.
'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
'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. 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
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without 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 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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rnaturalearthhires’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘StatDA’ in Rd xrefs
'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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘RandomFields’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:

  Warning: 'rgl::rgl.texts' is deprecated.
  Warning: 'rgl::rgl.texts' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Found the following files/directories:
  ‘Rpdb.pdb’
'LazyData' is specified without 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
'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
Package suggested but not available for checking: ‘evolqg’
Unknown package ‘evolqg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gdalUtils’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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. 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: ‘Vdgraph’
Unknown package ‘Vdgraph’ in Rd xrefs
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Running ‘testthat.R’ [14s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rstpm2)
  Loading required package: survival
  Loading required package: splines
  
  Attaching package: 'rstpm2'
  
  The following object is masked from 'package:survival':
  
      colon
  
  > 
  > test_check("rstpm2")
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 92 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_base.R:21'): offset ──────────────────────────────────────────
  max(abs(expr - value)) is not strictly less than `eps`. Difference: 0.995
  Backtrace:
      ▆
   1. └─rstpm2 (local) expect_eps(coef(fit)[1], -6.6465454, 1e-05) at test_base.R:21:4
   2.   └─testthat::expect_lt(max(abs(expr - value)), eps) at test_base.R:8:14
  ── Failure ('test_base.R:22'): offset ──────────────────────────────────────────
  max(abs(expr - value)) is not strictly less than `eps`. Difference: 0.00167
  Backtrace:
      ▆
   1. └─rstpm2 (local) expect_eps(coef(fit)[2], -0.3601438, 1e-05) at test_base.R:22:4
   2.   └─testthat::expect_lt(max(abs(expr - value)), eps) at test_base.R:8:14
  
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 92 ]
  Error: Test failures
  Execution halted
'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
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
GNU make is a SystemRequirements.
'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: ‘cmdstanr’
Unknown package ‘cmdstanr’ in Rd xrefs
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘Tsttwalk.dat’
'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
Running examples in ‘runexp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scrape
> ### Title: Softball Webscraper
> ### Aliases: scrape
> 
> ### ** Examples
> 
> url <-"https://wmubroncos.com/sports/softball/stats/2019"
> test <- scrape(url)
Error in open.connection(x, "rb") : 
  Recv failure: Connection reset by peer
Calls: scrape -> <Anonymous> -> read_html.default
Execution halted
Found the following files/directories:
  ‘results’
'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’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘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’
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
'LazyData' is specified without a 'data' directory
'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
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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘ssvd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘untitled_consensus_cluster’
'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 which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MC p-value.ps’ ‘Output.csv’ ‘Rh.ps’ ‘Th.ps’ ‘dataratio .Rdata’
  ‘featuresRmax.csv’ ‘featuresT.csv’
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
'LazyData' is specified without 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro-to-seecolor-package.Rmd’ using rmarkdown
Quitting from lines 49-60 (Intro-to-seecolor-package.Rmd) 
Error: processing vignette ‘Intro-to-seecolor-package.Rmd’ failed with diagnostics:
[1m[22m[36mℹ[39m In index: 1.
[1mCaused by error in `dplyr::if_else()`:[22m
[33m![39m `condition` must be a vector with type <logical>.
Instead, it has type <logical[,1]>.
--- failed re-building ‘Intro-to-seecolor-package.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro-to-seecolor-package.Rmd’

Error: Vignette re-building failed.
Execution halted
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Running examples in ‘seq2R-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: change.binary
> ### Title: Convert biological sequences into binary code
> ### Aliases: change.binary
> ### Keywords: binary AT GC
> 
> ### ** Examples
> 
> library(seq2R)
> 
> mthumanDNA <- read.genbank("NC_012920")
Warning in file(file, "r") :
  cannot open URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_012920&rettype=gb&retmode=text': HTTP status was '500 Internal Server Error'
Error in file(file, "r") : 
  cannot open the connection to 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_012920&rettype=gb&retmode=text'
Calls: read.genbank -> scan -> file
Execution halted
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [37s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sfnetworks)
  > 
  > test_check("sfnetworks")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 277 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_paths.R:242'): ... is passed correcly onto igraph::distances ──
  isTRUE(all.equal(cost_dijkstra, cost_johnson)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 277 ]
  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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’
'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:
  ‘ExportFigtree1.tre’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Found the following files/directories:
  ‘simu.pheno’ ‘usedpars.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
Found the following files/directories:
  ‘SimRAD-exampleRefSeq-Fasta.fa’ ‘SimRAD-exampleRefSeq.fa’
'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
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘SIPmg-vignette.Rmd’ using rmarkdown
Quitting from lines 248-256 (SIPmg-vignette.Rmd) 
Error: processing vignette ‘SIPmg-vignette.Rmd’ failed with diagnostics:
ℹ In argument: `grouped_seq_cov = purrr::map2(...)`.
Caused by error in `purrr::map2()`:
ℹ In index: 1.
Caused by error in `dplyr::na_if()`:
! Can't convert `y` <double> to match type of `x` <tbl_df>.
--- failed re-building ‘SIPmg-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'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
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Unknown package ‘InformationValue’ 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
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rPython’
'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_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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘r2cytoscape’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Unknown package ‘sparsebn’ in Rd xrefs
'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
Package suggested but not available for checking: ‘RStoolbox’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
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.
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'

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.
Package unavailable to check Rd xrefs: ‘RandomFields’
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'
Package unavailable to check Rd xrefs: ‘RandomFields’
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’
'LazyData' is specified without 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:
  ‘.neig’
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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
'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
Error(s) in re-building vignettes:
  ...
--- re-building ‘starschemar.Rmd’ using rmarkdown
Quitting from lines 354-363 (starschemar.Rmd) 
Error: processing vignette ‘starschemar.Rmd’ failed with diagnostics:
`x` must be a vector, not a <tbl_df/tbl/data.frame/dimension_table> object.
--- failed re-building ‘starschemar.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘starsdata’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘testmat.sdml’ ‘testmat2.sdml’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
'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: ‘INLA’
'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:
  ‘corrviz.html’
GNU make is a SystemRequirements.
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
Malformed Title field: should not end in a period.
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Package suggested but not available for checking: ‘extraTrees’
Unknown package ‘extraTrees’ in Rd xrefs
Package suggested but not available for checking: ‘extraTrees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
Unknown package ‘survJamda’ 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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘robets’
Unknown package ‘robets’ in Rd xrefs
Running examples in ‘sweep-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tidiers_robets
> ### Title: Tidying methods for robets (Robust Error, Trend, Seasonal)
> ###   exponential smoothing modeling of time series
> ### Aliases: tidiers_robets sw_tidy.robets sw_glance.robets
> ###   sw_augment.robets sw_tidy_decomp.robets
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(robets)
Error in library(robets) : there is no package called ‘robets’
Execution halted
Running ‘testthat.R’ [8s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sweep)
  > library(timetk)
  > library(forecast)
  > library(tidyverse)
  ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
  ✔ ggplot2 3.4.1     ✔ purrr   1.0.1
  ✔ tibble  3.1.8     ✔ dplyr   1.1.0
  ✔ tidyr   1.3.0     ✔ stringr 1.5.0
  ✔ readr   2.1.4     ✔ forcats 1.0.0
  ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
  ✖ readr::edition_get()   masks testthat::edition_get()
  ✖ dplyr::filter()        masks stats::filter()
  ✖ purrr::is_null()       masks testthat::is_null()
  ✖ dplyr::lag()           masks stats::lag()
  ✖ readr::local_edition() masks testthat::local_edition()
  ✖ dplyr::matches()       masks tidyr::matches(), testthat::matches()
  > library(robets)
  Error in library(robets) : there is no package called 'robets'
  Execution halted
Package suggested but not available for checking: ‘swephRdata’
Running examples in ‘SwimmeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: name_reorder
> ### Title: Orders all names as "Firstname Lastname"
> ### Aliases: name_reorder
> 
> ### ** Examples
> 
> name_reorder(
+ data.frame(
+ Name = c("King, Lilly",
+  "Lilly King",
+  NA,
+  "Richards Ross, Sanya",
+  "Phelps, Michael F")),
+ verbose = TRUE
+ )
Error in `dplyr::na_if()`:
! Can't convert `y` <character> to match type of `x` <data.frame>.
Backtrace:
     ▆
  1. ├─SwimmeR::name_reorder(...)
  2. │ └─... %>% ...
  3. ├─dplyr::mutate(...)
  4. ├─dplyr::na_if(., "")
  5. │ └─vctrs::vec_cast(x = y, to = x, x_arg = "y", to_arg = "x")
  6. ├─dplyr::mutate(...)
  7. ├─dplyr::na_if(., "")
  8. │ └─vctrs::vec_cast(x = y, to = x, x_arg = "y", to_arg = "x")
  9. └─vctrs (local) `<fn>`()
 10.   └─vctrs::vec_default_cast(...)
 11.     ├─base::withRestarts(...)
 12.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
 13.     │   └─base (local) doWithOneRestart(return(expr), restart)
 14.     └─vctrs::stop_incompatible_cast(...)
 15.       └─vctrs::stop_incompatible_type(...)
 16.         └─vctrs:::stop_incompatible(...)
 17.           └─vctrs:::stop_vctrs(...)
 18.             └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SwimmeR.Rmd’ using rmarkdown
Quitting from lines 60-66 (SwimmeR.Rmd) 
Error: processing vignette ‘SwimmeR.Rmd’ failed with diagnostics:
Can't convert `y` <character> to match type of `x` <data.frame>.
--- failed re-building ‘SwimmeR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘winpath.R’ [3s/5s]
Running the tests in ‘tests/winpath.R’ failed.
Complete output:
  > library(switchr)
  > ## if(getOption("repos")["CRAN"] == "@CRAN@")
  > ##     chooseCRANmirror(ind=1L)
  > graceful_inet(TRUE)
  [1] TRUE
  > checkUrlRoundtrip = function(pth) {
  +     pth = switchr:::normalizePath2(pth)
  +     furl = switchr:::makeFileURL(pth)
  +     pth2 = switchr:::fileFromFileURL(furl)
  +     if(pth != pth2)
  +         stop("Round trip result (", pth2, ") does not match original (", pth, ") when creating file URLs")
  + }
  > 
  > ## regression test to ensure that the roundtrip
  > ## between path and file url is working properly
  > checkUrlRoundtrip(getwd())
  > checkUrlRoundtrip(tempdir())
  > if(switchr:::isWindows())
  +     checkUrlRoundtrip("\\\\localhost\\c$")
  > 
  > ## regreossion test to ensure that package dependencies
  > ## are added to the dontunload list when a package
  > ## is specified
  > bef = switchrDontUnload()
  > af = switchrDontUnload("knitr")
  Switchr needs a default CRAN mirror set via R options. Using the cloud mirror. This happens only when no CRAN mirror is selected *and* the BiocInstaller package is not installed.
  > stopifnot(all(c("stringr", "stringi", "magrittr") %in% af))
  Error: all(c("stringr", "stringi", "magrittr") %in% af) is not TRUE
  Execution halted
'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
'LazyData' is specified without 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:
  ‘test.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
Found the following files/directories:
  ‘.xls’ ‘attenu.xls’ ‘chick1.xls’ ‘chick2.xls’ ‘generic1.xls’
  ‘hands.xls’ ‘table1.xls’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘tashudata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
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: ‘R2wd’
'LazyData' is specified without 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
'LazyData' is specified without 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
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘robets’
'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
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.
'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: ‘pca3d’
'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
'LazyData' is specified without a 'data' directory
'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'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘taxidata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘TreeDistData’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘treeplyr’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/treeplyr.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
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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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
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
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
Package which this enhances but not available for checking: ‘sl3’
'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
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MortalityLaws’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Package suggested but not available for checking: ‘USAboundariesData’
Package suggested but not available for checking: ‘USA.state.boundaries.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
'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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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’
'LazyData' is specified without a 'data' directory
Running examples in ‘wcep-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: wcep
> ### Title: Analysis of weighted composite endpoints
> ### Aliases: wcep
> 
> ### ** Examples
> 
> data(toyexample)
> #event weights
> EW <- data.frame(event = c('CHF','DTH','SHK','REMI'), weight = c(0.3,1,0.5,0.2))
> res1 <- wcep(toyexample, EW)
Error in `left_join()`:
! `...` must be empty.
✖ Problematic argument:
• stringsAsFactors = FALSE
Backtrace:
    ▆
 1. └─wcep::wcep(toyexample, EW)
 2.   └─wcep:::wcep_core(x[, 1:3], EW, alpha)
 3.     ├─dplyr::left_join(ew_h0, ew1, by = "event", stringsAsFactors = FALSE)
 4.     └─dplyr:::left_join.data.frame(ew_h0, ew1, by = "event", stringsAsFactors = FALSE)
 5.       └─rlang::check_dots_empty0(...)
 6.         └─rlang::check_dots_empty(call = call)
 7.           └─rlang:::action_dots(...)
 8.             ├─base (local) try_dots(...)
 9.             └─rlang (local) action(...)
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘prepr’
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ATE’
Unknown package ‘ATE’ 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
'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:
  ‘aphiainfo.csv’ ‘tax.csv’
'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.
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
'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:
  ‘RP2_data_1.txt’ ‘RP2_data_4.txt’ ‘RP2_qtl_1.txt’ ‘RP2_qtl_4.txt’
  ‘hp1_effect_qtl.txt’ ‘hp1_freq_mrk.txt’ ‘hp1_freq_qtl.txt’
  ‘hp1_genome.txt’ ‘hp1_last_hp_data.txt’ ‘hp1_lm_mrk.txt’
  ‘hp1_lm_qtl.txt’ ‘hp1_lm_qtl_mrk.txt’ ‘hp1_mrk.txt’ ‘hp1_qtl.txt’
  ‘hp2_effect_qtl.txt’ ‘hp2_freq_mrk.txt’ ‘hp2_freq_qtl.txt’
  ‘hp2_genome.txt’ ‘hp2_last_hp_data.txt’ ‘hp2_lm_mrk.txt’
  ‘hp2_lm_qtl.txt’ ‘hp2_lm_qtl_mrk.txt’ ‘hp2_mrk.txt’ ‘hp2_qtl.txt’
  ‘my_RP_data_1.txt’ ‘my_RP_data_4.txt’ ‘my_RP_mrk_1.txt’
  ‘my_RP_mrk_4.txt’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [95s/114s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xpose)
  Loading required package: ggplot2
  
