'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
'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 package ‘MHadaptive’ in Rd xrefs
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
checkRd: (-1) chickenk.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) multispati.Rd:54: Escaped LaTeX specials: \$
checkRd: (-1) randboot.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) kernelUD.Rd:210: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘filehash’
  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
Malformed Description field: should contain one or more complete sentences.
'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
File ‘ADMMnet/libs/ADMMnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘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
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘mFilter’ ‘regclass’ ‘writexl’
  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: ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'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: \&
checkRd: (-1) adapt.Rd:41: Escaped LaTeX specials: \$
File ‘ahaz/libs/ahaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘RandomFields’
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  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:
  ‘knitr’ ‘randomNames’ ‘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
Found the following files/directories:
  ‘ans_19-2.jpg’ ‘display2d_19-2.jpg’ ‘dist(3)_19-2.jpg’
  ‘dist(4)_19-2.jpg’ ‘dist(mirror)_19-2.jpg’ ‘dist(mirror2)_19-2.jpg’
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
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘AlgDesign/libs/AlgDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘alphabetr/libs/alphabetr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
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.
checkRd: (-1) varrob.Rd:44: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Zelig’
'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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Note: found 175 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Title field: should not end in a period.
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
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SportsAnalytics’
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/Anthropometry.Rcheck/00install.out’ for details.
Found the following significant warnings:
  header.h:50:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bicriterion_iterated_local_search_call.c:510:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/anticlust.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mcclust’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘aoristic-Ex.R’ failed
The error most likely occurred in:

> ### Name: aoristic.df
> ### Title: Calculate aoristic weights
> ### Aliases: aoristic.df
> 
> ### ** Examples
> 
> df <- aoristic.df(dcburglaries, 'X', 'Y', 'StartDateTime', 'EndDateTime')
Warning:  17 failed to parse.
Warning:  8 failed to parse.
Error in if (time.span >= 10080) { : 
  missing value where TRUE/FALSE needed
Calls: aoristic.df
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘dplyr’
  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:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
Found the following significant warnings:
  me.h:122:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  me.c:234:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ape.Rcheck/00install.out’ for details.
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
File ‘APIS/libs/APIS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘BayesianTools’
Problems with news in ‘NEWS.md’:
No news entries found.
Unknown package ‘BayesianTools’ in Rd xrefs
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’
checkRd: (-1) AQuadtree-package.Rd:11: Escaped LaTeX specials: \$
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
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:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
'LazyData' is specified without a 'data' directory
Note: found 1409 marked UTF-8 strings
Package which this enhances but not available for checking: ‘ARTP’
Found the following significant warnings:
  ARTP2_init.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ARTP2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ptree.c:47:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  warm.c:217:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/arules.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ptree.c:32:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ptree.c:192:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ptree.c:200:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ptree.c:768:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/arulesSequences.Rcheck/00install.out’ for details.
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Note: found 328 marked UTF-8 strings
Found the following significant warnings:
  /data/gannet/ripley/R/test-dev/processx/include/processx/unix-sockets.h:36:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/processx/include/processx/unix-sockets.c:118:29: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  asciicast.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  common.c:76:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  r.c:26:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/asciicast.Rcheck/00install.out’ for details.
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
File ‘ash/libs/ash.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MSToutput.txt’
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
'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’
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building ‘PeakSegDisk.Rmd’ using knitr
--- finished re-building ‘PeakSegDisk.Rmd’

--- re-building ‘binseg.Rmd’ using knitr
Quitting from lines 127-157 (binseg.Rmd) 
Error: processing vignette 'binseg.Rmd' failed with diagnostics:
'from' must be a finite number
--- failed re-building ‘binseg.Rmd’

--- re-building ‘cum_median.Rmd’ using knitr
--- finished re-building ‘cum_median.Rmd’

--- re-building ‘data.table.Rmd’ using knitr
--- finished re-building ‘data.table.Rmd’

--- re-building ‘git.Rmd’ using knitr
--- finished re-building ‘git.Rmd’

--- re-building ‘optseg.Rmd’ using knitr
--- finished re-building ‘optseg.Rmd’

--- re-building ‘regex.Rmd’ using knitr
--- finished re-building ‘regex.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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
Problems with news in ‘NEWS.md’:
No news entries found.
Unknown package ‘snpar’ in Rd xrefs
Found the following files/directories:
  ‘extrapackage’
'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
Found the following significant warnings:
  driver.c:114:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  driver.c:161:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  driver.c:199:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/audio.Rcheck/00install.out’ for details.
Note: found 1 marked UTF-8 string
Note: found 899 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
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
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘broom’ ‘tibble’ ‘usethis’
  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
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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘rclipboard’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
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.
Note: found 64209 marked UTF-8 strings
Note: found 133353 marked UTF-8 strings
Namespace in Imports field not imported from: ‘glpkAPI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘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.
Found the following files/directories:
  ‘exemplary_input1.txt’ ‘exemplary_input2.txt’
'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
Found the following significant warnings:
  utilities.h:67:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilities.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilities.h:83:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Ball_omp.h:6:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Ball_omp.h:7:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Ball_omp.h:8:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bd_gwas.c:260:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilities.c:1438:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilities.c:1446:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilities.c:1455:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/Ball.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘fs’ ‘testthat’
  All declared Imports should be used.
Found the following significant warnings:
  bamlss_functions.c:117:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/bamlss.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Note: found 148 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Note: found 13825 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
File ‘Barnard/libs/Barnard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
Found the following significant warnings:
  init.c:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/BART.Rcheck/00install.out’ for details.
File ‘base64enc/libs/base64enc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
Found the following significant warnings:
  bayesDccGarch.c:48:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bayesDccGarch.c:110:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bayesDccGarch.c:172:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/bayesDccGarch.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘StanHeaders’ ‘astsa’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppParallel’ ‘mlbench’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
File ‘bayesianETAS/libs/bayesianETAS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
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.
GNU make is a SystemRequirements.
Found the following significant warnings:
  rgig.c:42:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/BayesLN.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘bayesloglin/libs/bayesloglin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘FastGP’
  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 [112, 115] is out of the bounds [0, 112] of object ‘cbetaAllRow’ with type ‘arma::uvec’ {aka ‘arma::Col<unsigned int>’} [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/bayesm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘MCMCpack’ ‘R2WinBUGS’ ‘R2jags’ ‘carData’ ‘rjags’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppNumerical’
  All declared Imports should be used.
File ‘bayesQR/libs/bayesQR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
Note: found 1924 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘matrixcalc’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
File ‘BayesTree/libs/BayesTree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
checkRd: (-1) create_ThetaMatrix.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) create_ThetaMatrix.Rd:41: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘rgl’
  All declared Imports should be used.
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’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘locfit’ ‘secr’
  All declared Imports should be used.
File ‘BCBCSF/libs/BCBCSF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘fabiabreast.txt’
checkRd: (-1) tlsce.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:93: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'harmony', 'dlfUtils'
Namespace in Imports field not imported from: ‘splatter’
  All declared Imports should be used.
Note: found 72 marked UTF-8 strings
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
Found the following files/directories:
  ‘dump.txt’
Package suggested but not available for checking: ‘flowCore’
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘alist.txt’ ‘rpkg’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘forecast’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following significant warnings:
  load.c:11:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotime.h:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotime.h:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mark.c:75:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mark.c:118:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mark.c:119:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotime.c:61:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotime.c:71:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  process_memory.c:79:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/bench.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘BenfordTests/libs/BenfordTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘BiDAG’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 20 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘betategarch/libs/betategarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) scrHpd.Rd:30: Escaped LaTeX specials: \&
Note: found 10089 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
Note: found 582 marked UTF-8 strings
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
File ‘BiasedUrn/libs/BiasedUrn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
Note: found 1904 marked UTF-8 strings
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘DAAG’ ‘datasets’ ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
Found the following significant warnings:
  rbimax.c:326:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/biclust.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘RBGL’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ffbase’
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 940 marked Latin-1 strings
Found the following significant warnings:
  lib.h:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib.c:3:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/bigGP.Rcheck/00install.out’ for details.
File ‘biglm/libs/biglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Checking should be performed on sources prepared by ‘R CMD build’.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rename.h:420:41: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/BigQuic.Rcheck/00install.out’ for details.
File ‘bigReg/libs/bigReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘outputs’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bigrquery)
  > 
  > test_check("bigrquery")
  [ FAIL 1 | WARN 1 | SKIP 66 | PASS 128 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Authentication not available (8)
  • No BigQuery access credentials available (55)
  • On CRAN (1)
  • On Linux (1)
  • bq_authable() is not TRUE (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-bq-parse.R:37'): can parse date/times ──────────────────────────
  Error in `as.character.POSIXt(dt, "%Y-%m-%dT%H:%M:%S")`: 'digits' must be numeric, integer valued
  Backtrace:
      ▆
   1. ├─testthat::expect_identical(...) at test-bq-parse.R:37:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─bigrquery:::bq_parse_single(...)
   5. │ └─jsonlite::toJSON(value, auto_unbox = TRUE)
   6. │   └─base::force(x)
   7. ├─base::as.character(dt, "%Y-%m-%dT%H:%M:%S")
   8. └─base::as.character.POSIXt(dt, "%Y-%m-%dT%H:%M:%S")
  
  [ FAIL 1 | WARN 1 | SKIP 66 | PASS 128 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 660 marked UTF-8 strings
Found the following significant warnings:
  binarizeBASCA.h:37:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  TASC.c:258:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  TASC_min.c:256:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  binarizeBASCA.c:358:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/Binarize.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BinaryEPPM.Rd:159: Escaped LaTeX specials: \&
'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
File ‘binom/libs/binom.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘msa’
checkRd: (-1) core.find.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) core.find.Rd:87: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:89: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:91: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:93: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:95: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:97: Escaped LaTeX specials: \^
'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(BiocManager)
  Bioconductor does not yet build and check packages for R version 4.3; see
    https://bioconductor.org/install
  > 
  > test_check("BiocManager")
  [ FAIL 2 | WARN 0 | SKIP 25 | PASS 75 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (7)
  • mis-configuration, R 4.3.0, Bioconductor 3.16 (17)
  • too idiosyncratic for standardized testing (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_repositories.R:127'): '.repositories_base()' respects BiocManager.snapshot ──
  `.repositories_base()` did not throw an error.
  Backtrace:
      ▆
   1. ├─withr::with_options(...) at test_repositories.R:127:4
   2. │ └─base::force(code)
   3. └─testthat::expect_error(.repositories_base(), "BiocManager.snapshot")
  ── Failure ('test_repositories.R:131'): '.repositories_base()' respects BiocManager.snapshot ──
  `.repositories_base()` did not throw an error.
  Backtrace:
      ▆
   1. ├─withr::with_options(...) at test_repositories.R:131:4
   2. │ └─base::force(code)
   3. └─testthat::expect_error(.repositories_base(), "BiocManager.snapshot")
  
  [ FAIL 2 | WARN 0 | SKIP 25 | PASS 75 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Found the following files/directories:
  ‘Plots.pdf’
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘desc’ ‘lme4’ ‘mitml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘asreml’
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘bioPN/libs/bioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 46 marked UTF-8 strings
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘magrittr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Found the following significant warnings:
  bit.c:57:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bit.c:68:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/bit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  binarizeBASCA.h:37:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  TASC.c:258:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  TASC_min.c:256:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  binarizeBASCA.c:358:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/BiTrinA.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
Package suggested but not available for checking: ‘RQuantLib’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘digest’ ‘ergm’ ‘foreign’ ‘gWidgets2’ ‘gWidgets2tcltk’ ‘haven’
  ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
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 ‘nMaxCritMet’ with type ‘arma::rowvec’ {aka ‘arma::Row<double>’} [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/bmabasket.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
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
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.
File ‘BMRV/libs/BMRV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Found the following significant warnings:
  include/register.h:46:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  include/register.h:75:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  include/register.h:76:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  include/register.h:82:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  globals.c:15:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  globals.c:33:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  test.counter.c:26:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  test.counter.c:35:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/bnlearn.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘bnstruct.Rnw’ using knitr
Error: processing vignette 'bnstruct.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'bnstruct.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.211 \hldef
            {git\ clone\ https}\hlopt{://}\hldef{github.com}\hlopt{/}\hldef{...

? 
! Emergency stop.
l.211 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘bnstruct.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  common.c:15:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  random.h:12:22: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sat_search.c:106:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  symbolic_simulator.c:344:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/BoolNet.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘HSAUR3’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
File ‘bootruin/libs/bootruin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    modules 0.x
'LazyData' is specified without a 'data' directory
checkRd: (-1) bpca.Rd:85: Escaped LaTeX specials: \&
Found the following significant warnings:
  randomnumbers.h:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  randomnumbers.c:13:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/BPEC.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘BPEC.Rnw’ using Sweave
Error: processing vignette 'BPEC.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'BPEC.tex' failed.
LaTeX errors:
! Missing = inserted for \ifnum.
<to be read again> 
                   v
l.8 
    
! Emergency stop.
<to be read again> 
                   v
l.8 
    
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'BPEC.Rnw'

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Note: found 2487 marked UTF-8 strings
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
checkRd: (-1) R2txtJG.Rd:90: Escaped LaTeX specials: \#
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘Branching/libs/Branching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  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
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) brr-package.Rd:33: Escaped LaTeX specials: \&
Found the following significant warnings:
  BugsHelper.c:76:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BugsHelper.c:87:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BugsHelper.c:88:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/BRugs.Rcheck/00install.out’ for details.
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
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘grDevices’ ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘magrittr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘bvarsv/libs/bvarsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 179 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:
  ‘qgraph’ ‘reshape2’
  All declared Imports should be used.
Found the following significant warnings:
  defns.h:671:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  defns.h:761:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.h:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.h:27:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  getdata.c:47:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  hash.h:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  modelfiles.c:197:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  modelfiles.c:521:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  modelfiles.c:592:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  modelfiles.c:778:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rc50.c:42:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.c:46:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.c:191:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rsample.c:59:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  top.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utility.c:795:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/C50.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
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
Found the following significant warnings:
  cairobem.c:50:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Rapi.h:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Rapi.h:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cairotalk.c:661:23: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cairotalk.c:1552:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cairotalk.c:1588:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  xlib-backend.c:156:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/Cairo.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
Package suggested but not available for checking: ‘ReGenesees’
Note: found 58 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘CAMAN/libs/CAMAN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RxODE’
'LazyData' is specified without a 'data' directory
Note: found 287 marked UTF-8 strings
Note: found 512 marked UTF-8 strings
Note: found 23 marked UTF-8 strings
Found the following files/directories:
  ‘tmp.txt’
Found the following files/directories:
  ‘MDA231_tree.pdf’
checkRd: (-1) caic-class.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) caic-class.Rd:15: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘methods’ ‘readr’ ‘recipes’ ‘sf’ ‘stringr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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: ‘R.utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
checkRd: (-1) plot-methods.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) plot-methods.Rd:96: Escaped LaTeX specials: \_
Namespaces in Imports field not imported from:
  ‘igraph’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘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
Namespace in Imports field not imported from: ‘reshape’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GAMBoost’
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
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
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Found the following significant warnings:
  catnet_rexport.h:63:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/catnet.Rcheck/00install.out’ for details.
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: \&
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘epitools’ ‘forcats’ ‘purrr’
  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
Note: found 32 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CBPS’ ‘spelling’
  All declared Imports should be used.
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    News about the ccdf R package
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
Found the following files/directories:
  ‘hotcold.csv’
Namespace in Imports field not imported from: ‘formula.tools’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
File ‘CDLasso/libs/CDLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘urltools’
  All declared Imports should be used.
Found the following files/directories:
  ‘out.png’ ‘out1.txt’ ‘out2.txt’
Note: found 907 marked UTF-8 strings
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.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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.
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major refactoring of the code
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
File ‘cgAUC/libs/cgAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'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
Package suggested but not available for checking: ‘RxODE’
Error(s) in re-building vignettes:
--- re-building ‘CGNM-vignette.Rmd’ using rmarkdown
Quitting from lines 36-57 (CGNM-vignette.Rmd) 
Error: processing vignette 'CGNM-vignette.Rmd' failed with diagnostics:
there is no package called 'RxODE'
--- failed re-building ‘CGNM-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  graph.h:85:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  session.h:40:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  session.c:29:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/cgraph.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Found the following significant warnings:
  NPPELT.c:18:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  NPPELT.c:27:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  NPPELT.c:41:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  NPPELT.c:42:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  NPPELT.c:43:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  NPPELT.c:72:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/changepoint.np.Rcheck/00install.out’ for details.
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:
  ‘bench’ ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rappdirs’ ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘darts’
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinycssloaders’ ‘shinythemes’
  All declared Imports should be used.
checkRd: (-1) hyptis.Rd:31: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘stepres00.txt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 8119 marked UTF-8 strings
File ‘ChIPtest/libs/ChIPtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘cmdstanr’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
File ‘CHsharp/libs/CHsharp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘Matrix’ ‘stringr’
  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
'LazyData' is specified without a 'data' directory
File ‘CIFsmry/libs/CIFsmry.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘magrittr’
  All declared Imports should be used.
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
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
'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
'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.
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  cleancall.h:30:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cleancall.c:40:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  test.c:68:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/cleancall.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # ==================================================================== #
  > # TITLE                                                                #
  > # Fast and Easy Data Cleaning                                          #
  > #                                                                      #
  > # SOURCE                                                               #
  > # https://github.com/msberends/cleaner                                 #
  > #                                                                      #
  > # LICENCE                                                              #
  > # (c) 2021 Berends MS (m.s.berends@umcg.nl)                            #
  > #                                                                      #
  > # This R package is free software; you can freely use and distribute   #
  > # it for both personal and commercial purposes under the terms of the  #
  > # GNU General Public License version 2.0 (GNU GPL-2), as published by  #
  > # the Free Software Foundation.                                        #
  > #                                                                      #
  > # This R package was publicly released in the hope that it will be     #
  > # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
  > # ==================================================================== #
  > 
  > library(testthat)
  > library(cleaner)
  > 
  > test_check("cleaner")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 18 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-rdate.R:31'): random date generation works ───────────────────
  `rdate(42, -1)` did not throw an error.
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 18 ]
  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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ClickClust/libs/ClickClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) diagwl.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) diagwl.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clinfun (development version)
checkRd: (-1) coxphCPE.Rd:2: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataADaMCDISCP01.Rd:48: Escaped LaTeX specials: \&
Running ‘testthat.R’ [22s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clinUtils)
  > 
  > test_check("clinUtils")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 300 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_loadDataADaMSDTM.R:172'): An error is generated if the specified object to convert to date is not a date ──
  `convertToDateTime(c(1, 2))` did not throw an error.
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 300 ]
  Error: Test failures
  Execution halted
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
File ‘clogitboost/libs/clogitboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'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: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Found the following significant warnings:
  criteria.h:45:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  criteria.h:48:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/clusterCrit.Rcheck/00install.out’ for details.
possible bashism in cleanup line 15 (brace expansion):
  rm -f src/*.{o,so,mod}
  possible bashism in cleanup line 17 (brace expansion):
  rm -f config.{log,status}
  possible bashism in cleanup line 22 (brace expansion):
  rm -f vignettes/*.{tex,aux,bbl,blg,log,toc,idx,ind,ilg,out,synctex.gz}
checkRd: (-1) genRandomClust.Rd:228: Escaped LaTeX specials: \_
checkRd: (-1) genRandomClust.Rd:259: Escaped LaTeX specials: \_
checkRd: (-1) genRandomClust.Rd:327: Escaped LaTeX specials: \_
checkRd: (-1) plot1DProjection.Rd:95: Escaped LaTeX specials: \_ \_
checkRd: (-1) plot2DProjection.Rd:117: Escaped LaTeX specials: \_ \_
checkRd: (-1) simClustDesign.Rd:235: Escaped LaTeX specials: \_
checkRd: (-1) simClustDesign.Rd:268: Escaped LaTeX specials: \_
checkRd: (-1) simClustDesign.Rd:331: Escaped LaTeX specials: \_
Found the following files/directories:
  ‘clusterhap_reports’
File ‘clustering.sc.dp/libs/clustering.sc.dp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘methods’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) HINoV.Mod.rd:3: Escaped LaTeX specials: \&
checkRd: (-1) HINoV.Symbolic.rd:3: Escaped LaTeX specials: \&
checkRd: (-1) cluster.Gen.rd:14: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:18: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:29: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) cluster.Gen.rd:33: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:34: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:36: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:38: Escaped LaTeX specials: \_ \_
checkRd: (-1) cluster.Gen.rd:51: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:52: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:54: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:55: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:62: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) comparing.Partitions.rd:12: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.BC.rd:10: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.GDM.rd:33: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.SM.rd:10: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.C.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.G2.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.G3.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.H.rd:16: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.S.rd:12: Escaped LaTeX specials: \$ \_ \_
File ‘ClusterStability/libs/ClusterStability.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
File ‘ClustMMDD/libs/ClustMMDD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘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
Found the following significant warnings:
  optimal_assignment.c:47:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/clv.Rcheck/00install.out’ for details.
File ‘clv/libs/clv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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.
Found the following significant warnings:
  Rwrapper.c:84:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Rwrapper.c:184:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/cmfrec.Rcheck/00install.out’ for details.
Note: found 4622 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
File ‘cmprsk/libs/cmprsk.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Running examples in ‘cmsafops-Ex.R’ failed
The error most likely occurred in:

> ### Name: hourmean
> ### Title: Determine hourly means
> ### Aliases: hourmean
> 
> ### ** Examples
> 
> ## Create an example NetCDF file with a similar structure as used by CM
> ## SAF. The file is created with the ncdf4 package.  Alternatively
> ## example data can be freely downloaded here: <https://wui.cmsaf.eu/>
> 
> library(ncdf4)
> 
> ## create some (non-realistic) example data
> 
> lon <- seq(5, 15, 0.5)
> lat <- seq(45, 55, 0.5)
> 
> time <- seq(ISOdate(2000, 1, 1), ISOdate(2000, 1, 2), "mins")
> origin <- as.Date("1983-01-01 00:00:00")
> time <- as.numeric(difftime(time, origin, units = "min"))
> data <- array(250:350, dim = c(21, 21, 1441))
> ## create example NetCDF
> 
> x <- ncdim_def(name = "lon", units = "degrees_east", vals = lon)
> y <- ncdim_def(name = "lat", units = "degrees_north", vals = lat)
> t <- ncdim_def(name = "time", units = "minutes since 1983-01-01 00:00:00",
+               vals = time, unlim = TRUE)
> var1 <- ncvar_def("SIS", "W m-2", list(x, y, t), -1, prec = "short")
> vars <- list(var1)
> ncnew <- nc_create(file.path(tempdir(),"CMSAF_example_file.nc"), vars)
> ncvar_put(ncnew, var1, data)
> ncatt_put(ncnew, "lon", "standard_name", "longitude", prec = "text")
> ncatt_put(ncnew, "lat", "standard_name", "latitude", prec = "text")
> nc_close(ncnew)
> 
> ## Determine the hourly means of the example CM SAF NetCDF file
> ## and write the output to a new file.
> hourmean(var = "SIS", infile = file.path(tempdir(),"CMSAF_example_file.nc"), 
+  outfile = file.path(tempdir(),"CMSAF_example_file_hourmean.nc"))
Error in hourx_wrapper(1, var, infile, outfile, nc34, overwrite, verbose,  : 
  The time steps must be available at least every hour. Please try daysum for diurnal aggregation. 
Calls: hourmean -> hourx_wrapper
Execution halted
Running ‘spelling.R’
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...6c6
< NULL
---
> All Done!
  Running ‘testthat.R’ [166s/191s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cmsafops)
  > 
  > test_check("cmsafops")
  149016292920292920149016149016149016149028149016[ FAIL 3 | WARN 0 | SKIP 0 | PASS 9082 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_hourmean.R:8'): (code run outside of `test_that()`) ────────────
  Error in `hourx_wrapper(1, var, infile, outfile, nc34, overwrite, verbose, 
      nc = nc)`: The time steps must be available at least every hour. Please try daysum for diurnal aggregation. 
  Backtrace:
      ▆
   1. └─cmsafops::hourmean(...) at test_hourmean.R:8:0
   2.   └─cmsafops:::hourx_wrapper(...)
  ── Error ('test_hoursum.R:8'): (code run outside of `test_that()`) ─────────────
  Error in `hourx_wrapper(2, var, infile, outfile, nc34, overwrite, verbose, 
      nc = nc)`: The time steps must be available at least every hour. Please try daysum for diurnal aggregation. 
  Backtrace:
      ▆
   1. └─cmsafops::hoursum(...) at test_hoursum.R:8:0
   2.   └─cmsafops:::hourx_wrapper(...)
  ── Error ('test_mondaymean.R:8'): (code run outside of `test_that()`) ──────────
  Error in `mondaymean("SIS", file.path(data_dir, "ex_mondaymean.nc"), file_out)`: The time steps must be available every 15min (at least 12 days per month), 30min (at least 6 days per month) or 1h (at least 3 days per month). One or more time steps do not meet the requirements. The result of these time steps is NA. 
  Backtrace:
      ▆
   1. └─cmsafops::mondaymean(...) at test_mondaymean.R:8:0
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 9082 ]
  Error: Test failures
  Execution halted
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
Package suggested but not available for checking: ‘tobit1’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 14729 marked UTF-8 strings
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
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
Note: found 30244 marked UTF-8 strings
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘coenoflex/libs/coenoflex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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.
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Note: found 4186 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building ‘collin.Rnw’ using knitr
Error: processing vignette 'collin.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'collin.tex' failed.
LaTeX errors:
! Missing = inserted for \ifnum.
<to be read again> 
                   v
l.74 
     