  Attaching package: 'xpose'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("xpose")
  [ FAIL 1 | WARN 4 | SKIP 7 | PASS 521 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (7)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-xpose_save.R:33'): errors are returned for bad filename input ──
  `xpose_save(plot = plot, file = paths_1)` threw an error with unexpected message.
  Expected match: "device.+must be.+NULL.+string or a function"
  Actual message: "Unknown graphics device \"abcd\""
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-xpose_save.R:33:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─xpose::xpose_save(plot = plot, file = paths_1)
    7.   └─ggplot2::ggsave(...)
    8.     └─ggplot2:::plot_dev(device, filename, dpi = dpi)
    9.       └─cli::cli_abort("Unknown graphics device {.val {device}}", call = call)
   10.         └─rlang::abort(...)
  
  [ FAIL 1 | WARN 4 | SKIP 7 | PASS 521 ]
  Error: Test failures
  Execution halted
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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
Package suggested but not available for checking: ‘zdat’
Package suggested but not available for checking: ‘SDMTools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘acceldata2.RData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  'RGtk2', 'gWidgets2RGtk2'
'LazyData' is specified without 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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown packages ‘HI’, ‘MHadaptive’ 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
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
Found the following files/directories:
  ‘table_AeRobiology’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package which this enhances but not available for checking: ‘asreml’
'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
'LazyData' is specified without 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
Encountered the following conversion/validation errors:
as.data.frame.feem.Rd:11: condition must be plain text
cmf.Rd:16: condition must be plain text
feem.Rd:19: condition must be plain text
feemflame.Rd:55: condition must be plain text
feemife.Rd:78: condition must be plain text
feemindex.Rd:83: condition must be plain text
feemjackknife.Rd:78: condition must be plain text
feemparafac.Rd:82: condition must be plain text
feemscatter.Rd:36: condition must be plain text
feemsplithalf.Rd:43: condition must be plain text
marine.colours.Rd:46: condition must be plain text
whittaker2.Rd:45: condition must be plain text
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
'LazyData' is specified without 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:
  ‘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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘ARTP’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
GNU make is a SystemRequirements.
'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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/baggr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘exemplary_input1.txt’ ‘exemplary_input2.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
Package which this enhances but not available for checking: ‘rPython’
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bayesdfa.Rcheck/00install.out’ for details.
'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
'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
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘blavaan’
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘dump.txt’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/beanz.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘alist.txt’ ‘rpkg’
'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
'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: ‘SoDA’
'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: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
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’.
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’
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
'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
'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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/blavaan.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
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'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: 'RGtk2', 'cairoDevice'
'LazyData' is specified without 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: ‘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'.
Package required but not available: ‘blavaan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: ‘gvcm.cat’
Unknown package ‘gvcm.cat’ 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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RxODE’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tmp.txt’
Found the following files/directories:
  ‘MDA231_tree.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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘GAMBoost’
'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’
'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
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
Found the following files/directories:
  ‘hotcold.csv’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CirceR’
Found the following files/directories:
  ‘out.png’ ‘out1.txt’ ‘out2.txt’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Found the following files/directories:
  ‘stepres00.txt’
'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’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘clusterhap_reports’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘tobit1’
'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: ‘PopGenome’
'LazyData' is specified without a 'data' directory
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickdemo.Rmd’ using rmarkdown
Quitting from lines 38-46 (quickdemo.Rmd) 
Error: processing vignette ‘quickdemo.Rmd’ failed with diagnostics:
ℹ In argument: `his.lag = if_else(...)`.
ℹ In group 1: `ID = 1`.
Caused by error in `nth()`:
! Can't convert `default` <character> to match type of `x` <double>.
--- failed re-building ‘quickdemo.Rmd’

--- re-building ‘selectionbias.Rmd’ using rmarkdown
Quitting from lines 154-164 (selectionbias.Rmd) 
Error: processing vignette ‘selectionbias.Rmd’ failed with diagnostics:
ℹ In argument: `his.lag = if_else(...)`.
ℹ In group 1: `ID = 1001`.
Caused by error in `nth()`:
! Can't convert `default` <character> to match type of `x` <double>.
--- failed re-building ‘selectionbias.Rmd’

SUMMARY: processing the following files failed:
  ‘quickdemo.Rmd’ ‘selectionbias.Rmd’

Error: Vignette re-building failed.
Execution halted
'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’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
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
Found the following significant warnings:
  Warning: replacing previous import ‘geiger::rescale’ by ‘phytools::rescale’ when loading ‘convevol’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/convevol.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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘covfefe_inauguration.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
'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
'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: ‘baggr’
'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:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [37s/48s]
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(dail)
  > 
  > test_check("dail")
  No internet connection or data source broken.
  Downloading 2015 dataset.
  trying URL 'https://dadosabertos-download.cgu.gov.br/FalaBR/Arquivos_FalaBR_Filtrado/Arquivos_csv_2015.zip'
  Content type 'application/x-zip-compressed' length 45584203 bytes (43.5 MB)
  ==================================================
  downloaded 43.5 MB
  
  ℹ Using "','" as decimal and "'.'" as grouping mark. Use `read_delim()` for more control.
  Downloading 2016 dataset.
  trying URL 'https://dadosabertos-download.cgu.gov.br/FalaBR/Arquivos_FalaBR_Filtrado/Arquivos_csv_2016.zip'
  Content type 'application/x-zip-compressed' length 52095795 bytes (49.7 MB)
  ==================================================
  downloaded 49.7 MB
  
  ℹ Using "','" as decimal and "'.'" as grouping mark. Use `read_delim()` for more control.
  Ended query.
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-appeals.R:61'): test the arguments agency, year, answer and search ──
  nrow(df10) (`actual`) not equal to 5 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (5)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1 ]
  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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pca3d’
Package suggested but not available for checking: ‘dash’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dash’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dash’
Package suggested but not available for checking: ‘dash’
'LazyData' is specified without 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:
  ‘my new data set.rds’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘stubthat’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [113s/128s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dbplyr)
  > 
  > test_check("dbplyr")
  Registering testing src: sqlite OK
  [ FAIL 1 | WARN 0 | SKIP 294 | PASS 1312 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Need at least two srcs to compare (6)
  • No MariaDB (4)
  • No mssql (13)
  • No postgres (7)
  • On CRAN (258)
  • `grouped_df()` needs a `name_repair` argument (1)
  • identical(Sys.getenv("GITHUB_POSTGRES"), "true") is not TRUE (1)
  • not clear whether test makes sense (2)
  • not yet correctly supported (1)
  • tidyselect issue #221 (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-rows.R:767'): `rows_upsert()` works with `in_place = TRUE` and `returning` ──
  get_returned_rows(df_upserted) (`actual`) not equal to tibble(x = 4, y = 24) (`expected`).
  
    `attr(actual, 'row.names')`: 1 2 3
  `attr(expected, 'row.names')`: 1    
  
  actual vs expected
                  x  y
  - actual[1, ]   2 22
  - actual[2, ]   3 23
    actual[3, ]   4 24
  
    `actual$x`: 2 3 4
  `expected$x`:     4
  
    `actual$y`: 22 23 24
  `expected$y`:       24
  
  [ FAIL 1 | WARN 0 | SKIP 294 | PASS 1312 ]
  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
'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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-portable flags in variable ‘PKG_FFLAGS’:
  -std=f2008
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'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:
  ‘smd_table.docx’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Documentation.Rmd’ using rmarkdown
Quitting from lines 82-83 (Documentation.Rmd) 
Error: processing vignette ‘Documentation.Rmd’ failed with diagnostics:
Cannot load glue from the private library
--- failed re-building ‘Documentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
'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: ‘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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Package suggested but not available for checking: ‘rrelaxiv’
'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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘discreteMTP’
Unknown package ‘discreteMTP’ 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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
'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’.
Found the following calls to attach():
File ‘doSNOW/R/doSNOW.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Package suggested but not available for checking: ‘OpenMPController’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
'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
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [18s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dtplyr)
  > 
  > test_check("dtplyr")
  [ FAIL 1 | WARN 1 | SKIP 25 | PASS 603 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (24)
  • transmuting grouping vars with nesting is not supported (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-step-subset-slice.R:122'): slice_*() checks for empty ... ──────
  Error in `slice_head(dt, 5)`: `n` must be explicitly named.
  i Did you mean `slice_head(n = 5)`?
  Backtrace:
      ▆
   1. ├─testthat::expect_error(slice_head(dt, 5), class = "rlib_error_dots_nonempty") at test-step-subset-slice.R:122:2
   2. │ └─testthat:::expect_condition_matching(...)
   3. │   └─testthat:::quasi_capture(...)
   4. │     ├─testthat (local) .capture(...)
   5. │     │ └─base::withCallingHandlers(...)
   6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   7. └─dplyr::slice_head(dt, 5)
   8.   └─dplyr:::check_slice_unnamed_n_prop(..., n = n, prop = prop)
   9.     └─rlang::abort(bullets, call = error_call)
  
  [ FAIL 1 | WARN 1 | SKIP 25 | PASS 603 ]
  Error: Test failures
  Execution halted
'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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
'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
'LazyData' is specified without a 'data' directory
Codoc mismatches from documentation object ‘IQLearnFS_VHet-methods’:
\S4method{qqplot}{IQLearnFS_VHet}
  Code: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ...)
  Docs: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ..., conf.level =
                 NULL, conf.args = list(exact = NULL, simulate.p.value
                 = FALSE, B = 2000, col = NA, border = NULL))
  Argument names in docs not in code:
    conf.level conf.args
'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
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
'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
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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Package suggested but not available for checking: ‘osmar’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘file.path(temp_dir, gp2.csv)’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RStoolbox’
Found the following files/directories:
  ‘Environmental variables.csv’ ‘Inf.txt’ ‘List of species.csv’ ‘Mean
  overlap among taxa.csv’ ‘Overlap among taxa.csv’ ‘Pointsize.dat’
  ‘Polar coordinates.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
Package suggested but not available for checking: ‘epidict’
GNU make is a SystemRequirements.
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  Warning: replacing previous import ‘geiger::rescale’ by ‘phytools::rescale’ when loading ‘evobiR’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/evobiR.Rcheck/00install.out’ for details.
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
Package suggested but not available for checking: ‘ExactData’
'LazyData' is specified without a 'data' directory
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cec2013’
'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
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: ‘exuberdata’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘Bogota.tex’ ‘DogBreeds1.tex’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in ‘?.onAttach’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘default5.eps’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘coxKM’
'LazyData' is specified without 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 ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

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
.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
Package suggested but not available for checking: ‘NNLM’
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
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
Unexported objects imported by ‘:::’ calls:
  ‘fdapace:::GCVLwls1D1’ ‘fdapace:::GetSmoothedMeanCurve’
  ‘fdapace:::HandleNumericsAndNAN’ ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.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
'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: ‘MicrobeDS’
Package suggested but not available for checking: ‘RStoolbox’
Running examples in ‘fieldRS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rankPlots
> ### Title: rankPlots
> ### Aliases: rankPlots
> 
> ### ** Examples
> 
> {
+ 
+ require(raster)
+ require(RStoolbox)
+ require(ggplot2)
+ 
+ # read raster data
+ r <- brick(system.file("extdata", "ndvi.tif", package="fieldRS"))
+ 
+ # read road information
+ data(roads)
+ 
+ # unsupervised classification with kmeans
+ uc <- unsuperClass(r, nSamples=5000, nClasses=5)$map
+ 
+ # derive potential sampling plots
+ pp <- derivePlots(uc, 1000)
+ 
+ # plot ranking
+ pp@data <- rankPlots(uc, pp, roads)
+ 
+ # plot output
+ gp <- fortify(pp, region="ranking")
+ ggplot(gp, aes(x=long, y=lat, group=group, fill=as.numeric(id))) + 
+ geom_polygon() + scale_fill_continuous(name="Ranking")
+ 
+ }
Loading required package: raster
Loading required package: sp
Loading required package: RStoolbox
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘RStoolbox’
Loading required package: ggplot2
Error in unsuperClass(r, nSamples = 5000, nClasses = 5) : 
  could not find function "unsuperClass"
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fieldRS.Rmd’ using rmarkdown
Quitting from lines 21-28 (fieldRS.Rmd) 
Error: processing vignette ‘fieldRS.Rmd’ failed with diagnostics:
there is no package called 'RStoolbox'
--- failed re-building ‘fieldRS.Rmd’

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

Error: Vignette re-building failed.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
'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
Packages suggested but not available for checking:
  'benchden', '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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘flux.CH4.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
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
Running examples in ‘forceR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_strongest_peaks
> ### Title: Find Peaks
> ### Aliases: find_strongest_peaks
> 
> ### ** Examples
> 
> require(dplyr)
Loading required package: dplyr

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> # Using the forceR::df.all.200.tax dataset:
> 
> # reduce dataset
> df.all.200.tax_filtered <- forceR::df.all.200.tax %>%
+   filter(species == "species_A")
> 
> # find strongest peaks
> peaks.df <- find_strongest_peaks(df = df.all.200.tax_filtered,
+                                  no.of.peaks = 5)
Error in `slice()`:
! Arguments in `...` must be passed by position, not name.
✖ Problematic argument:
• n = 1
Backtrace:
    ▆
 1. ├─forceR::find_strongest_peaks(df = df.all.200.tax_filtered, no.of.peaks = 5)
 2. │ └─curr.plot.window %>% slice(n = 1) %>% pull(specimen)
 3. ├─dplyr::pull(., specimen)
 4. ├─dplyr::slice(., n = 1)
 5. └─dplyr:::slice.data.frame(., n = 1)
 6.   └─rlang::check_dots_unnamed()
 7.     └─rlang:::action_dots(...)
 8.       ├─base (local) try_dots(...)
 9.       └─rlang (local) action(...)
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘forceR.Rmd’ using rmarkdown
Quitting from lines 518-523 (forceR.Rmd) 
Error: processing vignette ‘forceR.Rmd’ failed with diagnostics:
Arguments in `...` must be passed by position, not name.
✖ Problematic argument:
• n = 1
--- failed re-building ‘forceR.Rmd’

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

Error: Vignette re-building failed.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: 'dggrids', 'INLA'
Unknown package ‘frm’ in Rd xrefs
Unknown package ‘frm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
'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
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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘checkdata.csv’ ‘gbmforest.sas’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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.
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
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’.
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
Malformed Description field: should contain one or more complete sentences.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘RGtk2’
Package suggested but not available for checking: ‘condSURV’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 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
'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: ‘ggOceanMapsData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  'nlmixr', '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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Unknown package ‘IC2’ 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
Package suggested but not available for checking: ‘mlr3proba’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 objects imported by ‘:::’ calls:
  ‘gargle:::secret_can_decrypt’ ‘gargle:::secret_read’
  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
Unexported objects imported by ‘:::’ calls:
  ‘gargle:::secret_can_decrypt’ ‘gargle:::secret_read’
  See the note in ?`:::` about the use of this operator.
'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’
Unknown package ‘gvcm.cat’ 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
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
'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:
  'taxstats', 'taxstats1516'
'LazyData' is specified without a 'data' directory
Running examples in ‘GREMLINS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotMBM
> ### Title: Plot the mesoscopic view of the estimated MBM
> ### Aliases: plotMBM
> 
> ### ** Examples
> 
> namesFG <- c('A','B')
> list_pi <- list(c(0.5,0.5),c(0.3,0.7)) # prop of blocks in each FG
> E  <-  rbind(c(1,2),c(2,2)) # architecture of the multipartite net.
> typeInter <- c( "inc","diradj")
> v_distrib <- c('gaussian','bernoulli')
> list_theta <- list()
> list_theta[[1]] <- list()
> list_theta[[1]]$mean  <- matrix(c(6.1, 8.9, 6.6, 3), 2, 2)
> list_theta[[1]]$var  <-  matrix(c(1.6, 1.6, 1.8, 1.5),2, 2)
> list_theta[[2]] <- matrix(c(0.7,1.0, 0.4, 0.6),2, 2)
> list_Net <- rMBM(v_NQ = c(30,30),E , typeInter, v_distrib, list_pi,
+                 list_theta, namesFG = namesFG, seed = 2)$list_Net
> res_MBMsimu <- multipartiteBM(list_Net, v_distrib,
+                               namesFG = c('A','B'), v_Kinit = c(2,2),
+                               nbCores = 2,initBM = FALSE)
[1] "------------Nb of entities in each functional group--------------"
 A  B 
30 30 
[1] "------------Probability distributions on each network--------------"
[1] "gaussian"  "bernoulli"
[1] "-------------------------------------------------------------------"
[1] " ------ Searching the numbers of blocks starting from [ 2 2 ] blocks"
[1] "ICL : -2028.78 . Nb of blocks: [ 2 2 ]"
[1] "Best model------ ICL : -2028.78 . Nb of clusters: [ 2 2 ] for [ A , B ] respectively"
> plotMBM(res_MBMsimu)
Error in i_set_edge_attr(graph = graph, name = name, value = value, check = FALSE) : 
  Length of new attribute value must be 1 or 0, the number of target edges, not 8
Calls: plotMBM -> %>% -> set_edge_attr -> i_set_edge_attr
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EcologicalNetwork.Rmd’ using rmarkdown
Quitting from lines 130-131 (EcologicalNetwork.Rmd) 
Error: processing vignette ‘EcologicalNetwork.Rmd’ failed with diagnostics:
Length of new attribute value must be 1 or 0, the number of target edges, not 14
--- failed re-building ‘EcologicalNetwork.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
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.
'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
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’
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
'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
Found the following problems:
GWASinlps.Rd:187:1: Warning: trimming empty <h4>
'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:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [9s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hablar)
  > test_check("hablar")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 418 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test.ifs.R:53'): if_else_ ─────────────────────────────────────────
  `if_else_(c(T, F, NA), 1, 1L)` did not throw an error.
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 418 ]
  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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘helda-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kmeans_procedure
> ### Title: K-means procedure
> ### Aliases: kmeans_procedure
> ### Keywords: cluster kmeans sizes
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> data <- iris %>% select(Sepal.Length, Sepal.Width, Petal.Length, Petal.Width)
> features <- colnames(data)
> result <- kmeans_procedure(data = data, columns = features, threshold_min = 2, threshold = 10,
+ verbose=FALSE, seed=10)
Error in `between()`:
! Can't combine `x` <table[1d]> and `left` <double>.
Backtrace:
     ▆
  1. ├─helda::kmeans_procedure(...)
  2. │ └─dplyr::between(...)
  3. │   └─vctrs::vec_cast_common(!!!args)
  4. └─vctrs (local) `<fn>`()
  5.   └─vctrs::vec_default_ptype2(...)
  6.     ├─base::withRestarts(...)
  7.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
  8.     │   └─base (local) doWithOneRestart(return(expr), restart)
  9.     └─vctrs::stop_incompatible_type(...)
 10.       └─vctrs:::stop_incompatible(...)
 11.         └─vctrs:::stop_vctrs(...)
 12.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘synbreed’
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
‘:::’ call which should be ‘::’: ‘ggplot2:::guide_axis’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ‘:::’ calls:
  ‘ggplot2:::build_guides’ ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘colorfulVennPlot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 suggested but not available for checking: ‘trackr’
Package which this enhances but not available for checking: ‘HadoopStreaming’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘glmmADMB’
Package suggested but not available for checking: ‘ROI.plugin.mosek’
'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: 'RGtk2', 'cairoDevice'
'LazyData' is specified without 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
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
'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:
  ‘AIC.txt’ ‘AICc.txt’ ‘IAS.pdf’ ‘IAS2.pdf’ ‘IAS3.pdf’
  ‘P.microlepis-AIC.txt’ ‘P.microlepis-AICc.txt’ ‘P.microlepis-IAS.pdf’
  ‘P.microlepis-IAS2.pdf’ ‘P.microlepis-IAS3.pdf’
'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: ‘SparkR’
'LazyData' is specified without 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: ‘icd’
Package suggested but not available for checking: ‘ICBayes’
'LazyData' is specified without 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 suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘blavaan’
Running examples in ‘insol-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hillshading
> ### Title: Intensity of illumination over a surface
> ### Aliases: hillshading
> 
> ### ** Examples
> 
> ## Not run: 
> ##D ## From the "Obligatory Mathematical surface" in persp3d {rgl}
> ##D ## this shows the cast shdows clearly, but there is some interference with rgl internal
> ##D ## lit parameters
> ##D require(rgl)
> ##D x = seq(-10, 10, length= 300)
> ##D y = x
> ##D f = function(x,y) { r <- sqrt(x^2+y^2); 10 * sin(r)/r }
> ##D z = outer(x, y, f)
> ##D z[is.na(z)] = 1
> ##D zgr = cgrad(z,2/30)
> ##D sv = normalvector(55,315)
> ##D hsh = zgr[,,1]*sv[1]+zgr[,,2]*sv[2]+zgr[,,3]*sv[3]
> ##D hsh = (hsh+abs(hsh))/2
> ##D sh = doshade(z,sv,2/30)
> ##D hshsh = hsh*sh
> ##D hshsh = t(hshsh[nrow(hshsh):1,])
> ##D open3d()
> ##D rgl.light(viewpoint.rel = F, ambient = "#FFFFFF", diffuse = "#FFFFFF", specular = "#000000")
> ##D persp3d(x, y, z, col=grey(hshsh))
> ## End(Not run)
> 
> ## Hillshading on mountain terrain, sun at NW, 35 degrees elevation
> zipfile = tempfile()
> download.file("https://meteoexploration.com/R/insol/data/dempyrenees.asc.zip",zipfile)
trying URL 'https://meteoexploration.com/R/insol/data/dempyrenees.asc.zip'
Warning in download.file("https://meteoexploration.com/R/insol/data/dempyrenees.asc.zip",  :
  URL 'https://meteoexploration.com/R/insol/data/dempyrenees.asc.zip': status was 'SSL peer certificate or SSH remote key was not OK'
Error in download.file("https://meteoexploration.com/R/insol/data/dempyrenees.asc.zip",  : 
  cannot open URL 'https://meteoexploration.com/R/insol/data/dempyrenees.asc.zip'
Execution halted
Malformed Title field: should not end in a period.
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘surveyspec’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
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'
'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
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
'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: ‘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
'LazyData' is specified without 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:
  ‘song.wav’ ‘song4karaoke.wav’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘Killed after ’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘VARSEDIG’
Unknown package ‘VARSEDIG’ in Rd xrefs
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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:
  Warning: replacing previous import ‘dplyr::where’ by ‘imager::where’ when loading ‘LARGB’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/LARGB.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘example.llo’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ergm.userterms’
Unknown package ‘ergm.userterms’ in Rd xrefs
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tidySEM’
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
--- finished re-building ‘example.Rmd’