! Emergency stop.
<to be read again> 
                   v
l.74 
     
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘collin.Rnw’

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

Error: Vignette re-building failed.
Execution halted
File ‘collUtils/libs/collUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'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
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
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:
  ‘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
Package suggested but not available for checking: ‘CAM’
File ‘compareC/libs/compareC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) compareGroups-package.Rd:52: Escaped LaTeX specials: \~
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  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
checkRd: (-1) HouseholdExp.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) HouseholdExp.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) mix2compositions.Rd:28: Escaped LaTeX specials: \$
checkRd: (-1) mixRead.Rd:30: Escaped LaTeX specials: \$ \$
checkRd: (-1) mixRead.Rd:31: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘ConConPiWiFun/libs/ConConPiWiFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 92 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Deprecation
'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:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
File ‘condmixt/libs/condmixt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
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.
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) plotMCC.Rd:19: Escaped LaTeX specials: \_
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
File ‘ConsReg/libs/ConsReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
Found the following significant warnings:
  brentmin.c:237:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ContaminatedMixt.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
File ‘contoureR/libs/contoureR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
File ‘cord/libs/cord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) poss_local.Rd:21: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
Note: found 6 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
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: \&
Note: found 1187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 578 marked UTF-8 strings
checkRd: (-1) sgt.Rd:16: Escaped LaTeX specials: \&
Note: found 438 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) egde.Rd:26: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
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
Found the following significant warnings:
  bb.c:719:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ibb.c:78:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/countdata.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 139613 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
Running examples in ‘covatest-Ex.R’ failed
The error most likely occurred in:

> ### Name: read.STdata
> ### Title: Imports a text file in R
> ### Aliases: read.STdata
> 
> ### ** Examples
> 
> #example 1: import a text file, with dates stored in a single column (the 4th)
> # and fill missing time points in monthly time series, with time lag equal to one
> 
> file_date <- system.file("extdata", "file_date.txt", package = "covatest")
> db.date <- read.STdata(file = file_date, header = TRUE, iclx = 2, icly = 3, iclt = 0,
+ icldate = c(icl.date = 4, iclty = 0, icltm = 0, icltd = 0),
+ icltime = c(icl.time = 0, icltH =0, icltM = 0, icltS = 0),
+ iclvr = 5, iclsp = 1, missing.v = -99999, save.as = "data.frame",
+ date.format = c("Date", "%d-%m-%Y"), bytime = "%m", tlag = 1)

Execution halted
File ‘covBM/libs/covBM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘colourpicker’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘covfefe_inauguration.txt’
Note: found 1934235 marked UTF-8 strings
Note: found 2385 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘CoxPlus/libs/CoxPlus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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
Found the following significant warnings:
  bcplm.c:84:22: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/cplm.Rcheck/00install.out’ for details.
File ‘cpm/libs/cpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Non-visible changes:
'LazyData' is specified without a 'data' directory
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  crf/src/crfsuite_internal.h:169:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  crf/src/params.h:36:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  crf/src/crf1d_encode.c:1031:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  crf/src/crf1d_feature.c:77:22: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  crf/src/quark.h:39:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  crf/src/params.c:252:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  crf/src/quark.c:72:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/crfsuite.Rcheck/00install.out’ for details.
Note: found 34 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building ‘cricinfo.Rmd’ using rmarkdown
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
Warning: Removed 2574 rows containing non-finite values (stat_smooth).
Warning: Removed 2574 rows containing missing values (geom_point).
--- finished re-building ‘cricinfo.Rmd’

--- re-building ‘cricsheet.Rmd’ using rmarkdown
Quitting from lines 112-148 (cricsheet.Rmd) 
Error: processing vignette 'cricsheet.Rmd' failed with diagnostics:
Aesthetics must be either length 1 or the same as the data (1): colour and fill
--- failed re-building ‘cricsheet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘gbm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
‘cleanup’: /bin/bash is not portable
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
download_terraclimate.html:20:1 (download_terraclimate.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
download_terraclimate.html:20:1 (download_terraclimate.Rd:6): Warning: <img> proprietary attribute "logo"
eto_calibration.html:20:1 (eto_calibration.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
eto_calibration.html:20:1 (eto_calibration.Rd:6): Warning: <img> proprietary attribute "logo"
loadROI.html:20:1 (loadROI.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
loadROI.html:20:1 (loadROI.Rd:6): Warning: <img> proprietary attribute "logo"
monthly_stack.html:20:1 (monthly_stack.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
monthly_stack.html:20:1 (monthly_stack.Rd:6): Warning: <img> proprietary attribute "logo"
plot_AWC.html:20:1 (plot_AWC.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
plot_AWC.html:20:1 (plot_AWC.Rd:6): Warning: <img> proprietary attribute "logo"
ppt_calibration.html:20:1 (ppt_calibration.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
ppt_calibration.html:20:1 (ppt_calibration.Rd:6): Warning: <img> proprietary attribute "logo"
see_brazil_biomes.html:20:1 (see_brazil_biomes.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
see_brazil_biomes.html:20:1 (see_brazil_biomes.Rd:6): Warning: <img> proprietary attribute "logo"
see_brazil_states.html:20:1 (see_brazil_states.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
see_brazil_states.html:20:1 (see_brazil_states.Rd:6): Warning: <img> proprietary attribute "logo"
waterDemand.html:20:1 (waterDemand.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
waterDemand.html:20:1 (waterDemand.Rd:6): Warning: <img> proprietary attribute "logo"
'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
Found the following HTML validation problems:
ccrop_zoning.html:20:1 (ccrop_zoning.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
ccrop_zoning.html:20:1 (ccrop_zoning.Rd:6): Warning: <img> proprietary attribute "logo"
download_terraclimate.html:20:1 (download_terraclimate.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
download_terraclimate.html:20:1 (download_terraclimate.Rd:6): Warning: <img> proprietary attribute "logo"
loadROI.html:20:1 (loadROI.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
loadROI.html:20:1 (loadROI.Rd:6): Warning: <img> proprietary attribute "logo"
plot_ccrop_zoning.html:20:1 (plot_ccrop_zoning.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
plot_ccrop_zoning.html:20:1 (plot_ccrop_zoning.Rd:6): Warning: <img> proprietary attribute "logo"
see_brazil_biomes.html:20:1 (see_brazil_biomes.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
see_brazil_biomes.html:20:1 (see_brazil_biomes.Rd:6): Warning: <img> proprietary attribute "logo"
see_brazil_states.html:20:1 (see_brazil_states.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
see_brazil_states.html:20:1 (see_brazil_states.Rd:6): Warning: <img> proprietary attribute "logo"
tmax_calibration.html:20:1 (tmax_calibration.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
tmax_calibration.html:20:1 (tmax_calibration.Rd:6): Warning: <img> proprietary attribute "logo"
tmean.html:20:1 (tmean.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
tmean.html:20:1 (tmean.Rd:6): Warning: <img> proprietary attribute "logo"
tmean_monthly_stack.html:20:1 (tmean_monthly_stack.Rd:6): Warning: <img> attribute "width" has invalid value "auto"
tmean_monthly_stack.html:20:1 (tmean_monthly_stack.Rd:6): Warning: <img> proprietary attribute "logo"
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  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:
    Major features
    Minor features
checkRd: (-1) handmovement.Rd:9: Escaped LaTeX specials: \_ \_
File ‘crrSC/libs/crrSC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 500 marked UTF-8 strings
'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
Found the following significant warnings:

  Warning: ! Deprecation: Argument 'ncores' is deprecated.
  Warning: ! Deprecation: Argument 'ncores' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
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
Found the following significant warnings:
  structs.h:44:29: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vector.c:125:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ctl.Rcheck/00install.out’ for details.
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/ctmcd.Rcheck/00install.out’ for details.
'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
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘par-7269706c6579’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Hello.csv’
Found the following significant warnings:
  ../inst/include/cuba.h:75:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/cuba.h:76:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/cubature.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  redefine.h:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.h:27:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  getdata.c:44:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  hash.h:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rcubist.c:40:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.c:46:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.c:191:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  top.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/Cubist.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 459 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
'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:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
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
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'
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    CVXR pre-0.94-4
File ‘cycleRtools/libs/cycleRtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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
checkRd: (-1) dspg.Rd:29: Escaped LaTeX specials: \^ \^
checkRd: (-1) dspgd2015.Rd:31: Escaped LaTeX specials: \^ \^
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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.
File ‘DALY/libs/DALY.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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
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
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: ‘R6’
  All declared Imports should be used.
'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
Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: ‘stubthat’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Note: found 8 marked Latin-1 strings
Found the following significant warnings:
  init.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:30:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:36:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:37:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/datastructures.Rcheck/00install.out’ for details.
‘cleanup’: ‘env bash’ is not portable as bash need not be installed
Namespaces in Imports field not imported from:
  ‘R6’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
Package suggested but not available for checking: ‘msa’
Note: found 2596 marked UTF-8 strings
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 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
Found the following significant warnings:
  ../include/external/random.h:53:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../include/external/random.h:54:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  randomBase.c:363:21: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  randomBase.c:381:26: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../include/misc/adaptiveRadixTree.h:54:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  adaptiveRadixTree.c:195:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  simd.c:53:24: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/dbarts.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dblog’
Found the following significant warnings:
  d011ch.c:17:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:41:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:42:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:44:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:45:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:352:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:427:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:520:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:531:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:686:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:698:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ma.c:7:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  urnew010.c:17:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  urnew010.c:36:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  urnew010.c:37:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wur.c:23:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/dblcens.Rcheck/00install.out’ for details.
File ‘dblcens/libs/dblcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
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
'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
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘bslib’ ‘knitr’ ‘matrixStats’ ‘rmarkdown’ ‘shinythemes’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
Note: found 38 marked UTF-8 strings
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Found the following significant warnings:
  difeq.h:65:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  difeq.c:123:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dopri.h:208:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dopri.c:245:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/dde.Rcheck/00install.out’ for details.
Found the following significant warnings:
  DDHFm.c:101:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  DDHFm.c:122:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  DDHFm.c:199:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/DDHFm.Rcheck/00install.out’ for details.
File ‘DDHFm/libs/DDHFm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘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
Found the following significant warnings:
  globals.h:139:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/deBif.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
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘smd_table.docx’
checkRd: (-1) lifetable.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Running examples in ‘dendRoAnalyst-Ex.R’ failed
The error most likely occurred in:

> ### Name: daily.data
> ### Title: Calculation of daily statistics for dendrometer data
> ### Aliases: daily.data
> 
> ### ** Examples
> 
> library(dendRoAnalyst)
> data(nepa17)
> daily_stats<-daily.data(df=nepa17, TreeNum=1)
Error in daily.data(df = nepa17, TreeNum = 1) : 
  Date not in the right format
Execution halted
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘methods’ ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rdonlp2’
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘Rdonlp2’
File ‘depth/libs/depth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  deque.h:73:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  constructor.c:43:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  deque.c:31:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dequer_native.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/dequer.Rcheck/00install.out’ for details.
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
checkRd: (-1) geom_axis.Rd:10: Escaped LaTeX specials: \_
'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’
Found the following significant warnings:
  ranksort.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ranksort.c:49:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ranksort.c:76:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/DescTools.Rcheck/00install.out’ for details.
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
Found the following significant warnings:
  deSolve.h:95:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_init_deSolve.c:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_init_deSolve.c:60:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  deSolve_utils.c:76:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ex_CCL4model.c:51:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ex_CCL4model.c:74:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/deSolve.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  DetSel_init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  GetData.c:33:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/DetSel.Rcheck/00install.out’ for details.
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
Found the following significant warnings:
  void_dev.c:103:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  void_dev.c:182:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  void_dev.c:197:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/devoid.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  arms.h:50:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/dfcomb.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) phihat.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) anova.dglm.Rd:41: Escaped LaTeX specials: \&
Package which this enhances but not available for checking: ‘BayesianTools’
'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
File ‘diffIRT/libs/diffIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

> ### Name: resample_dgm
> ### Title: Change the sampling of a digiRhythm friendly dataset
> ### Aliases: resample_dgm
> 
> ### ** Examples
> 
> data("df516b_2", package = "digiRhythm")
> df <- df516b_2
> df <- remove_activity_outliers(df)
> new_sampling <- 30
> new_dgm <- resample_dgm(df, new_sampling)
Error in if ((new_sampling%%original_sampling) != 0) { : 
  missing value where TRUE/FALSE needed
Calls: resample_dgm
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Actgram_diurnality_avg_activity.Rmd’ using rmarkdown
Quitting from lines 30-36 (Actgram_diurnality_avg_activity.Rmd) 
Error: processing vignette 'Actgram_diurnality_avg_activity.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘Actgram_diurnality_avg_activity.Rmd’

--- re-building ‘DFC_and_HP_and_changing_plots.Rmd’ using rmarkdown
Quitting from lines 20-26 (DFC_and_HP_and_changing_plots.Rmd) 
Error: processing vignette 'DFC_and_HP_and_changing_plots.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘DFC_and_HP_and_changing_plots.Rmd’

--- re-building ‘Loading_and_preprocessing_data_in_DigiRhythm.Rmd’ using rmarkdown
trying URL 'https://raw.githubusercontent.com/nasserdr/digiRhythm_sample_datasets/main/516b_2.csv'
Content type 'text/plain; charset=utf-8' length 2655404 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

Quitting from lines 118-120 (Loading_and_preprocessing_data_in_DigiRhythm.Rmd) 
Error: processing vignette 'Loading_and_preprocessing_data_in_DigiRhythm.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘Loading_and_preprocessing_data_in_DigiRhythm.Rmd’

SUMMARY: processing the following files failed:
  ‘Actgram_diurnality_avg_activity.Rmd’
  ‘DFC_and_HP_and_changing_plots.Rmd’
  ‘Loading_and_preprocessing_data_in_DigiRhythm.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  dipm.c:3577:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dipm.c:3654:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dipm.c:3998:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/dipm.Rcheck/00install.out’ for details.
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
File ‘DIRECT/libs/DIRECT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
checkRd: (-1) sammy.Rd:51: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
'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
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
'LazyData' is specified without 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:
  ‘csim’ ‘xyz’ ‘xyz.sav’ ‘xyz.sav.comment’
Found the following files/directories:
  ‘csim.mean’ ‘csim.mean.comment’
'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.
Found the following significant warnings:
  rfftw.h:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rfftw.c:149:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.c:231:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/diversitree.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘BOLTSSIRR’
Packages suggested but not available for checking: 'sendplot', 'HWxtest'
checkRd: (-1) fastDivPart.Rd:13: Escaped LaTeX specials: \_
checkRd: (-1) inCalc.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) inCalc.Rd:13: Escaped LaTeX specials: \_
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘dkDNA/libs/dkDNA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Found the following significant warnings:
  arms-R.c:83:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  arms-R.c:811:30: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 4 has type ‘POINT *’ {aka ‘struct point *’} [-Wformat=]
  arms-R.c:821:26: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘POINT *’ {aka ‘struct point *’} [-Wformat=]
  arms-R.c:821:38: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 4 has type ‘struct point *’ [-Wformat=]
  arms-R.c:821:51: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 5 has type ‘struct point *’ [-Wformat=]
  arms-R.c:832:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dlm.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dlm.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dlm.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dlm.c:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dlm.c:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dlm.c:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dlm.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dlm.c:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dlm.c:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dlm.c:53:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dlm.c:54:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/dlm.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
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
GNU make is a SystemRequirements.
checkRd: (-1) block.catlg.Rd:61: Escaped LaTeX specials: \^ \^
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 10 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘rjson’ ‘uuid’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Note: found 100 marked UTF-8 strings
Found the following significant warnings:
  alive.c:200:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  alive.c:277:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/doRedis.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘DoseFinding’ ‘ggplot2’ ‘lattice’ ‘latticeExtra’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘OpenMPController’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
Note: found 2 marked UTF-8 strings
Unknown package ‘broomExtra’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘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
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘ggplot2’ ‘nloptr’
  All declared Imports should be used.
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
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’
  All declared Imports should be used.
File ‘dse/libs/dse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 149 marked UTF-8 strings
Note: found 4891 marked UTF-8 strings
Package suggested but not available for checking: ‘dsBaseClient’
'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
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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘dualtrees/libs/dualtrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2854 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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
Found the following significant warnings:
  nwout.c:49:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/DynamicGP.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘NatureSounds’ ‘av’ ‘magrittr’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lle’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
File ‘dynpred/libs/dynpred.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  arms.c:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  arms.c:902:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/dynsurv.Rcheck/00install.out’ for details.
Note: found 9 marked UTF-8 strings
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
File ‘EasyABC/libs/EasyABC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    20181118
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bayestestR’ ‘correlation’ ‘datawizard’ ‘effectsize’ ‘modelbased’
  ‘parameters’ ‘performance’ ‘report’ ‘see’
  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.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    breaking changes
    major changes
    minor changes
    Internal
Namespace in Imports field not imported from: ‘qcr’
  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 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.
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
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Found the following significant warnings:
  include/ecos_bb.h:161:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ecos_bb/ecos_bb_preproc.c:298:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ecos/include/ecos_bb.h:161:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ECOSolveR.Rcheck/00install.out’ for details.
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
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
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.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
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
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: ‘progress’
  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
'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
GNU make is a SystemRequirements.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  eicm.h:70:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/eicm.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
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
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
GNU make is a SystemRequirements.
Found the following significant warnings:
  zeroin.c:54:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/EL.Rcheck/00install.out’ for details.
File ‘elsa/libs/elsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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
Found the following significant warnings:
  emd-rubner.c:143:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  emd-rubner.c:153:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  emd-rubner.c:640:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  emd-rubner.c:810:20: warning: ‘minI’ is used uninitialized [-Wuninitialized]
  emd-rubner.c:810:26: warning: ‘minJ’ is used uninitialized [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/emdist.Rcheck/00install.out’ for details.
File ‘emdist/libs/emdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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
checkRd: (-1) freudenstein_roth_func.Rd:29: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘osmar’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  utilities.h:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilities.c:14:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/emoa.Rcheck/00install.out’ for details.
File ‘emoa/libs/emoa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 9451 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.
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘sp’ ‘testthat’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’
  All declared Imports should be used.
File ‘EntropyEstimation/libs/EntropyEstimation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) check_several.Rd:34: Escaped LaTeX specials: \#
checkRd: (-1) check_several.Rd:35: Escaped LaTeX specials: \#
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
checkRd: (-1) calibrate.Rd:151: Escaped LaTeX specials: \&
checkRd: (-1) cdfCompareCensored.Rd:299: Escaped LaTeX specials: \&
checkRd: (-1) detectionLimitCalibrate.Rd:149: Escaped LaTeX specials: \&
checkRd: (-1) ecdfPlotCensored.Rd:169: Escaped LaTeX specials: \&
checkRd: (-1) egammaAltCensored.Rd:344: Escaped LaTeX specials: \&
checkRd: (-1) egammaCensored.Rd:340: Escaped LaTeX specials: \&
checkRd: (-1) elnormAltCensored.Rd:694: Escaped LaTeX specials: \&
checkRd: (-1) elnormCensored.Rd:270: Escaped LaTeX specials: \&
checkRd: (-1) enormCensored.Rd:852: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:343: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:358: Escaped LaTeX specials: \&
checkRd: (-1) epoisCensored.Rd:354: Escaped LaTeX specials: \&
checkRd: (-1) ppointsCensored.Rd:406: Escaped LaTeX specials: \&
checkRd: (-1) predIntGammaSimultaneous.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) predIntGammaSimultaneous.Rd:171: Escaped LaTeX specials: \&
checkRd: (-1) predIntLnormSimultaneous.Rd:136: Escaped LaTeX specials: \&
checkRd: (-1) predIntLnormSimultaneous.Rd:137: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneous.Rd:204: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneous.Rd:205: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:277: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:278: Escaped LaTeX specials: \&
checkRd: (-1) qqPlotCensored.Rd:261: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTest.Rd:276: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:324: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:331: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
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.
GNU make is a SystemRequirements.
Running ‘testthat.R’ [91s/105s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(epidemia)
  > 
  > test_check("epidemia")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 426 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-data.R:59'): check_time_as_date ──────────────────────────────
  `check_time_as_date(rt, df)` did not throw an error.
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 426 ]
  Error: Test failures
  Execution halted
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
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.
Package suggested but not available for checking: ‘epidict’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_state.h:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:380:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:381:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:382:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_wtstate.h:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:585:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:586:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:587:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/EpiModel.Rcheck/00install.out’ for details.
'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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘knitr’ ‘plyr’ ‘tidyverse’ ‘tokenizers’ ‘xml2’
  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.
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
File ‘equivalence/libs/equivalence.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘methods’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_state.h:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:380:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:381:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:382:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_wtstate.h:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:585:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:586:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:587:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ergm.count.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_state.h:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:380:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:381:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:382:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_wtstate.h:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:585:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:586:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:587:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ergm.ego.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_state.h:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:380:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:381:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:382:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_wtstate.h:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:585:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:586:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:587:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ergm.rank.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ../inst/include/ergm_state.h:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  MPLE.c:28:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ergm_omp.c:36:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ergm_state.c:107:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/ergm_wtstate.h:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ergm_wtstate.c:107:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:35:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:36:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:40:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ergm.Rcheck/00install.out’ for details.
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
'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
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
File ‘EstHer/libs/EstHer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘matrixStats’
  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
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.
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:
  ‘RColorBrewer’ ‘curl’ ‘scales’ ‘stringr’ ‘tidyquant’
  All declared Imports should be used.
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘sample .nwk’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ExactData’
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 342 marked UTF-8 strings
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
File ‘exif/libs/exif.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'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.
Package suggested but not available for checking: ‘cec2013’
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  expint.c:536:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  expint.c:604:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/expint.Rcheck/00install.out’ for details.
'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
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘exuberdata’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
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.
File ‘ezglm/libs/ezglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘BiocStyle’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Bogota.tex’ ‘DogBreeds1.tex’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 5 marked Latin-1 strings
'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.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘base’ ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
File ‘falcon/libs/falcon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  chli.c:5:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/fame.Rcheck/00install.out’ for details.
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'.
File ‘fame/libs/fame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ezprof.c:16:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/fanc.Rcheck/00install.out’ for details.
File ‘fanc/libs/fanc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 179 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1430 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘FastBandChol/libs/FastBandChol.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  lu.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lu.c:828:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/fastclime.Rcheck/00install.out’ for details.
File ‘fastclime/libs/fastclime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘default5.eps’
File ‘fastcmh/libs/fastcmh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘coxKM’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/fastmap.Rcheck/00install.out’ for details.
'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’
File ‘fastmatch/libs/fastmatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Scent.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) Traffic.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
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 ‘/data/gannet/ripley/R/packages/tests-devel/FastRWeb.Rcheck/00install.out’ for details.
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
File ‘FastRWeb/libs/null.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NNLM’
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘collapse’ ‘data.table’ ‘fst’ ‘kit’ ‘magrittr’ ‘matrixStats’
  All declared Imports should be used.
Found the following significant warnings:
  gld.c:439:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/fBasics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  fbati_init.c:35:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:36:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:37:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:39:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:50:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:52:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:53:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/fbati.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'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.
Note: found 75 marked UTF-8 strings
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘FastGP’ ‘MASS’ ‘fdapace’
  All declared Imports should be used.
Note: found 76 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘usethis’ ‘utils’
  All declared Imports should be used.
Note: found 1 marked Latin-1 string
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘FD/libs/FD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘vert.txt’
'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
Found the following files/directories:
  ‘treesAll.txt’
'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
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
File ‘fechner/libs/fechner.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘panelView’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New Stuff
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 43825 marked UTF-8 strings
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘FFD/libs/FFD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ff.h:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  r_ff.h:62:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  r_ff.h:63:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  r_ff.h:64:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  r_ff.c:289:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  r_ff.c:298:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  r_ff.c:309:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ff.Rcheck/00install.out’ for details.
checkRd: (-1) dimnames.ff.rd:18: Escaped LaTeX specials: \_
checkRd: (-1) ff.rd:120: Escaped LaTeX specials: \_
checkRd: (-1) names.ff.rd:22: Escaped LaTeX specials: \_
Namespace in Imports field not imported from: ‘nflreadr’
  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 significant warnings:
  f2c.h:185:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:186:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:187:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:188:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:189:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:190:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:191:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:192:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:193:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:194:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:195:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/FGSG.Rcheck/00install.out’ for details.
File ‘FGSG/libs/FGSG.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘numDeriv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MicrobeDS’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 7 marked UTF-8 strings
File ‘fishMod/libs/fishMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'benchden', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Note: found 584 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
checkRd: (-1) fk_regression.Rd:32: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘evaluate’ ‘ggplot2’
  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.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
File ‘flashClust/libs/flashClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
checkRd: (-1) cclust.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) randIndex.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:28: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  flexiblas_api_standalone.c:64:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  flexiblas_api_standalone.c:86:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  flexiblas_api_standalone.c:452:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrapper.c:25:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrapper.c:34:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrapper.c:47:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrapper.c:58:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrapper.c:74:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrapper.c:132:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/flexiblas.Rcheck/00install.out’ for details.
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
Found the following significant warnings:
  float_native.c:40:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  float_native.c:41:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  float_native.c:53:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  machine.c:7:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  NA.c:20:21: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  NA.c:76:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  NA.c:88:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/float.Rcheck/00install.out’ for details.
File ‘flock/libs/flock.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘flux.CH4.txt’
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pseudoOptim.Rd:27: Escaped LaTeX specials: \$
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
checkRd: (-1) write.AFNI.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) write.AFNI.Rd:17: Escaped LaTeX specials: \_
checkRd: (-1) write.AFNI.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) write.AFNI.Rd:22: Escaped LaTeX specials: \_
Found the following significant warnings:
  BDSTest.c:84:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BDSTest.c:104:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BDSTest.c:129:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BDSTest.c:153:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BDSTest.c:192:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BDSTest.c:219:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BDSTest.c:227:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BDSTest.c:245:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BDSTest.c:257:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/fNonlinear.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘foghorn-Ex.R’ failed
The error most likely occurred in:

> ### Name: cran_results
> ### Title: Table of the CRAN check results
> ### Aliases: cran_results
> 
> ### ** Examples
> 
>   if (curl::has_internet()) {
+     cran_results(pkg="MASS")
+   }
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  restarting interrupted promise evaluation
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  restarting interrupted promise evaluation
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  restarting interrupted promise evaluation
Error: Something went wrong with getting data for package name(s): ‘MASS’
  Error in open.connection(x, "rb") : Could not resolve host: web
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘foghorn.Rmd’ using rmarkdown
Quitting from lines 23-25 (foghorn.Rmd) 
Error: processing vignette 'foghorn.Rmd' failed with diagnostics:
Something went wrong with getting data with email address(es): 'francois.michonneau@gmail.com'
  Error in open.connection(x, "rb") : Could not resolve host: web

--- failed re-building ‘foghorn.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Note: found 154 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 234 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
checkRd: (-1) forecTheta-package.Rd:11: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘RColorBrewer’
  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:
    Previous versions (not tagged nor released)
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rgeos’ ‘viridis’
  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
Namespace in Imports field not imported from: ‘RCSF’
  All declared Imports should be used.
Note: found 31 marked UTF-8 strings
Namespace in Imports field not imported from: ‘spatstat’
  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: ‘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'
File ‘fpow/libs/fpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘fable’ ‘fabletools’ ‘feasts’ ‘ggplot2’ ‘lubridate’ ‘tibble’
  ‘tidyr’ ‘tsibble’ ‘tsibbledata’ ‘urca’
  All declared Imports should be used.
Found the following significant warnings:
  fracdiff.h:39:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fdcore.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/fracdiff.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘fractional/libs/fractional.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
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
checkRd: (-1) CatalogueAccessors.Rd:249: Escaped LaTeX specials: \^ \^
checkRd: (-1) FrF2.Rd:574: Escaped LaTeX specials: \^
checkRd: (-1) FrF2.Rd:629: Escaped LaTeX specials: \^ \^
checkRd: (-1) IAPlot.Rd:87: Escaped LaTeX specials: \$
checkRd: (-1) block.Rd:121: Escaped LaTeX specials: \^
checkRd: (-1) block.Rd:150: Escaped LaTeX specials: \^ \^
checkRd: (-1) blockpick.Rd:114: Escaped LaTeX specials: \^ \^
Running ‘testthat.R’ [20s/118s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(frictionless)
  > 
  > test_check("frictionless")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 352 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-add_resource.R:257'): add_resource() can add resource from local, relative, absolute,
             remote or compressed CSV file, readable by read_resource() ──
  Error in `open.connection(con, "rb")`: Timeout was reached: [github.com] SSL connection timeout
  Backtrace:
      ▆
   1. └─frictionless::add_resource(p, "remote", remote_path, schema) at test-add_resource.R:257:2
   2.   └─readr::guess_encoding(last_file, n_max = 1000)
   3.     ├─base::unlist(read_lines_raw(file, n_max = n_max))
   4.     └─readr::read_lines_raw(file, n_max = n_max)
   5.       └─readr::datasource(...)
   6.         └─readr:::datasource_connection(...)
   7.           └─readr:::read_connection(path)
   8.             ├─base::open(con, "rb")
   9.             └─base::open.connection(con, "rb")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 352 ]
  Error: Test failures
  Execution halted
Note: found 50 marked UTF-8 strings
Package suggested but not available for checking: ‘dggrids’
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'
Found the following significant warnings:
  init.c:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/FSelectorRcpp.Rcheck/00install.out’ for details.
'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.
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
checkRd: (-1) mean.fts.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) median.fts.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) plot.fm.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) residuals.fm.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) sd.fts.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) var.fts.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'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’
File ‘futureheatwaves/libs/futureheatwaves.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  gamlr.c:87:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/gamlr.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
Found the following significant warnings:
  loessc.c:74:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:76:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:78:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:80:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:82:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:84:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:86:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:88:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:90:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/gam.Rcheck/00install.out’ for details.
'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
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
Note: found 2 marked UTF-8 strings
checkRd: (-1) meyer.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) mia.Rd:39: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘gausscov/libs/gausscov.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘gbp/libs/gbp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gputools’
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
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘arm’ ‘usethis’
  All declared Imports should be used.
File ‘GCPM/libs/GCPM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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: ‘sp’
  All declared Imports should be used.
checkRd: (-1) plot_summary.Rd:14: Escaped LaTeX specials: \_
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’
Namespace in Imports field not imported from: ‘DOSE’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
File ‘genepi/libs/genepi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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) SandP500.Rd:4: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
Running examples in ‘GenEst-Ex.R’ failed
The error most likely occurred in:

> ### Name: averageSS
> ### Title: Tabulate an average search schedule from a multi-unit SS data
> ###   table
> ### Aliases: averageSS
> 
> ### ** Examples
> 
>   data(mock)
>   avgSS <- averageSS(mock$SS)
Error in prepSS(data_SS, SSdate = SSdate) : 
  more than 1 date column in data_SS, and SSdate does not specify which to use.
Calls: averageSS -> prepSS
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘GenEstGUI.Rmd’ using rmarkdown
--- finished re-building ‘GenEstGUI.Rmd’

--- re-building ‘command-line-example.Rmd’ using rmarkdown
Quitting from lines 381-390 (command-line-example.Rmd) 
Error: processing vignette 'command-line-example.Rmd' failed with diagnostics:
more than 1 date column in data_SS, and SSdate does not specify which to use.
--- failed re-building ‘command-line-example.Rmd’

--- re-building ‘solar-examples.Rmd’ using rmarkdown
Quitting from lines 286-293 (solar-examples.Rmd) 
Error: processing vignette 'solar-examples.Rmd' failed with diagnostics:
more than 1 date column in data_SS, and SSdate does not specify which to use.
--- failed re-building ‘solar-examples.Rmd’

--- re-building ‘wind-examples.Rmd’ using rmarkdown
Quitting from lines 277-283 (wind-examples.Rmd) 
Error: processing vignette 'wind-examples.Rmd' failed with diagnostics:
more than 1 date column in data_SS, and SSdate does not specify which to use.
--- failed re-building ‘wind-examples.Rmd’

SUMMARY: processing the following files failed:
  ‘command-line-example.Rmd’ ‘solar-examples.Rmd’ ‘wind-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
  ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgeos’
  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: ‘methods’
  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.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  init.c:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/GenSA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  arms.c:99:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  arms.c:900:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/genscore.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  gensvm/include/gensvm_rand.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gensvm/src/gensvm_rand.c:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gensvm/src/gensvm_rand.c:112:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gensvm/src/gensvm_rand.c:153:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/gensvm.Rcheck/00install.out’ for details.
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
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
Note: found 76726 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/geohashTools.Rcheck/00install.out’ for details.
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
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  GeoModels_init.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  GeoModels_init.c:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Utility.c:1057:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Utility.c:1144:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/GeoModels.Rcheck/00install.out’ for details.
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
Found the following significant warnings:
  init.c:179:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:181:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:182:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:183:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:380:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:394:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:401:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/geos.Rcheck/00install.out’ for details.
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.
Namespaces in Imports field not imported from:
  ‘iterators’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  getip_native.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ip_internal.c:71:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ip_internal.c:292:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/getip.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘pipeR’ ‘rlang’
  All declared Imports should be used.
checkRd: (-1) getopt.Rd:60: Escaped LaTeX specials: \#
Namespaces in Imports field not imported from:
  ‘scales’ ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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/gettz.Rcheck/00install.out’ for details.
checkRd: (-1) gexp.Rd:123: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘RGtk2’
checkRd: (-1) estGF.Rd:106: Escaped LaTeX specials: \&
checkRd: (-1) estGF.Rd:107: Escaped LaTeX specials: \&
'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
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    earlier versions
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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘do’ ‘survival’
  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.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 2356 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without 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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘productplots’ ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggsci’ ‘memes’ ‘universalmotif’
  All declared Imports should be used.
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
Namespace in Imports field not imported from: ‘cowplot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
checkRd: (-1) diamonds.Rd:10: Escaped LaTeX specials: \$ \$
Found the following HTML validation problems:
ggplot2-package.html:23:4 (ggplot2-package.Rd:9): Warning: <img> attribute "align" not allowed for HTML5
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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    History
'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
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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug fixes
'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.
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.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘hexbin’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 138 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
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.
Problems with news in ‘NEWS.md’:
No news entries found.
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
Found the following significant warnings:
  rgig.c:127:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ghyp.Rcheck/00install.out’ for details.
'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
Namespaces in Imports field not imported from:
  ‘aTSA’ ‘mvtnorm’
  All declared Imports should be used.
'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
File ‘GiRaF/libs/GiRaF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1178 marked UTF-8 strings
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.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  gld.rs.fx.c:62:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gld.rs.fx.c:121:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/gld.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘mlr3proba’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  phytr.c:419:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:2327:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3266:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3268:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3298:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3302:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3307:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3316:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3319:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3322:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3325:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/glinvci.Rcheck/00install.out’ for details.
File ‘gllm/libs/gllm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ordinal’
  All declared Imports should be used.
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘GMMBoost’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
checkRd: (-1) basal.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) basal.Rd:33: Escaped LaTeX specials: \_ \_ \_
Found the following significant warnings:
  pb.c:27:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/glmnet.Rcheck/00install.out’ for details.
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
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘cplexAPI’
Found the following significant warnings:
  rho_rho_excess.c:16:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/globalKinhom.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
File ‘globalOptTests/libs/globalOptTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
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
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Found the following significant warnings:
  glpkAPI.h:81:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:84:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:87:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:101:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:104:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:107:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:460:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:491:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:433:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:446:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:459:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:722:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:791:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:825:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:3400:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/glpkAPI.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2629 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) barleyHeights.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) barleyHeights.Rd:22: Escaped LaTeX specials: \&
'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.
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
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
'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.
Found the following significant warnings:
  R_register_native.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_register_native.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gower.c:60:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gower.c:72:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gower.c:83:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/gower.Rcheck/00install.out’ for details.
checkRd: (-1) rotations.Rd:103: Escaped LaTeX specials: \^
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘utils’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gvcm.cat’
Unknown package ‘gvcm.cat’ in Rd xrefs
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘gplm/libs/gplm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
checkRd: (-1) GPoM.FDLyapu-package.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) Plague.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) lyapFDGrond.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) lyapFDGrond.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) lyapFDGrond.Rd:69: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed 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.
Namespace in Imports field not imported from: ‘lfc’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘PairedData’ ‘RColorBrewer’ ‘agricolae’ ‘corrplot’ ‘desplot’
  ‘dplyr’ ‘ggplot2’ ‘ggpubr’ ‘gridGraphics’ ‘gtools’ ‘kableExtra’
  ‘knitr’ ‘magrittr’ ‘pastecs’ ‘reshape2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘summarytools’
  All declared Imports should be used.
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) gen_graph_indep.Rd:126: Escaped LaTeX specials: \&
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) mlGraphicalVAR.Rd:79: Escaped LaTeX specials: \~
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.
Namespaces in Imports field not imported from:
  ‘methods’ ‘quadmesh’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
Found the following significant warnings:
  Offset.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  omp_diagnose.c:5:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  omp_diagnose.c:18:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/grattan.Rcheck/00install.out’ for details.
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/gRc.Rcheck/00install.out’ for details.
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.
Problems with news in ‘NEWS.md’:
No news entries found.
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.
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘groupRemMap/libs/groupRemMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘MASS’ ‘rjags’
  All declared Imports should be used.
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
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
File ‘grr/libs/grr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
File ‘gsmoothr/libs/gsmoothr.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  smolyak.c:58:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  smolyak.c:79:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  smolyak.c:227:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  smolyak.c:477:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/gss.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
checkRd: (-1) gsym.point.Rd:143: Escaped LaTeX specials: \&
Note: found 116 marked UTF-8 strings
Note: found 269 marked UTF-8 strings
Note: found 42384 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RRprof.out’
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
checkRd: (-1) GUTS-package.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:201: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:209: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
File ‘GWASExactHW/libs/GWASExactHW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
checkRd: (-1) luzdat.Rd:21: Escaped LaTeX specials: \~
File ‘GWEX/libs/GWEX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘gwfa/libs/gwfa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘attempt’ ‘corpcor’ ‘glue’ ‘htmltools’ ‘pkgload’ ‘processx’
  ‘tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [10s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hablar)
  > test_check("hablar")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 416 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test.convert.R:118'): from Date ───────────────────────────────────
  tibble(a = as.Date(c("1970-05-03", NA, "1987-04-20"))) %>% convert(dtm(a)) not equal to tibble(a = as.POSIXct(as.Date(c("1970-05-03", NA, "1987-04-20")))).
  Component "a": 'tzone' attributes are inconsistent ('Europe/London' and 'UTC')
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 416 ]
  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
Namespaces in Imports field not imported from:
  ‘DT’ ‘gsubfn’ ‘stringr’
  All declared Imports should be used.
Found the following significant warnings:
  haplo.stats_init.c:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  haplo_em_pin.h:107:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  haplo_em_pin.c:1143:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  seqhap.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  seqhap.c:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  seqhap.c:110:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  seqhap.c:627:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  seqhap.c:807:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/haplo.stats.Rcheck/00install.out’ for details.
checkRd: (-1) haplo.design.Rd:33: Escaped LaTeX specials: \$
checkRd: (-1) haplo.design.Rd:42: Escaped LaTeX specials: \$
checkRd: (-1) haplo.glm.Rd:176: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) haplo.glm.Rd:178: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) haplo.glm.Rd:283: Escaped LaTeX specials: \$ \$
checkRd: (-1) haplo.glm.Rd:292: Escaped LaTeX specials: \$ \$
checkRd: (-1) haplo.glm.Rd:324: Escaped LaTeX specials: \$ \$
Note: found 8248 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) HWClrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/harmony.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hash-accessors.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) hash-class.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) hash-class.Rd:45: Escaped LaTeX specials: \$
checkRd: (-1) hash-package.Rd:39: Escaped LaTeX specials: \#
Found the following significant warnings:
  readstat/readstat_bits.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/readstat_bits.c:11:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/readstat_variable.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/readstat_variable.c:8:25: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/sas/../readstat_bits.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/sas/ieee.c:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/sas/ieee.c:99:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/sas/readstat_sas.c:123:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/sas/readstat_xport_read.c:48:21: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/spss/readstat_por.h:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/spss/readstat_por.c:67:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/spss/readstat_por_write.c:170:25: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/spss/../readstat_bits.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/stata/../readstat_bits.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/haven.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
File ‘hawkes/libs/hawkes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) prm09.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) prm09.Rd:26: Escaped LaTeX specials: \&
Note: found 3 marked UTF-8 strings
Note: found 104392 marked UTF-8 strings
checkRd: (-1) schools.Rd:18: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
  H5Error.h:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  datatype_export.c:64:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  H5Error.c:122:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/hdf5r.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
File ‘HDGLM/libs/HDGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘ggjoy’ ‘isotone’ ‘questionr’ ‘rprojroot’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘TidyDensity’ ‘healthyR’ ‘healthyR.ai’ ‘healthyR.data’ ‘healthyR.ts’
  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
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘synbreed’
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:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
checkRd: (-1) erode.hexbin.Rd:43: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
Found the following significant warnings:
  jack-n.c:203:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  jack-n.c:206:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  jack-n.c:219:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  jack-n.c:220:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  jack-n.c:259:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  jack-n.c:260:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  jack-n.c:303:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  jack-n.c:327:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  jack-n.c:890:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  jack-n.c:937:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  jack-n.c:1721:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  jack-n.c:1727:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rk.c:48:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  so3_nc.c:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  so3_nc.c:116:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/hgm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘spatstat.linnet’
  All declared Imports should be used.
File ‘HiCseg/libs/HiCseg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
':::' 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.
File ‘hierarchicalSets/libs/hierarchicalSets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RiskPortfolios’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
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
Found the following significant warnings:
  arms-R.c:83:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  arms-R.c:811:30: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 4 has type ‘POINT *’ {aka ‘struct point *’} [-Wformat=]
  arms-R.c:821:26: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘POINT *’ {aka ‘struct point *’} [-Wformat=]
  arms-R.c:821:38: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 4 has type ‘struct point *’ [-Wformat=]
  arms-R.c:821:51: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 5 has type ‘struct point *’ [-Wformat=]
  arms-R.c:832:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/HI.Rcheck/00install.out’ for details.
checkRd: (-1) trans.dens.Rd:47: Escaped LaTeX specials: \&
Found the following significant warnings:
  registerDynamicSymbol.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:23:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/hisse.Rcheck/00install.out’ for details.
checkRd: (-1) Snow.Rd:118: Escaped LaTeX specials: \&
checkRd: (-1) Snow.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) Yeast.Rd:56: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
File ‘hit/libs/hit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘HadoopStreaming’
Note: found 9638 marked UTF-8 strings
File ‘hkevp/libs/hkevp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘FGN’
File ‘HKprocess/libs/HKprocess.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
Found the following significant warnings:
  ranksort.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ranksort.c:49:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ranksort.c:76:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/Hmisc.Rcheck/00install.out’ for details.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ROI.plugin.mosek’
'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
Note: found 124 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
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
checkRd: (-1) attributes_speclib.Rd:73: Escaped LaTeX specials: \$
checkRd: (-1) get_reflectance.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  useful.h:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/hSDM.Rcheck/00install.out’ for details.
File ‘hsphase/libs/hsphase.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  htree.c:126:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:135:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:324:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:362:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:408:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:517:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:693:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:711:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:813:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1476:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1494:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1528:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1679:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1754:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1839:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1869:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1909:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:2906:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:3696:6: 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/htree.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘humaniformat/libs/humaniformat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  humanleague_init.c:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/humanleague.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: ‘hurricaneexposuredata’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘xml2’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
checkRd: (-1) Trancura9414001.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) Trancura9414001.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) hydroPSO.Rd:390: Escaped LaTeX specials: \&
checkRd: (-1) hydroPSO.Rd:408: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:7: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘flowCore’
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26215 marked UTF-8 strings
Note: found 1058038 marked UTF-8 strings
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’
File ‘iBATCGH/libs/iBATCGH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘gutenbergr’
Note: found 1 marked UTF-8 string
Note: found 359 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ibdreg_init.c:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mcmemory.h:188:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:85:29: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:88:29: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:90:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:303:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:814:22: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:877:29: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:1018:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ibdreg.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘ibmcraftr/libs/ibmcraftr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘SparkR’
File ‘ibm/libs/ibm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Registration problems:
  symbol ‘nom1’ in the local frame:
   .C(nom1, as.double(xord), as.integer(length(xord)), as.double(yord), 
       as.double(gridbw), as.integer(length(gridbw)), as.integer(effold), 
       as.integer(neffold), double(length(gridbw)), double(length(gridbw)))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1), double(n))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1), double(length(newdata)))
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
File ‘icapca/libs/icapca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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
'LazyData' is specified without a 'data' directory
Note: found 329984 marked UTF-8 strings
Package suggested but not available for checking: ‘icd’
Note: found 55 marked UTF-8 strings
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Namespaces in Imports field not imported from:
  ‘digest’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 10 marked UTF-8 strings
Found the following files/directories:
  ‘Crashpad’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
'LazyData' is specified without a 'data' directory
checkRd: (-1) pulmonary.Rd:13: Escaped LaTeX specials: \_
'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
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
File ‘ieeeround/libs/ieeeround.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘optiRum’
Namespace in Imports field not imported from: ‘testit’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 40 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘pritikin-schmidt.Rnw’ using knitr