--- re-building ‘fullworkflow.Rmd’ using rmarkdown
Quitting from lines 245-255 (fullworkflow.Rmd) 
Error: processing vignette ‘fullworkflow.Rmd’ failed with diagnostics:
The package `tidySEM` is required for this function.
--- failed re-building ‘fullworkflow.Rmd’

--- re-building ‘indirect.Rmd’ using rmarkdown
Quitting from lines 53-71 (indirect.Rmd) 
Error: processing vignette ‘indirect.Rmd’ failed with diagnostics:
The package `tidySEM` is required for this function.
--- failed re-building ‘indirect.Rmd’

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

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

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

SUMMARY: processing the following files failed:
  ‘fullworkflow.Rmd’ ‘indirect.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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:
  'gWidgets', 'gWidgetsRGtk2', '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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘tTestTable.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Dependence on R version ‘4.0.3’ not with patchlevel 0
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kerdiest’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘test’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
'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: ‘RGtk2’
'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: ‘scrubr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘flashier’
'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’
Package suggested but not available for checking: ‘gurobi’
Error(s) in re-building vignettes:
  ...
--- re-building ‘MatchIt.Rmd’ using rmarkdown
--- finished re-building ‘MatchIt.Rmd’

--- re-building ‘assessing-balance.Rmd’ using rmarkdown
--- finished re-building ‘assessing-balance.Rmd’

--- re-building ‘estimating-effects.Rmd’ using rmarkdown
Quitting from lines 247-255 (estimating-effects.Rmd) 
Error: processing vignette ‘estimating-effects.Rmd’ failed with diagnostics:
The `wts` argument must be a numeric vector of length 882, or a string which matches a column name in `newdata`. If you did not supply a `newdata` explicitly, `marginaleffects` extracted it automatically from the model object, and the `wts` variable may not have been available. The easiest strategy is often to supply a data frame such as the original data to `newdata` explicitly, and to make sure that it includes an appropriate column of weights, identified by the `wts` argument.
--- failed re-building ‘estimating-effects.Rmd’

--- re-building ‘matching-methods.Rmd’ using rmarkdown
--- finished re-building ‘matching-methods.Rmd’

--- re-building ‘sampling-weights.Rmd’ using rmarkdown
--- finished re-building ‘sampling-weights.Rmd’

SUMMARY: processing the following file failed:
  ‘estimating-effects.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without 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
Found the following files/directories:
  ‘utilities.R’
'LazyData' is specified without 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:
  ‘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
'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: ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MethylCapSig’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘genuMet’
'LazyData' is specified without a 'data' directory
Running examples in ‘metacore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check_inconsistent_labels
> ### Title: Optional checks to consistency of metadata
> ### Aliases: check_inconsistent_labels check_inconsistent_types
> ###   check_inconsistent_formats
> 
> ### ** Examples
> 
> ## EXAMPLE WITH DUPLICATES
> # Loads in a metacore obj called metacore
> load(metacore_example("pilot_ADaM.rda"))
> check_inconsistent_labels(metacore)
Error in `mutate()`:
ℹ In argument: `across(...)`.
ℹ In group 3: `var1 = "CHG"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
     ▆
  1. ├─metacore::check_inconsistent_labels(metacore)
  2. │ └─metacore:::basic_check(label, metacore)
  3. │   └─... %>% select(variable = var1, everything())
  4. ├─dplyr::select(., variable = var1, everything())
  5. ├─dplyr::summarise(...)
  6. ├─dplyr::group_by(...)
  7. ├─dplyr::mutate(...)
  8. ├─dplyr:::mutate.data.frame(...)
  9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
 10. │   ├─base::withCallingHandlers(...)
 11. │   └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 12. │     ├─base::withCallingHandlers(...)
 13. │     └─mask$eval_all_mutate(quo)
 14. │       └─dplyr (local) eval()
 15. └─dplyr:::dplyr_internal_error("dplyr:::mutate_incompatible_size", `<named list>`)
 16.   └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
Execution halted
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.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
'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
Package unavailable to check Rd xrefs: ‘DAPAR’
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without 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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/MIRES.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘AnalyzeFMRI’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mixRasch’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
Found the following significant warnings:
  ./mlpack/core/data/save_impl.hpp:107:40: warning: ‘bool arma::Mat<eT>::quiet_save(std::ostream&, arma::file_type) const [with eT = long unsigned int; std::ostream = std::basic_ostream<char>]’ is deprecated [-Wdeprecated-declarations]
  ./mlpack/core/data/save_impl.hpp:128:43: warning: ‘bool arma::Mat<eT>::quiet_save(std::ostream&, arma::file_type) const [with eT = long unsigned int; std::ostream = std::basic_ostream<char>]’ is deprecated [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/mlpack.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘Flury’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alstructure’

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Package suggested but not available for checking: ‘ArchR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘corpus.useR.2008.abstracts’
'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
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
'LazyData' is specified without 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:
  ‘test.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [421s/481s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(multicolor)
  Colors cannot be applied in this environment. Please use another application, such as RStudio or a color-enabled terminal.
  Colors cannot be applied in this environment. Please use another application, such as RStudio or a color-enabled terminal.
  > 
  > test_check("multicolor")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 29 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • use_color() is not TRUE (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-multicolor.R:103'): colors(), including grays, rainbow, and rbg work ──
  `suppressMessages(...)` produced warnings.
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 29 ]
  Error: Test failures
  Execution halted
'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: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘asreml’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
'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
'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: ‘re2r’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Running examples in ‘netmeta-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: netcontrib
> ### Title: Contribution matrix in network meta-analysis
> ### Aliases: netcontrib print.netcontrib
> ### Keywords: contribution
> 
> ### ** Examples
> 
> # Use the Woods dataset
> #
> data("Woods2010")
> p1 <- pairwise(treatment, event = r, n = N,
+   studlab = author, data = Woods2010, sm = "OR")
> 
> net1 <- netmeta(p1)
> cm <- netcontrib(net1)
Error: node stack overflow
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
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'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘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
'LazyData' is specified without 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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without 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:
  'originr', 'parallelsugar'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘openNLPmodels.en’
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘result.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘CorShrink’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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’
Found the following files/directories:
  ‘Minimal-concordance.tex’ ‘Minimal.Rnw’ ‘Minimal.pdf’
  ‘Minimal.synctex.gz’ ‘Minimal.tex’ ‘figure’
'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
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
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
'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
'LazyData' is specified without 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: ‘crrstep’
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘blavaan’
Package suggested but not available for checking: ‘dendextendRcpp’
'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
Found the following files/directories:
  ‘animation.gif’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.pdf’
Running ‘testthat.R’ [226s/260s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PHEindicatormethods)
  > 
  > test_check("PHEindicatormethods")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 452 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('testLifeExpectancy.R:315'): LE - warnings are generated when invalid arguments are used ──
  wideci_warning\[2\] does not match "some life expectancy values have a 95% confidence interval > 20 years; these values have been suppressed to NAs".
  Actual value: "Each row in `x` is expected to match at most 1 row in `y`\.\\nℹ Row 1 of `x` matches multiple rows\.\\nℹ If multiple matches are expected, set `multiple = "all"` to silence this\\n  warning\."
  Backtrace:
      ▆
   1. └─testthat::expect_match(wideci_warning[2], "some life expectancy values have a 95% confidence interval > 20 years; these values have been suppressed to NAs") at testLifeExpectancy.R:315:2
   2.   └─testthat:::expect_match_(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 452 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘ggsubplot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘RStoolbox’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
Packages suggested but not available for checking:
  'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘plsdepot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
Package unavailable to check Rd xrefs: ‘INLA’
'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: ‘pollimetrydata’
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: ‘RClone’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘advclust’ 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
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
'LazyData' is specified without 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:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: ‘gurobi’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProFit’
'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
'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: ‘cin’
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’
'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
Package suggested but not available for checking: ‘fulltext’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘exampleplot_1_blockdist_1.png’ ‘exampleplot_1_blockdist_2.png’
  ‘exampleplot_1_blockdist_3.png’ ‘exampleplot_1_bootdist.png’
  ‘exampleplot_1_dist.png’ ‘exampleplot_1_histogramtest_EMD.png’
  ‘exampleplot_1_roc_dynamic.png’ ‘exampleplot_1_slidedist_1.png’
  ‘exampleplot_1_slidedist_2.png’ ‘exampleplot_1_slidedist_3.png’
  ‘exampleplot_1_trimmeddist.png’ ‘exampleplot_blockdist_1.png’
  ‘exampleplot_blockdist_2.png’ ‘exampleplot_blockdist_3.png’
  ‘exampleplot_bootdist.png’ ‘exampleplot_dist.png’
  ‘exampleplot_lim_dyn.png’ ‘exampleplot_lim_sig.png’
  ‘exampleplot_lim_sta.png’ ‘exampleplot_noc.png’
  ‘exampleplot_roc_dyn.png’ ‘exampleplot_roc_sta.png’
  ‘exampleplot_slidedist_1.png’ ‘exampleplot_slidedist_2.png’
  ‘exampleplot_slidedist_3.png’ ‘exampleplot_trimmeddist.png’
  ‘myworkflow_result.xml’ ‘test_2_roc_dynamic.png’ ‘test_4_dist.png’
  ‘test_5_blockdist_1.png’ ‘test_5_blockdist_2.png’
  ‘test_5_blockdist_3.png’ ‘test_6_slidedist_1.png’
  ‘test_6_slidedist_2.png’ ‘test_6_slidedist_3.png’
  ‘test_7_trimmeddist.png’ ‘test_8_bootdist.png’ ‘test_emd_1d.png’
  ‘test_emd_2d.png’ ‘test_jsd_1d.png’ ‘test_jsd_2d.png’
  ‘test_kld_1d.png’ ‘test_kld_2d.png’ ‘test_ms_1d.png’ ‘test_ms_2d.png’
  ‘test_rms_1d.png’ ‘test_rms_2d.png’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘lambda.pdf’ ‘qqplot.pdf’
'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
GNU make is a SystemRequirements.
'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
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'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
'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
Found the following files/directories:
  ‘blcs.dot’ ‘ex1.dot’ ‘ex1bridge1.dot’ ‘ex1bridge2.dot’
  ‘ex1bridge3.dot’ ‘ex1effect1.dot’ ‘ex1effect2.dot’ ‘gcmlinear.dot’
  ‘latent.dot’ ‘lcs.dot’ ‘mimic.dot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘googlesheets’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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'
'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
GNU make is a SystemRequirements.
Running ‘testthat.R’ [4s/176s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rbioapi)
  > 
  > test_check("rbioapi")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 116 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-api_calls_rba_skeleton.R:40'): .rba_skeleton works ─────────────
  Error: The server returned HTTP Status '504' (Redirection: Gateway Timeout).
  Backtrace:
      ▆
   1. ├─testthat::expect_null(object = .rba_skeleton(input_call = request)) at test-api_calls_rba_skeleton.R:40:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─rbioapi:::.rba_skeleton(input_call = request)
   5.   └─rbioapi:::.rba_api_call(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 116 ]
  Error: Test failures
  Execution halted
'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
Found the following files/directories:
  ‘rcanvec.cache’
'LazyData' is specified without a 'data' directory
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
'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’
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rredis’
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
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
'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:
  ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘pbdRPC’
'LazyData' is specified without 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: ‘blavaan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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'
'LazyData' is specified without 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.
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:
  /tmp/Rtmp9Iy9ce/R.INSTALL217efb413e3f48/riot/src/vtk-src/Common/DataModel/vtkCellTreeLocator.cxx:312:7: warning: ‘detail::CellTreeBuilder<long long int>::Bucket::Cnt’ will be initialized after [-Wreorder]
  /tmp/Rtmp9Iy9ce/R.INSTALL217efb413e3f48/riot/src/vtk-src/Common/DataModel/vtkCellTreeLocator.cxx:310:12: warning:   ‘double detail::CellTreeBuilder<long long int>::Bucket::Min’ [-Wreorder]
  /tmp/Rtmp9Iy9ce/R.INSTALL217efb413e3f48/riot/src/vtk-src/Common/DataModel/vtkCellTreeLocator.cxx:314:5: warning:   when initialized here [-Wreorder]
  /tmp/Rtmp9Iy9ce/R.INSTALL217efb413e3f48/riot/src/vtk-src/Common/DataModel/vtkCellTreeLocator.cxx:312:7: warning: ‘detail::CellTreeBuilder<int>::Bucket::Cnt’ will be initialized after [-Wreorder]
  /tmp/Rtmp9Iy9ce/R.INSTALL217efb413e3f48/riot/src/vtk-src/Common/DataModel/vtkCellTreeLocator.cxx:310:12: warning:   ‘double detail::CellTreeBuilder<int>::Bucket::Min’ [-Wreorder]
  /tmp/Rtmp9Iy9ce/R.INSTALL217efb413e3f48/riot/src/vtk-src/Common/DataModel/vtkPolyhedron.cxx:1501:23: warning: array subscript 2 is outside array bounds of ‘long long int [2]’ [-Warray-bounds]
  /tmp/Rtmp9Iy9ce/R.INSTALL217efb413e3f48/riot/src/vtk-src/Common/DataModel/vtkPolyhedron.cxx:1491:23: warning: array subscript 2 is outside array bounds of ‘long long int [2]’ [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/riot.Rcheck/00install.out’ for details.
'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
'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. 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
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without 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 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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rnaturalearthhires’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘StatDA’ in Rd xrefs
'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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘RandomFields’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:

  Warning: 'rgl::rgl.texts' is deprecated.
  Warning: 'rgl::rgl.texts' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Found the following files/directories:
  ‘Rpdb.pdb’
'LazyData' is specified without 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
'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
Package suggested but not available for checking: ‘evolqg’
Unknown package ‘evolqg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gdalUtils’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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. 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: ‘Vdgraph’
Unknown package ‘Vdgraph’ in Rd xrefs
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Running ‘testthat.R’ [14s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rstpm2)
  Loading required package: survival
  Loading required package: splines
  
  Attaching package: 'rstpm2'
  
  The following object is masked from 'package:survival':
  
      colon
  
  > 
  > test_check("rstpm2")
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 92 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_base.R:21'): offset ──────────────────────────────────────────
  max(abs(expr - value)) is not strictly less than `eps`. Difference: 0.995
  Backtrace:
      ▆
   1. └─rstpm2 (local) expect_eps(coef(fit)[1], -6.6465454, 1e-05) at test_base.R:21:4
   2.   └─testthat::expect_lt(max(abs(expr - value)), eps) at test_base.R:8:14
  ── Failure ('test_base.R:22'): offset ──────────────────────────────────────────
  max(abs(expr - value)) is not strictly less than `eps`. Difference: 0.00167
  Backtrace:
      ▆
   1. └─rstpm2 (local) expect_eps(coef(fit)[2], -0.3601438, 1e-05) at test_base.R:22:4
   2.   └─testthat::expect_lt(max(abs(expr - value)), eps) at test_base.R:8:14
  
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 92 ]
  Error: Test failures
  Execution halted
'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
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
GNU make is a SystemRequirements.
'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: ‘cmdstanr’
Unknown package ‘cmdstanr’ in Rd xrefs
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘Tsttwalk.dat’
'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:
  ‘results’
'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’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [7s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(safedata)
  SAFE package reminder: Please set SAFE data directory using set_safe_dir()
  > 
  > test_check("safedata")
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 47 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-safedata_network.R:57'): URL errors fails gracefully ─────────
  attr\(success, "fail_msg"\) does not match "URL error".
  Actual value: "URL timed out"
  Backtrace:
      ▆
   1. └─testthat::expect_match(attr(success, "fail_msg"), regexp = "URL error") at test-safedata_network.R:57:4
   2.   └─testthat:::expect_match_(...)
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 47 ]
  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
'LazyData' is specified without a 'data' directory
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’
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
'LazyData' is specified without a 'data' directory
'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
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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘ssvd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘untitled_consensus_cluster’
'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 which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MC p-value.ps’ ‘Output.csv’ ‘Rh.ps’ ‘Th.ps’ ‘dataratio .Rdata’
  ‘featuresRmax.csv’ ‘featuresT.csv’
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
'LazyData' is specified without 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro-to-seecolor-package.Rmd’ using rmarkdown
Quitting from lines 49-60 (Intro-to-seecolor-package.Rmd) 
Error: processing vignette ‘Intro-to-seecolor-package.Rmd’ failed with diagnostics:
[1m[22m[36mℹ[39m In index: 1.
[1mCaused by error in `dplyr::if_else()`:[22m
[33m![39m `condition` must be a vector with type <logical>.
Instead, it has type <logical[,1]>.
--- failed re-building ‘Intro-to-seecolor-package.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro-to-seecolor-package.Rmd’

Error: Vignette re-building failed.
Execution halted
'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
'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: ‘blavaan’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [38s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sfnetworks)
  > 
  > test_check("sfnetworks")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 277 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_paths.R:242'): ... is passed correcly onto igraph::distances ──
  isTRUE(all.equal(cost_dijkstra, cost_johnson)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 277 ]
  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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’
'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:
  ‘ExportFigtree1.tre’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Found the following files/directories:
  ‘simu.pheno’ ‘usedpars.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
Found the following files/directories:
  ‘SimRAD-exampleRefSeq-Fasta.fa’ ‘SimRAD-exampleRefSeq.fa’
'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
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘SIPmg-vignette.Rmd’ using rmarkdown
Quitting from lines 455-460 (SIPmg-vignette.Rmd) 
Error: processing vignette ‘SIPmg-vignette.Rmd’ failed with diagnostics:
could not open file ‘/tmp/RtmpI0ZGIe/file3a079f33a4def0’
--- failed re-building ‘SIPmg-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'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
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Unknown package ‘InformationValue’ 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
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rPython’
'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_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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘r2cytoscape’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Unknown package ‘sparsebn’ in Rd xrefs
'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
Package suggested but not available for checking: ‘RStoolbox’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
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.
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'

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.
Package unavailable to check Rd xrefs: ‘RandomFields’
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'
Package unavailable to check Rd xrefs: ‘RandomFields’
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’
'LazyData' is specified without 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:
  ‘.neig’
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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
'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
Error(s) in re-building vignettes:
  ...
--- re-building ‘starschemar.Rmd’ using rmarkdown
Quitting from lines 354-363 (starschemar.Rmd) 
Error: processing vignette ‘starschemar.Rmd’ failed with diagnostics:
`x` must be a vector, not a <tbl_df/tbl/data.frame/dimension_table> object.
--- failed re-building ‘starschemar.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘starsdata’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘testmat.sdml’ ‘testmat2.sdml’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
'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: ‘INLA’
'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:
  ‘corrviz.html’
GNU make is a SystemRequirements.
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
Malformed Title field: should not end in a period.
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Package suggested but not available for checking: ‘extraTrees’
Unknown package ‘extraTrees’ in Rd xrefs
Package suggested but not available for checking: ‘extraTrees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
Unknown package ‘survJamda’ 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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘robets’
Unknown package ‘robets’ in Rd xrefs
Running examples in ‘sweep-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tidiers_robets
> ### Title: Tidying methods for robets (Robust Error, Trend, Seasonal)
> ###   exponential smoothing modeling of time series
> ### Aliases: tidiers_robets sw_tidy.robets sw_glance.robets
> ###   sw_augment.robets sw_tidy_decomp.robets
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(robets)
Error in library(robets) : there is no package called ‘robets’
Execution halted
Running ‘testthat.R’ [6s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sweep)
  > library(timetk)
  > library(forecast)
  > library(tidyverse)
  ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
  ✔ dplyr     1.1.0     ✔ readr     2.1.4
  ✔ forcats   1.0.0     ✔ stringr   1.5.0
  ✔ ggplot2   3.4.1     ✔ tibble    3.1.8
  ✔ lubridate 1.9.2     ✔ tidyr     1.3.0
  ✔ purrr     1.0.1     
  ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
  ✖ readr::edition_get()   masks testthat::edition_get()
  ✖ dplyr::filter()        masks stats::filter()
  ✖ purrr::is_null()       masks testthat::is_null()
  ✖ dplyr::lag()           masks stats::lag()
  ✖ readr::local_edition() masks testthat::local_edition()
  ✖ dplyr::matches()       masks tidyr::matches(), testthat::matches()
  ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
  > library(robets)
  Error in library(robets) : there is no package called 'robets'
  Execution halted
Package suggested but not available for checking: ‘swephRdata’
Running examples in ‘SwimmeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: name_reorder
> ### Title: Orders all names as "Firstname Lastname"
> ### Aliases: name_reorder
> 
> ### ** Examples
> 
> name_reorder(
+ data.frame(
+ Name = c("King, Lilly",
+  "Lilly King",
+  NA,
+  "Richards Ross, Sanya",
+  "Phelps, Michael F")),
+ verbose = TRUE
+ )
Error in `dplyr::na_if()`:
! Can't convert `y` <character> to match type of `x` <data.frame>.
Backtrace:
     ▆
  1. ├─SwimmeR::name_reorder(...)
  2. │ └─... %>% ...
  3. ├─dplyr::mutate(...)
  4. ├─dplyr::na_if(., "")
  5. │ └─vctrs::vec_cast(x = y, to = x, x_arg = "y", to_arg = "x")
  6. ├─dplyr::mutate(...)
  7. ├─dplyr::na_if(., "")
  8. │ └─vctrs::vec_cast(x = y, to = x, x_arg = "y", to_arg = "x")
  9. └─vctrs (local) `<fn>`()
 10.   └─vctrs::vec_default_cast(...)
 11.     ├─base::withRestarts(...)
 12.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
 13.     │   └─base (local) doWithOneRestart(return(expr), restart)
 14.     └─vctrs::stop_incompatible_cast(...)
 15.       └─vctrs::stop_incompatible_type(...)
 16.         └─vctrs:::stop_incompatible(...)
 17.           └─vctrs:::stop_vctrs(...)
 18.             └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SwimmeR.Rmd’ using rmarkdown
Quitting from lines 60-66 (SwimmeR.Rmd) 
Error: processing vignette ‘SwimmeR.Rmd’ failed with diagnostics:
Can't convert `y` <character> to match type of `x` <data.frame>.
--- failed re-building ‘SwimmeR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘winpath.R’ [3s/6s]
Running the tests in ‘tests/winpath.R’ failed.
Complete output:
  > library(switchr)
  > ## if(getOption("repos")["CRAN"] == "@CRAN@")
  > ##     chooseCRANmirror(ind=1L)
  > graceful_inet(TRUE)
  [1] TRUE
  > checkUrlRoundtrip = function(pth) {
  +     pth = switchr:::normalizePath2(pth)
  +     furl = switchr:::makeFileURL(pth)
  +     pth2 = switchr:::fileFromFileURL(furl)
  +     if(pth != pth2)
  +         stop("Round trip result (", pth2, ") does not match original (", pth, ") when creating file URLs")
  + }
  > 
  > ## regression test to ensure that the roundtrip
  > ## between path and file url is working properly
  > checkUrlRoundtrip(getwd())
  > checkUrlRoundtrip(tempdir())
  > if(switchr:::isWindows())
  +     checkUrlRoundtrip("\\\\localhost\\c$")
  > 
  > ## regreossion test to ensure that package dependencies
  > ## are added to the dontunload list when a package
  > ## is specified
  > bef = switchrDontUnload()
  > af = switchrDontUnload("knitr")
  Switchr needs a default CRAN mirror set via R options. Using the cloud mirror. This happens only when no CRAN mirror is selected *and* the BiocInstaller package is not installed.
  > stopifnot(all(c("stringr", "stringi", "magrittr") %in% af))
  Error: all(c("stringr", "stringi", "magrittr") %in% af) is not TRUE
  Execution halted
'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
'LazyData' is specified without 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:
  ‘test.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
Found the following files/directories:
  ‘.xls’ ‘attenu.xls’ ‘chick1.xls’ ‘chick2.xls’ ‘generic1.xls’
  ‘hands.xls’ ‘table1.xls’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘tashudata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
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: ‘R2wd’
'LazyData' is specified without 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
'LazyData' is specified without 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
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without 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: ‘blavaan’

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
Package suggested but not available for checking: ‘robets’
'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
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.
'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: ‘pca3d’
'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
'LazyData' is specified without a 'data' directory
'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'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘taxidata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘TreeDistData’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘treeplyr’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/treeplyr.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
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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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
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
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
Package which this enhances but not available for checking: ‘sl3’
'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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Package suggested but not available for checking: ‘USAboundariesData’
Package suggested but not available for checking: ‘USA.state.boundaries.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
'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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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’
'LazyData' is specified without a 'data' directory
Running examples in ‘wcep-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: wcep
> ### Title: Analysis of weighted composite endpoints
> ### Aliases: wcep
> 
> ### ** Examples
> 
> data(toyexample)
> #event weights
> EW <- data.frame(event = c('CHF','DTH','SHK','REMI'), weight = c(0.3,1,0.5,0.2))
> res1 <- wcep(toyexample, EW)
Error in `left_join()`:
! `...` must be empty.
✖ Problematic argument:
• stringsAsFactors = FALSE
Backtrace:
    ▆
 1. └─wcep::wcep(toyexample, EW)
 2.   └─wcep:::wcep_core(x[, 1:3], EW, alpha)
 3.     ├─dplyr::left_join(ew_h0, ew1, by = "event", stringsAsFactors = FALSE)
 4.     └─dplyr:::left_join.data.frame(ew_h0, ew1, by = "event", stringsAsFactors = FALSE)
 5.       └─rlang::check_dots_empty0(...)
 6.         └─rlang::check_dots_empty(call = call)
 7.           └─rlang:::action_dots(...)
 8.             ├─base (local) try_dots(...)
 9.             └─rlang (local) action(...)
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘prepr’
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ATE’
Unknown package ‘ATE’ 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
'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:
  ‘aphiainfo.csv’ ‘tax.csv’
'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.
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
'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:
  ‘RP2_data_1.txt’ ‘RP2_data_4.txt’ ‘RP2_qtl_1.txt’ ‘RP2_qtl_4.txt’
  ‘hp1_effect_qtl.txt’ ‘hp1_freq_mrk.txt’ ‘hp1_freq_qtl.txt’
  ‘hp1_genome.txt’ ‘hp1_last_hp_data.txt’ ‘hp1_lm_mrk.txt’
  ‘hp1_lm_qtl.txt’ ‘hp1_lm_qtl_mrk.txt’ ‘hp1_mrk.txt’ ‘hp1_qtl.txt’
  ‘hp2_effect_qtl.txt’ ‘hp2_freq_mrk.txt’ ‘hp2_freq_qtl.txt’
  ‘hp2_genome.txt’ ‘hp2_last_hp_data.txt’ ‘hp2_lm_mrk.txt’
  ‘hp2_lm_qtl.txt’ ‘hp2_lm_qtl_mrk.txt’ ‘hp2_mrk.txt’ ‘hp2_qtl.txt’
  ‘my_RP_data_1.txt’ ‘my_RP_data_4.txt’ ‘my_RP_mrk_1.txt’
  ‘my_RP_mrk_4.txt’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [93s/110s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xpose)
  Loading required package: ggplot2
  
  Attaching package: 'xpose'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("xpose")
  [ FAIL 1 | WARN 4 | SKIP 7 | PASS 521 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (7)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-xpose_save.R:33'): errors are returned for bad filename input ──
  `xpose_save(plot = plot, file = paths_1)` threw an error with unexpected message.
  Expected match: "device.+must be.+NULL.+string or a function"
  Actual message: "Unknown graphics device \"abcd\""
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-xpose_save.R:33:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─xpose::xpose_save(plot = plot, file = paths_1)
    7.   └─ggplot2::ggsave(...)
    8.     └─ggplot2:::plot_dev(device, filename, dpi = dpi)
    9.       └─cli::cli_abort("Unknown graphics device {.val {device}}", call = call)
   10.         └─rlang::abort(...)
  