Quitting from lines 1645-1650 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
The job for model 'container1' exited abnormally with the error message: User interrupt
--- failed re-building ‘pritikin-schmidt.Rnw’

SUMMARY: processing the following file failed:
  ‘pritikin-schmidt.Rnw’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘IFCdata’
File ‘IFP/libs/IFP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ../inst/include/ut_debug.h:188:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ut_debug.c:102:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ifultools.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  core/core/error.c:65:29: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vendor/plfit/gss.h:132:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vendor/plfit/gss.c:60:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vendor/plfit/mt.c:20:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vendor/plfit/platform.c:36:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rrandom.h:26:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:104:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rinterface.c:2506:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rinterface.c:2522:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rinterface.c:9433:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rrandom.c:108:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/igraph.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  common.c:62:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utils.c:9:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ijtiff.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /data/gannet/ripley/R/test-dev/RNifti/include/RNifti.h:58:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RNifti_shim.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/RNifti/include/RNiftiAPI.h:268:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RNifti_shim.c:39:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  print.h:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  core.c:717:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/imbibe.Rcheck/00install.out’ for details.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘haven’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  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
Note: found 151 marked UTF-8 strings
Namespace in Imports field not imported from: ‘optimr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Found the following significant warnings:
  keyplayer-utils.c:24:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/influenceR.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
BugReports field should be the URL of a single webpage
Package which this enhances but not available for checking: ‘gurobi’
File ‘infotheo/libs/infotheo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  DefinePolygons.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  DefinePolygons.c:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/inlmisc.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
File ‘INSPIRE/libs/INSPIRE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO for future releases:
Found the following files/directories:
  ‘pkgbuild’
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘splines2’
  All declared Imports should be used.
'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’
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Running ‘testthat.R’ [13s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(intensegRid)
  > 
  > test_check("intensegRid")
  [ FAIL 1 | WARN 8 | SKIP 0 | PASS 66 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-other.R:34'): get_stats() works ──────────────────────────────
  `get_stats(10, 20)` did not throw an error.
  
  [ FAIL 1 | WARN 8 | SKIP 0 | PASS 66 ]
  Error: Test failures
  Execution halted
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:
  ‘grDevices’ ‘methods’ ‘mlbench’ ‘parallel’ ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘readxl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Intervals-class.Rd:109: Escaped LaTeX specials: \_
checkRd: (-1) Intervals-class.Rd:110: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:68: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:76: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:77: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:78: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:79: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:81: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:88: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:89: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) sgd.Rd:12: Escaped LaTeX specials: \_
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
Note: found 12106 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:
  ‘fdrtool’ ‘nimble’
  All declared Imports should be used.
Note: found 102 marked UTF-8 strings
'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’
File ‘iotools/libs/iotools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gmodels’ ‘lmtest’ ‘testthat’ ‘tidyverse’ ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘iRafNet/libs/iRafNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘glmnet’
  All declared Imports should be used.
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Found the following significant warnings:
  phi.h:33:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/IRon.Rcheck/00install.out’ for details.
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
checkRd: (-1) pine.Rd:20: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
Note: found 104 marked UTF-8 strings
File ‘isingLenzMC/libs/isingLenzMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  trace_islasso.c:39:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/islasso.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7528 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘modules’
  All declared Imports should be used.
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 1 marked UTF-8 string
Found the following files/directories:
  ‘RMTplot.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: ‘gurobi’
Note: found 58 marked UTF-8 strings
Package suggested but not available for checking: ‘locClass’
checkRd: (-1) ivmodel.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) ivmodelFormula.Rd:79: Escaped LaTeX specials: \&
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
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:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘fBasics’ ‘reshape’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Note: found 2261 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 461377 marked UTF-8 strings
Note: found 1984 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘mcmcplots’ ‘tidyverse’
  All declared Imports should be used.
Found the following significant warnings:
  jGDtalk.c:116:16: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  jGDtalk.c:797:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  javaGD.c:373:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  javaGD.c:382:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/JavaGD.Rcheck/00install.out’ for details.
Output from running autoreconf:
  configure.ac:4: warning: The macro `AC_CONFIG_HEADER' is obsolete.
  configure.ac:4: You should run autoupdate.
  ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
  configure.ac:4: the top level
  configure.ac:24: warning: The macro `AC_HEADER_STDC' is obsolete.
  configure.ac:24: You should run autoupdate.
  ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
  configure.ac:24: the top level
  configure.ac:30: warning: The macro `AC_HEADER_TIME' is obsolete.
  configure.ac:30: You should run autoupdate.
  ./lib/autoconf/headers.m4:743: AC_HEADER_TIME is expanded from...
  configure.ac:30: the top level
  configure.ac:34: warning: The macro `AC_TYPE_SIGNAL' is obsolete.
  configure.ac:34: You should run autoupdate.
  ./lib/autoconf/types.m4:776: AC_TYPE_SIGNAL is expanded from...
  configure.ac:34: the top level
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘JavaGD/libs/JavaGD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘GA’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ids’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘knitr’ ‘markdown’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 85 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘dplyr’ ‘emmeans’ ‘ggrepel’ ‘ggridges’ ‘lavaan’
  ‘multcomp’ ‘mvnormtest’ ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    joineR <1.1
Package which this enhances but not available for checking: ‘remMap’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘boot’ ‘fds’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
Found the following significant warnings:
  rjcommon.h:75:31: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/jpeg.Rcheck/00install.out’ for details.
Note: found 461377 marked UTF-8 strings
Note: found 176 marked UTF-8 strings
File ‘JRF/libs/JRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  push_parser.h:1:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  yajl/yajl_tree.c:523:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/jsonlite.Rcheck/00install.out’ for details.
Note: found 17 marked UTF-8 strings
checkRd: (-1) summ.rq.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) summ.rq.Rd:108: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
Namespaces in Imports field not imported from:
  ‘Superpower’ ‘pwr’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘kappalab/libs/kappalab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘my.Mobius.set.func.csv’ ‘my.card.set.func.csv’ ‘my.set.func.csv’
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
Namespace in Imports field not imported from: ‘gifski’
  All declared Imports should be used.
Found the following HTML validation problems:
math_to_rd.html:81:2153 (math_to_rd.Rd:45): Warning: <svg> attribute "width" has invalid value "400em"
math_to_rd.html:81:2153 (math_to_rd.Rd:45): Warning: <svg> attribute "height" has invalid value "1.08em"
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘EQL’ ‘univariateML’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /usr/include/c++/12/array:61:36: warning: array subscript 18446744073709551615 is above array bounds of ‘std::__array_traits<double, 1>::_Type’ {aka ‘const double [1]’} [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/kdtools.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
File ‘Kendall/libs/Kendall.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) ionosphere.Rd:22: Escaped LaTeX specials: \&
checkRd: (-1) ionosphere.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘KernSmoothIRT/libs/KernSmoothIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  keypress-unix.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  keypress-win.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/keypress.Rcheck/00install.out’ for details.
Found the following significant warnings:
  init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:30:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  keyring_macos.c:523:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  keyring_secret_service.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  keyring_secret_service.c:15:21: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  keyring_secret_service.c:59:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  keyring_secret_service.c:91:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  keyring_secret_service.c:394:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  keyring_wincred.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/keyring.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘Rsamtools’ ‘rtracklayer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fitdistrplus’ ‘plotly’
  All declared Imports should be used.
Found the following significant warnings:
  kit.h:92:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utils.c:21:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/kit.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
File ‘kknn/libs/kknn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘rkward’
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘SnowballC’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cld1.Rdata’ ‘main.tex’ ‘myCld.Rdata’ ‘myCld3d.Rdata’ ‘scene.asy’
File ‘kml/libs/kml.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘cld1.Rdata’ ‘ld.Rdata’ ‘myCld.Rdata’
checkRd: (-1) pathFrechet.Rd:54: Escaped LaTeX specials: \&
File ‘kmlShape/libs/kmlShape.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Killed after ’
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘VARSEDIG’
Unknown package ‘VARSEDIG’ in Rd xrefs
Note: found 9 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘mice’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
'LazyData' is specified without a 'data' directory
checkRd: (-1) kstIO-package.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) read_kbase.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) read_kdata.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) read_kfamset.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) read_kspace.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) read_kstructure.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) read_surmiserelation.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) write_kbase.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) write_kdata.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) write_kspace.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) write_kstructure.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) write_surmiserelation.Rd:36: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘DF7.bas’ ‘DF7.dat’ ‘DF7.rel’ ‘DF7.spc’ ‘DF7.struct’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
checkRd: (-1) alphaOnly.Rd:25: Escaped LaTeX specials: \^
checkRd: (-1) alphaOnly.Rd:26: Escaped LaTeX specials: \$
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
checkRd: (-1) natlongsurv.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
File ‘labdsv/libs/labdsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/laGP.Rcheck/00install.out’ for details.
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
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  init.c:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/largeList.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘example.llo’
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘LassoNet/libs/LassoNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘ergm.userterms’
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package ‘ergm.userterms’ in Rd xrefs
GNU make is a SystemRequirements.
Found the following significant warnings:
  init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:27:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/later.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rmarkdown’
  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.
Found the following significant warnings:
  lrsmp.h:147:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lrsmp.c:40:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/LatticeDesign.Rcheck/00install.out’ for details.
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gof', 'lava.tobit'
checkRd: (-1) Col.Rd:17: Escaped LaTeX specials: \#
checkRd: (-1) regression-set.Rd:103: Escaped LaTeX specials: \$
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘raster’
  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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) goodnessfit.Rd:105: Escaped LaTeX specials: \&
checkRd: (-1) lba.Rd:252: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    lcars.0.3.1
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  lcopula-init.c:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/lcopula.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘utf8’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘chinese.misc’ ‘dplyr’ ‘factoextra’ ‘glasso’
  ‘highcharter’ ‘htmlwidgets’ ‘ldatuning’ ‘qgraph’ ‘quanteda’ ‘rvest’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinycssloaders’
  ‘shinydashboard’ ‘shinyjs’ ‘stringr’ ‘textmineR’ ‘textplot’ ‘tidyr’
  ‘topicmodels’
  All declared Imports should be used.
File ‘lda/libs/lda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘beepr’ ‘broom’ ‘chinese.misc’ ‘dplyr’ ‘highcharter’
  ‘htmlwidgets’ ‘ldatuning’ ‘parallel’ ‘plotly’ ‘purrr’ ‘quanteda’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinycssloaders’ ‘shinyjs’
  ‘stringr’ ‘textmineR’ ‘tidyr’ ‘tidytext’ ‘topicmodels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RcppProgress’ ‘rgen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 75 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Note: found 1096 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:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) leaps.Rd:38: Escaped LaTeX specials: \&
File ‘leaps/libs/leaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 78 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Note: found 51 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Found the following significant warnings:
  rigraph/src/plfit/gss.h:132:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/plfit/gss.c:60:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/plfit/platform.c:36:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/plfit/mt.c:20:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/init.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/init.c:104:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/rinterface.c:2354:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/rinterface.c:2370:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/rinterface.c:9538:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/glpk_support.c:95:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/leidenbase.Rcheck/00install.out’ for details.
Found the following significant warnings:
  lemna.c:98:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lemna.c:109:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lemna.c:120:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lemna.c:129:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lemna.c:138:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/lemna.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
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:
  ‘cli’ ‘glue’ ‘stringr’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
Running ‘spelling.R’
  Running ‘testthat.R’ [46s/191s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("LexisNexisTools")
  LexisNexisTools Version 0.3.5
  > 
  > test_check("LexisNexisTools")
  