  [ FAIL 1 | WARN 4 | SKIP 7 | PASS 521 ]
  Error: Test failures
  Execution halted
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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
Package suggested but not available for checking: ‘zdat’
Package suggested but not available for checking: ‘SDMTools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    libs  29.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 95.9Mb
  sub-directories of 1Mb or more:
    libs  94.9Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 134469 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R  14.1Mb
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Packages required but not available:
  'BSgenome.Hsapiens.UCSC.hg19', 'BSgenome.Hsapiens.UCSC.hg38',
  'BSgenome.Mmusculus.UCSC.mm9', 'BSgenome.Mmusculus.UCSC.mm10'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
'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
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   3.0Mb
    libs   2.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    data    1.3Mb
    files   1.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.9Mb
Package suggested but not available for checking: ‘maptools’
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data  10.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Package suggested but not available for checking: ‘HiTC’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘mFilter’ ‘regclass’ ‘writexl’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Biostrings’
Package unavailable to check Rd xrefs: ‘Biostrings’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’
  ‘utils’
  All declared Imports should be used.
Note: found 53 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       2.0Mb
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  24.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 231 marked UTF-8 strings
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 31.7Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    30.2Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.6Mb
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    R  36.1Mb
Package suggested but not available for checking: ‘rhdf5’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    test_v8    2.0Mb
    testdata   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mcclust’
  All declared Imports should be used.
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.8Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Note: found 76 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘bannerCommenter’ ‘config’ ‘feather’ ‘here’ ‘knitr’ ‘log4r’ ‘ps’
  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘methods’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'affxparser', 'oligo', 'oligoClasses', 'pdInfoBuilder',
  'AffymetrixDataTestFiles'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R             3.1Mb
    help          1.1Mb
    testScripts   1.1Mb
Packages unavailable to check Rd xrefs: ‘affxparser’, ‘oligo’, ‘oligoClasses’
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 85.4Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    libs  79.8Mb
Note: found 1409 marked UTF-8 strings
Package which this enhances but not available for checking: ‘ARTP’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘asteRiskData’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.5Mb
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘lubridate’ ‘openair’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘lubridate’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Note: found 552 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.rsp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘readxl’ ‘reshape2’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘rclipboard’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    java   8.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MixAll’ ‘dplyr’ ‘lqmm’ ‘matrixcalc’ ‘rmutil’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Package suggested but not available for checking: ‘lixoftConnectors’
Note: found 64209 marked UTF-8 strings
Note: found 133353 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
installed size is 91.4Mb
  sub-directories of 1Mb or more:
    libs  89.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 260 marked UTF-8 strings
installed size is 86.7Mb
  sub-directories of 1Mb or more:
    libs  85.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fs’ ‘testthat’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    data   1.3Mb
    doc    1.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
Note: found 148 marked UTF-8 strings
Package suggested but not available for checking: ‘ArrayExpress’
'LazyData' is specified without a 'data' directory
Note: found 13825 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.4Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dbplyr’ ‘dotenv’ ‘googleAuthR’ ‘writexl’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Biobase', 'GO.db', 'GSEABase', 'org.Hs.eg.db', 'reactome.db'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Namespace in Imports field not imported from: ‘vtable’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
installed size is 64.2Mb
  sub-directories of 1Mb or more:
    libs  62.2Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘utils’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 97.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  96.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   6.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  13.7Mb
installed size is 70.3Mb
  sub-directories of 1Mb or more:
    libs  68.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘StanHeaders’ ‘astsa’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 96.7Mb
  sub-directories of 1Mb or more:
    libs  95.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppParallel’ ‘mlbench’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘shinytest’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
GNU make is a SystemRequirements.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  15.2Mb
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  23.2Mb
'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     1.9Mb
    doc   3.9Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘MCMCpack’ ‘R2WinBUGS’ ‘R2jags’ ‘carData’ ‘rjags’
  All declared Imports should be used.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Note: found 1924 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘matrixcalc’ ‘stats’
  All declared Imports should be used.
installed size is 86.3Mb
  sub-directories of 1Mb or more:
    libs  86.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  15.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 385 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
GNU make is a SystemRequirements.
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
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Package suggested but not available for checking: ‘Biostrings’
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Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Namespaces in Imports field not imported from:
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Package suggested but not available for checking: ‘DNAcopy’
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Package suggested but not available for checking: ‘BRugs’
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Package suggested but not available for checking: ‘webshot2’
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Packages suggested but not available for checking:
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Namespace in Imports field not imported from: ‘splatter’
  All declared Imports should be used.
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Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Note: found 2666 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘flowCore’
installed size is 94.9Mb
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Namespace in Imports field not imported from: ‘rstantools’
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is 49.9Mb
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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
installed size is 42.6Mb
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Namespace in Imports field not imported from: ‘rstantools’
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.9Mb
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Namespace in Imports field not imported from: ‘BiDAG’
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Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
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Namespaces in Imports field not imported from:
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Namespace in Imports field not imported from: ‘nycflights13’
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Namespace in Imports field not imported from: ‘httr’
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Package suggested but not available for checking: ‘INLA’
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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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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
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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
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GNU make is a SystemRequirements.
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Namespaces in Imports field not imported from:
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Package which this enhances but not available for checking: ‘asreml’
Package required but not available: ‘MEIGOR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Namespace in Imports field not imported from: ‘Rcpp’
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Namespaces in Imports field not imported from:
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Package suggested but not available for checking: ‘IHW’
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
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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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Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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Package suggested but not available for checking: ‘cmdstanr’
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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Namespace in Imports field not imported from: ‘shiny’
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Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘INLA’
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GNU make is a SystemRequirements.
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Namespace in Imports field not imported from: ‘dplyr’
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Package suggested but not available for checking: ‘sangerseqR’
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GNU make is a SystemRequirements.
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Namespace in Imports field not imported from: ‘dplyr’
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘kableExtra’
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Package suggested but not available for checking: ‘cmdstanr’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Packages suggested but not available for checking: 'graph', 'Rgraphviz'
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'LazyData' is specified without a 'data' directory
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Namespaces in Imports field not imported from:
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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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Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘doMPI’
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Namespace in Imports field not imported from: ‘RcppEigen’
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 179 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘ReGenesees’
Note: found 58 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
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Package required but not available: ‘org.Dr.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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Packages suggested but not available for checking:
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Package unavailable to check Rd xrefs: ‘GenomicRanges’
Package required but not available: ‘bluster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
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Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
converting counts to integer mode
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
>   
> data.mageck = stat.mageck(untreated.list = list(CONTROL1, CONTROL2),
+ treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+ norm.fun="median", extractpattern=expression("^(.+?)(_.+)"),
+ mageckfolder=NULL, sort.criteria="neg", adjust.method="fdr", filename = "TEST" , fdr.pval = 0.05)
sh: mageck: command not found
Warning in system(mageckstring) : error in running command
Warning in file(file, "rt") :
  cannot open file 'TEST.gene_summary.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: stat.mageck -> load.file -> read.table -> file
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CaRpools.Rmd’ using rmarkdown
sh: mageck: command not found
Quitting from lines 1956-1959 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘CaRpools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  18.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GAMBoost’
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc  37.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespaces in Imports field not imported from:
  ‘epitools’ ‘forcats’ ‘purrr’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CBPS’ ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 29.5Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs  27.0Mb
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  37.4Mb
GNU make is a SystemRequirements.
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘salso’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.3Mb
'LazyData' is specified without a 'data' directory
installed size is 160.0Mb
  sub-directories of 1Mb or more:
    libs  159.5Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Namespace in Imports field not imported from: ‘statmod’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CirceR’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.4Mb
Note: found 907 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.2Mb
    libs  10.2Mb
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 104 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘batchtools’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘htmltools’
  ‘jsonlite’ ‘magrittr’ ‘methods’ ‘plotly’ ‘reshape’ ‘rlang’ ‘shiny’
  ‘shinyWidgets’ ‘shinyjqui’ ‘shinyjs’ ‘shinymaterial’ ‘sortable’ ‘ssh’
  ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
installed size is 124.7Mb
  sub-directories of 1Mb or more:
    libs  124.4Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bench’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘multtest’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'GenomicInteractions', 'GenomicRanges', 'Gviz', 'countreg'
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 8119 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘cmdstanr’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Note: found 10 marked UTF-8 strings
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Packages required but not available:
  'ChIPseeker', 'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 28982 marked UTF-8 strings
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘networkD3’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
Note: found 29 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.5Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 9 marked UTF-8 strings
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.8Mb
installed size is  5.5Mb
  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  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...{C}=c\mathbf {U}\cdot \operatorname 
                                                  {diag}(\mathbf {s}) + \mat...
l.149 \mathbf{1}\,\mathbf{o}^T}{}
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Package required but not available: ‘IsoGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespaces in Imports field not imported from:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 5626 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Biobase', 'annotate', 'GO.db', 'moe430a.db'
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FNN’ ‘R.utils’ ‘SearchTrees’ ‘colorspace’ ‘colourpicker’
  ‘data.table’ ‘fields’ ‘mapproj’ ‘maps’ ‘maptools’ ‘ncdf4’ ‘raster’
  ‘rworldxtra’ ‘shinyFiles’ ‘shinyWidgets’ ‘shinyjs’ ‘shinythemes’ ‘sp’
  ‘tcltk’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.9Mb
  sub-directories of 1Mb or more:
    libs  34.6Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package required but not available: ‘GenomicInteractions’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 14729 marked UTF-8 strings
Package suggested but not available for checking: ‘limma’
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
Note: found 19 marked UTF-8 strings
Package suggested but not available for checking: ‘userfriendlyscience’
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘formatR’ ‘jsonlite’ ‘yaml’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
Note: found 4186 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 742 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  15.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'pcalg', 'CAM'
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  28.3Mb
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Note: found 92 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘lwgeom’ ‘s2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
installed size is 60.6Mb
  sub-directories of 1Mb or more:
    libs  59.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   2.6Mb
    libs   3.3Mb
Package suggested but not available for checking: ‘cec2005benchmark’
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs          2.7Mb
    sample_data   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Note: found 1187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 578 marked UTF-8 strings
Note: found 438 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProData’
Package suggested but not available for checking: ‘xcms’
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ICAMS’
Package unavailable to check Rd xrefs: ‘ICAMS’
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
Note: found 59 marked UTF-8 strings
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.7Mb
Note: found 139613 marked UTF-8 strings
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colourpicker’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Note: found 1934235 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘gsl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘SeqArray’

Package suggested but not available for checking: ‘GENESIS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘qvalue’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.3Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
Package suggested but not available for checking: ‘NMF’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v79’
Running ‘testthat.R’ [21s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error in `loadNamespace(x)`: there is no package called 'EnsDb.Hsapiens.v79'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(length(as_gene_symbol(entrez_test)), length(entrez_test)) at test-utils.R:16:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─crosstalkr::as_gene_symbol(entrez_test)
   5. └─base::loadNamespace(x)
   6.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     └─base (local) withOneRestart(expr, restarts[[1L]])
   8.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 2 | SKIP 8 | PASS 89 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 500 marked UTF-8 strings
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    libs  26.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘geosphere’ ‘mapdata’ ‘maps’ ‘marmap’ ‘shinydashboard’
  ‘shinyjs’ ‘stringr’ ‘swfscDAS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘future’
  All declared Imports should be used.
Note: found 282 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
Note: found 3031 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 1350 marked UTF-8 strings
installed size is 151.4Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    data    1.6Mb
    doc     1.2Mb
    libs  146.3Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘pbdMPI’
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 459 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    doc    1.2Mb
    help   1.0Mb
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    demos         4.3Mb
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘plyr’ ‘simpleboot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 109157 marked UTF-8 strings
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
Note: found 2020 marked UTF-8 strings
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 212 marked Latin-1 strings
  Note: found 12719 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘fs’ ‘googleCloudStorageR’
  All declared Imports should be used.
installed size is 30.6Mb
  sub-directories of 1Mb or more:
    libs  28.5Mb
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'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:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    deps  10.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    deps   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.9Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 36560 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 8 marked Latin-1 strings
installed size is 56.3Mb
  sub-directories of 1Mb or more:
    libs  55.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs    1.4Mb
    tests   1.5Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 54315 marked UTF-8 strings
Note: found 1 marked Latin-1 string
  Note: found 360 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
Package required and available but unsuitable version: ‘methods’

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: ‘dblog’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.5Mb
Namespace in Imports field not imported from: ‘html5’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘RedeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘lubridate’ ‘tseries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 122 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘bslib’ ‘knitr’ ‘matrixStats’ ‘rmarkdown’ ‘shinythemes’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BRugs’
Package suggested but not available for checking: ‘INLA’
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    libs  51.7Mb
Note: found 38 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  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
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-portable flags in variable 'PKG_FFLAGS':
  -std=f2008
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 37.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  34.9Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 5764 marked UTF-8 strings
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.8Mb
    help   1.5Mb
    libs   3.1Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
Note: found 47 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.2Mb
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.7Mb
GNU make is a SystemRequirements.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘plyr’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
installed size is 54.7Mb
  sub-directories of 1Mb or more:
    libs  54.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  14.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Note: found 8014 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
    doc  10.8Mb
'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:
    libs  10.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: ‘zinbwave’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
installed size is 58.3Mb
  sub-directories of 1Mb or more:
    libs  57.5Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:158'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:161'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  
  [ FAIL 36 | WARN 1 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘biomartr’
Package unavailable to check Rd xrefs: ‘biomartr’
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggmulti’ ‘loon’ ‘loon.data’ ‘loon.ggplot’ ‘loon.shiny’ ‘loon.tourr’
  ‘stats’ ‘zenplots’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Package suggested but not available for checking: ‘BOLTSSIRR’
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
'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
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.4Mb
Note: found 9796 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs  11.6Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rjson’ ‘uuid’
  All declared Imports should be used.
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
Note: found 100 marked UTF-8 strings
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘doMPI’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘parallel’ ‘rgdal’ ‘sp’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘ggplot2’ ‘nloptr’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    tutorials   5.2Mb
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
Package required but not available: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   8.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’
  All declared Imports should be used.
installed size is 66.8Mb
  sub-directories of 1Mb or more:
    libs  66.3Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> f:\mathbb 
                     {R}^K \to \mathbb {R}^L, (x_{n1},x_{n2},...,x_{nK}) \ma...
l.2282 ...) \mapsto f(x_{n1},x_{n2},...,x_{nK})}{}
                                                   be differentiable up to o...
! Undefined control sequence.
<argument> f:\mathbb {R}^K \to \mathbb 
                                       {R}^L, (x_{n1},x_{n2},...,x_{nK}) \ma...
l.2282 ...) \mapsto f(x_{n1},x_{n2},...,x_{nK})}{}
                                                   be differentiable up to o...
Note: found 149 marked UTF-8 strings
Note: found 4891 marked UTF-8 strings
Package suggested but not available for checking: ‘dsBaseClient’
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.6Mb
Note: found 1 marked Latin-1 string
'LazyData' is specified without a 'data' directory
Note: found 281 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'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:
    htmlwidgets   4.8Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.4Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.0Mb
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 310.9Mb
  sub-directories of 1Mb or more:
    libs  310.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2854 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GenEst’ ‘expint’ ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    doc    1.7Mb
    libs  25.9Mb
Package suggested but not available for checking: ‘cmdstanr’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    data   7.1Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
Namespaces in Imports field not imported from:
  ‘NatureSounds’ ‘av’ ‘magrittr’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   3.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Codoc mismatches from documentation object 'IQLearnFS_VHet-methods':
\S4method{qqplot}{IQLearnFS_VHet}
  Code: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ...)
  Docs: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ..., conf.level =
                 NULL, conf.args = list(exact = NULL, simulate.p.value
                 = FALSE, B = 2000, col = NA, border = NULL))
  Argument names in docs not in code:
    conf.level conf.args
Note: found 9 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   8.5Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘eaf/libs/eaf.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘eaf/io.o’, ‘mo-tools/hv.o’
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘eaf/io.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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs        9.1Mb
    shiny_app   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  11.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: ‘diffcoexp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AnnotationDbi', 'org.Hs.eg.db', 'qvalue'
Package unavailable to check Rd xrefs: ‘AnnotationDbi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qcr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without 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 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Note: found 1409 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lmtest’ ‘sandwich’ ‘urca’
  All declared Imports should be used.
installed size is 106.0Mb
  sub-directories of 1Mb or more:
    libs  105.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘econet.tex’ using tex
Error: processing vignette 'econet.tex' failed with diagnostics:
Running 'texi2dvi' on 'econet.tex' failed.
LaTeX errors:
! LaTeX Error: File `orcidlink.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \graphicspath
                 {{Figures/}}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘econet.tex’

SUMMARY: processing the following file failed:
  ‘econet.tex’

Error: Vignette re-building failed.
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘opGMMassessment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
Package suggested but not available for checking: ‘eggCountsExtra’
installed size is 95.1Mb
  sub-directories of 1Mb or more:
    libs  94.5Mb
GNU make is a SystemRequirements.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(EGRETci)
  > test_check("EGRETci")
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (10)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('tests_boot_tests.R:112'): paVector ────────────────────────────────
  `paIndexWinter` not equal to 11:13.
  Lengths differ: 4 is not 3
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  Error: Test failures
  Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
installed size is 142.4Mb
  sub-directories of 1Mb or more:
    libs  142.3Mb
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
'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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 60.4Mb
  sub-directories of 1Mb or more:
    libs  59.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rtsne’ ‘uwot’
  All declared Imports should be used.
Note: found 155 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 50 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  17.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
Note: found 16919 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 23639 marked Latin-1 strings
Namespace in Imports field not imported from: ‘BBmisc’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
'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      3.1Mb
    help   4.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 1 marked Latin-1 string
  Note: found 1508 marked UTF-8 strings
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   2.8Mb
Package suggested but not available for checking: ‘epidict’
installed size is 126.6Mb
  sub-directories of 1Mb or more:
    help    1.5Mb
    libs  124.2Mb
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: ‘taskscheduleR’
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘knitr’ ‘plyr’ ‘rgdal’ ‘tidyverse’ ‘tokenizers’ ‘xml2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘graph’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mzR’
Namespaces in Imports field not imported from:
  ‘methods’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    libs   2.4Mb
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘EMMAgeo’ ‘limSolve’ ‘shinyFiles’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.9Mb
Note: found 595 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘curl’ ‘scales’ ‘stringr’ ‘tidyquant’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package suggested but not available for checking: ‘ExactData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 342 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    exiftool  14.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
installed size is 93.6Mb
  sub-directories of 1Mb or more:
    libs  91.4Mb
GNU make is a SystemRequirements.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc      3.4Mb
    images   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
'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: ‘exuberdata’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 5 marked Latin-1 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘jss.Rmd’ using rmarkdown
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
! LaTeX Error: File `orcidlink.sty' not found.

! Emergency stop.
<read *> 

Error: processing vignette 'jss.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.2/fairadapt.Rcheck/vign_test/fairadapt/vignettes/jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See jss.log for more info.
--- failed re-building ‘jss.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘data.table’
  All declared Imports should be used.
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in '?.onAttach'.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    doc    1.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.6Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     2.9Mb
installed size is 47.4Mb
  sub-directories of 1Mb or more:
    libs  47.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    libs  38.6Mb
Package suggested but not available for checking: ‘coxKM’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

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
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
'LazyData' is specified without a 'data' directory
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data  16.0Mb
.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
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.5Mb
Package suggested but not available for checking: ‘NNLM’
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   5.1Mb
GNU make is a SystemRequirements.
Running ‘testthat.R’ [29s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  • Too variable (1)
  • long checking function (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-distributions.R:574'): likert labels ─────────────────────────
  cumsum(counts$n) not equal to floor(unname(p) * 100) + 1.
  Lengths differ: 6 is not 5
  Backtrace:
      ▆
   1. └─global expect_equal(cumsum(counts$n), floor(unname(p) * 100) + 1) at test-distributions.R:574:2
   2.   └─testthat::expect_equal(..., check.environment = FALSE)
  
  [ FAIL 1 | WARN 17 | SKIP 13 | PASS 1349 ]
  Error: Test failures
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   6.7Mb
Unexported objects imported by ':::' calls:
  ‘fdapace:::GCVLwls1D1’ ‘fdapace:::GetSmoothedMeanCurve’
  ‘fdapace:::HandleNumericsAndNAN’ ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Note: found 75 marked UTF-8 strings
installed size is 40.2Mb
  sub-directories of 1Mb or more:
    libs  38.4Mb
Namespaces in Imports field not imported from:
  ‘FastGP’ ‘MASS’ ‘fdapace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.2Mb
Note: found 76 marked UTF-8 strings
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘lattice’ ‘randomForest’ ‘tibble’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespace in Imports field not imported from: ‘panelView’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 43825 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.8Mb
    libs      1.3Mb
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MicrobeDS’
installed size is 39.5Mb
  sub-directories of 1Mb or more:
    libs  37.9Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R         5.0Mb
    doc       1.9Mb
    extdata   2.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.2Mb
'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
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'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
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 7 marked UTF-8 strings
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs  28.3Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    lib   10.4Mb
    libs  19.5Mb
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbitScraper-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Note: found 584 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    3.6Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   3.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘xtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Note: found 82 marked UTF-8 strings
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 300.6Mb
  sub-directories of 1Mb or more:
    libs  299.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc   9.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'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
Note: found 446 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘minet’
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 234 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘Rcpp’ ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.6Mb
    libs   7.5Mb
Note: found 31 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘LaplacesDemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
    libs   5.7Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.5Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R   6.0Mb
Note: found 50 marked UTF-8 strings
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 81.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.7Mb
    libs  73.5Mb
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'foba', 'rrlda'
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 39 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 120 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without 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  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'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
Package suggested but not available for checking: ‘WGCNA’
Package suggested but not available for checking: ‘IRanges’
Package unavailable to check Rd xrefs: ‘IRanges’
'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:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘cBioPortalData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 41.7Mb
  sub-directories of 1Mb or more:
    libs  41.6Mb
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gargle’ ‘getProxy’ ‘rappsflyer’ ‘rfacebookstat’ ‘rgoogleads’
  ‘rmytarget’ ‘rvkstat’ ‘ryandexdirect’ ‘rym’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘webshot’
  All declared Imports should be used.
Package suggested but not available for checking: ‘DAAGbio’
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   5.6Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Package which this enhances but not available for checking: ‘doMPI’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
installed size is 48.9Mb
  sub-directories of 1Mb or more:
    doc   44.3Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  10.2Mb
installed size is 84.8Mb
  sub-directories of 1Mb or more:
    libs  84.3Mb
GNU make is a SystemRequirements.
installed size is 65.2Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     61.6Mb
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.7Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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.
Package suggested but not available for checking: ‘gputools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 298.0Mb
  sub-directories of 1Mb or more:
    L8NY18    2.2Mb
    libs    294.6Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Namespace in Imports field not imported from: ‘badger’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lifecycle’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.4Mb
    libs      1.5Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘genderdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘R.utils’ ‘markdown’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rrvgo’
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
Malformed Description field: should contain one or more complete sentences.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
  ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   4.3Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 58 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   3.0Mb
    libs      4.3Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pander’ ‘readr’ ‘tidyr’
  All declared Imports should be used.
Note: found 80 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘phonTools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Note: found 646 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   4.5Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    R        10.0Mb
    extdata   2.5Mb
    help      3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 50.0Mb
  sub-directories of 1Mb or more:
    libs  48.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Note: found 64 marked Latin-1 strings
  Note: found 25 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘GWmodel’ ‘beepr’ ‘cartography’ ‘dplyr’ ‘raster’ ‘readxl’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinyjs’ ‘sp’
  ‘spdep’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pipeR’ ‘rlang’
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...s ,C_k)^\top = \mathbf {0}\,\,\text 
                                                  {and}\,\,\mathcal H_0: \ma...
l.238 ...H} (B_1,\ldots,B_k)^\top = \mathbf{0},}{}
                                                  
! Undefined control sequence.
<argument> ...\mathbf {C} = \mathbf {0}\,\, \text 
                                                  {or}\,\,\mathcal H_{0,\ell...
l.249 ...{B} = \mathbf{0}, \,\,\ell=1,\ldots,q,}{}
                                                  
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.251 ...s \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.252 \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                             , respectively, are calculated.
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.265 ...r \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.266 for \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                                 , the test statistics and c...
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘googlesheets4’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Package required but not available: ‘ggbio’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘do’ ‘survival’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 2356 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘grDevices’ ‘scales’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  18.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘productplots’ ‘scales’
  All declared Imports should be used.
Packages required but not available: 'memes', 'universalmotif'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘sna’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggOceanMapsData’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   1.9Mb
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lixoftConnectors’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.3Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘RPostgres’ ‘colourpicker’ ‘dplyr’
  ‘ggpmisc’ ‘ggpubr’ ‘ggrepel’ ‘gridExtra’ ‘markdown’ ‘plotly’
  ‘quantreg’ ‘rlang’ ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘survival’
  ‘survminer’ ‘table1’ ‘tidyr’ ‘zoo’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   2.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Note: found 6242 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘nomogramFormula’ ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 138 marked UTF-8 strings
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
Note: found 203 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘class’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘graphics’ ‘refund’ ‘stats’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.3Mb
'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:
    libs   6.4Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MCMCpack’ ‘ggplot2’ ‘moments’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 159.3Mb
  sub-directories of 1Mb or more:
    doc     1.4Mb
    libs  157.0Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Namespace in Imports field not imported from: ‘ordinal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 48.9Mb
  sub-directories of 1Mb or more:
    libs  48.2Mb
GNU make is a SystemRequirements.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespace in Imports field not imported from: ‘GMMBoost’
  All declared Imports should be used.
installed size is 54.9Mb
  sub-directories of 1Mb or more:
    libs  53.9Mb
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  24.9Mb
installed size is 64.0Mb
  sub-directories of 1Mb or more:
    libs           59.2Mb
    test_data       2.2Mb
    vignette_data   1.1Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
Namespaces in Imports field not imported from:
  ‘AER’ ‘MASS’ ‘Matrix’ ‘censReg’ ‘effects’ ‘foreign’ ‘lme4’ ‘lmtest’
  ‘nnet’ ‘pBrackets’ ‘plm’ ‘pscl’ ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rnaturalearthdata’
  All declared Imports should be used.
Note: found 1191 marked UTF-8 strings
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.4Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘preprocessCore’
Packages suggested but not available for checking: 'graph', 'mutoss'
'LazyData' is specified without a 'data' directory
Note: found 2629 marked UTF-8 strings
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
GNU make is a SystemRequirements.
Package required but not available: ‘SeqArray’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'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
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 1352 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘future’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    libs  29.7Mb
installed size is 143.4Mb
  sub-directories of 1Mb or more:
    libs  142.5Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.4Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'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’
Namespace in Imports field not imported from: ‘lfc’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘monocle’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘PairedData’ ‘RColorBrewer’ ‘agricolae’ ‘corrplot’ ‘desplot’
  ‘dplyr’ ‘ggplot2’ ‘ggpubr’ ‘gridGraphics’ ‘gtools’ ‘kableExtra’
  ‘knitr’ ‘magrittr’ ‘pastecs’ ‘reshape2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘summarytools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   3.2Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cubature’ ‘magicaxis’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Note: found 989 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mclust’
  All declared Imports should be used.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.6Mb
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    libs  31.7Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.