    |                                                  | 0 % ~calculating  
    |+++++                                             | 10% ~00s          
    |++++++++++                                        | 20% ~00s          
    |+++++++++++++++                                   | 30% ~00s          
    |++++++++++++++++++++                              | 40% ~00s          
    |+++++++++++++++++++++++++                         | 50% ~00s          
    |++++++++++++++++++++++++++++++                    | 60% ~00s          
    |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
    |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
    |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
    |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
    adding: sample.DOCX (deflated 45%)
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 99 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • !dir.exists("/home/johannes/Dropbox/LexisNexis_sample_files/") is TRUE (1)
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-lnt_convert.R:16'): Convert LNToutput to rDNA ────────────────
  {
      ...
  } not equal to readRDS("../files/rDNA.RDS").
  Component "date": 'tzone' attributes are inconsistent ('UTC' and '')
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 99 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  lfe.h:121:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lfe.h:122:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utils.c:195:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utils.c:208:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/lfe.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
File ‘lgarch/libs/lgarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  init.c:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/lhs.Rcheck/00install.out’ for details.
Note: found 22 marked UTF-8 strings
Found the following significant warnings:
  trainLinear.c:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  trainLinear.c:93:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/LiblineaR.ACF.Rcheck/00install.out’ for details.
File ‘LiblineaR.ACF/libs/LiblineaR.ACF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  trainLinear.c:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  trainLinear.c:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  trainLinear.c:100:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  trainLinear.c:130:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/LiblineaR.Rcheck/00install.out’ for details.
File ‘LiblineaR/libs/LiblineaR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/liGP.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ddpcr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) LIMEcoli.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) Read.Rd:88: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:92: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:98: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:104: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:105: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:106: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:107: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:108: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:109: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:110: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:111: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:112: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:114: Escaped LaTeX specials: \# \#
'LazyData' is specified without 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 ‘linERR/libs/linERR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 60596 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RColorBrewer’
  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: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 435 marked UTF-8 strings
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Note: found 266 marked UTF-8 strings
File ‘ljr/libs/ljr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1 marked UTF-8 string
checkRd: (-1) MHDI.Rd:23: 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.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘agridat’ ‘ggplot2’ ‘maps’ ‘sp’
  All declared Imports should be used.
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
File ‘lmPerm/libs/lmPerm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) hatr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tTestTable.rda’
Note: found 4 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘base’ ‘qpdf’
  All declared Imports should be used.
checkRd: (-1) SPSloess.Rd:71: Escaped LaTeX specials: \^ \^
File ‘localgauss/libs/localgauss.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  CPkPlj.c:160:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  CPkPlj.c:324:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  CcovI.c:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/locits.Rcheck/00install.out’ for details.
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) ACS.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) EmployedACS.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSale.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCA.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCanton.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleNY.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:24: Escaped LaTeX specials: \$
checkRd: (-1) SalaryGender.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) SandP500.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts2.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) TrafficFlow.Rd:18: Escaped LaTeX specials: \#
Namespace in Imports field not imported from: ‘lestat’
  All declared Imports should be used.
Found the following significant warnings:
  locpol.c:101:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/locpol.Rcheck/00install.out’ for details.
checkRd: (-1) KernelChars.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) Kernels.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) PRDenEstC.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) compKernVals.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) denCVBwSelC.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) equivKernel.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) kernelCtes.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) locPolWeights.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) locpol.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) locpol.Rd:82: Escaped LaTeX specials: \&
checkRd: (-1) locpolSmoothers.Rd:54: Escaped LaTeX specials: \&
checkRd: (-1) pluginBw.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) regCVBwSelC.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) thumbBw.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
File ‘loe/libs/loe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘modules’
  All declared Imports should be used.
Found the following significant warnings:
  logconweights.c:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  logconweights.c:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  logconweights.c:27:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  solvoptweights.c:63:16: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  solvoptweights.c:64:16: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  solvoptweights.c:66:16: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  solvoptweights.c:68:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  solvoptweights.c:129:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  solvoptweights.c:697:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  solvoptweights.c:700:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  useful.c:59:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/LogConcDEAD.Rcheck/00install.out’ for details.
Note: found 12 marked UTF-8 strings
Found the following significant warnings:
  clogic.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  clogic.c:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  clogic.c:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  clogic.c:17:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  clogic.c:59:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  clogic.c:69:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  clogic.c:80:16: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  swrite.c:2:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  swrite.c:14:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/LogicReg.Rcheck/00install.out’ for details.
checkRd: (-1) logreg.myown.Rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:20: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:24: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:99: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:120: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:132: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:133: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:134: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:172: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:182: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:184: Escaped LaTeX specials: \_ \_
Found the following significant warnings:
  veclib.h:316:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/logistf.Rcheck/00install.out’ for details.
File ‘logisticPCA/libs/logisticPCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'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.
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: ‘utils’
  All declared Imports should be used.
Found the following files/directories:
  ‘main.tex’ ‘scene.asy’
'LazyData' is specified without a 'data' directory
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.nri.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.s.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.s.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) nri.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) roc.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) roc.s.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.s.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 994 marked Latin-1 strings
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.
File ‘lorec/libs/lorec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  LowRankQP.c:278:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  LowRankQP_init.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/LowRankQP.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lpepa.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:90: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:65: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../inst/include/RlpSolveLink.h:288:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RlpSolveLink.c:2442:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/lpSolveAPI.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
File ‘LRcontrast/libs/LRcontrast.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  period.c:116:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/lubridate.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rpostgis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  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’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  proj_conf_test.c:5:5: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  proj_conf_test.c:4:5: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  liblwgeom/liblwgeom.h:305:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  liblwgeom/lwboundingcircle.c:36:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  liblwgeom/lwboundingcircle.c:217:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lwin_wkt_lex.l:16:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/lwgeom.Rcheck/00install.out’ for details.
Found the following significant warnings:
  map_lib.h:42:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  map_lib.c:45:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/lxb.Rcheck/00install.out’ for details.
File ‘lxb/libs/lxb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Note: found 134 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘rlang’ ‘torch’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘maptools’ ‘sp’
  All declared Imports should be used.
checkRd: (-1) read.magpie.Rd:20: Escaped LaTeX specials: \_ \_
checkRd: (-1) read.magpie.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) read.magpie.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) read.magpie.Rd:36: Escaped LaTeX specials: \_
checkRd: (-1) read.magpie.Rd:65: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:24: Escaped LaTeX specials: \_ \_
checkRd: (-1) write.magpie.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:42: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:43: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:70: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) cilleruelo.Rd:36: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Note: found 41 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘nomnoml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17524 marked UTF-8 strings
File ‘MAMS/libs/MAMS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 55 marked UTF-8 strings
Found the following significant warnings:
  libCEigen.c:76:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ManlyMix.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 3058 marked UTF-8 strings
Note: found 11396 marked UTF-8 strings
Found the following significant warnings:
  Gmake.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Gmake.c:26:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Gmake.c:36:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Gmake.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Gmake.c:66:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Gmake.c:88:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Gmake.c:93:16: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Gmake.c:113:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Gmake.c:128:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Gmake.c:174:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Gmake.c:211:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Lmake.c:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Lmake.c:26:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Lmake.c:36:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Lmake.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Lmake.c:73:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Lmake.c:96:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Lmake.c:119:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Lmake.c:172:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Lmake.c:224:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/mapdata.Rcheck/00install.out’ for details.
checkRd: (-1) china.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) china.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) japan.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) japan.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) nzHires.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) nzHires.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) rivers.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) rivers.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) world2Hires.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) world2Hires.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) worldHires.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) worldHires.Rd:52: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
'LazyData' is specified without a 'data' directory
Note: found 29618 marked UTF-8 strings
Namespace in Imports field not imported from: ‘pbmcapply’
  All declared Imports should be used.
Found the following significant warnings:
  mapproject.c:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mapproject.c:20:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mapproject.c:67:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mapproject.c:111:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mapproject.c:130:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/mapproj.Rcheck/00install.out’ for details.
checkRd: (-1) mapproject.Rd:203: Escaped LaTeX specials: \_
checkRd: (-1) mapproject.Rd:204: Escaped LaTeX specials: \_
checkRd: (-1) mapproject.Rd:210: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scrubr’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    To do
Note: found 55 marked UTF-8 strings
Note: found 996 marked UTF-8 strings
Note: found 13062 marked UTF-8 strings
Note: found 1763 marked UTF-8 strings
checkRd: (-1) county.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) county.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) france.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) france.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) italy.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) italy.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) match.map.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) nz.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) nz.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) state.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) state.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) state.carto.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) state.carto.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) state.vbm.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) state.vbm.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) usa.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) usa.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) world.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) world.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) world2.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) world2.Rd:54: Escaped LaTeX specials: \&
Note: found 1 marked UTF-8 string
checkRd: (-1) sw_sfac.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) Interpolation-class.Rd:41: Escaped LaTeX specials: \#
checkRd: (-1) MareyMap-class.Rd:85: Escaped LaTeX specials: \_
checkRd: (-1) MareyMap-methods.Rd:11: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) MareyMap-methods.Rd:12: Escaped LaTeX specials: \_
checkRd: (-1) SpeciesMaps-methods.Rd:11: Escaped LaTeX specials: \_
checkRd: (-1) interpolation-methods.Rd:13: Escaped LaTeX specials: \_
Note: found 5210 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘kableExtra’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘flashr’
'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
checkRd: (-1) GerberGreenImai.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) GerberGreenImai.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) GerberGreenImai.Rd:34: Escaped LaTeX specials: \#
checkRd: (-1) GerberGreenImai.Rd:35: Escaped LaTeX specials: \#
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
Found the following significant warnings:
  libCEigen.c:76:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/MatManlyMix.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
GNU make is a SystemRequirements.
Found the following significant warnings:
  t_sparseVector.c:83:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chm_common.h:72:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chm_common.h:93:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chm_common.h:94:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chm_common.c:8:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chm_common.c:25:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chm_common.c:50:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/Matrix.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  allocMatrix2.c:10:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  allocMatrix2.c:16:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/matrixStats.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘utilities.R’
'LazyData' is specified without a 'data' directory
checkRd: (-1) maxControl.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'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
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Note: found 18 marked UTF-8 strings
Note: found 17 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
Note: found 66 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:
  ‘effsize’ ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 6 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
File ‘mbrglm/libs/mbrglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cplexAPI’
checkRd: (-1) salamander.Rd:22: Escaped LaTeX specials: \&
File ‘mcemGLM/libs/mcemGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘boot.heterogeneity’
  All declared Imports should be used.
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
Note: found 46 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  chMatrix.c:162:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mcmcsae_init.c:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/mcmcsae.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Checking should be performed on sources prepared by ‘R CMD build’.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘covr’ ‘curl’ ‘devtools’ ‘gh’ ‘git2r’ ‘grDevices’ ‘httr’
  ‘knitr’ ‘openssl’ ‘pkgbuild’ ‘rlang’ ‘rmarkdown’ ‘roxygen2’
  ‘spelling’ ‘testthat’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) glass.Rd:23: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) glass.Rd:24: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) glass.Rd:25: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) glass.Rd:26: Escaped LaTeX specials: \_ \_ \_ \_
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  threat-safe-random.h:58:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  threat-safe-random.h:70:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/mdgc.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mriTest.Rd:9: Escaped LaTeX specials: \&
checkRd: (-1) riTest.Rd:9: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MethylCapSig’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  meanr_native.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  meanr_nthreads.c:9:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  meanr_nthreads.c:31:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  hashtable/poshash.h:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  hashtable/poshash.h:124:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  hashtable/neghash.h:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  hashtable/neghash.h:131:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/meanr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mebootSpear.Rd:88: Escaped LaTeX specials: \_
checkRd: (-1) ullwan.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ullwan.Rd:8: Escaped LaTeX specials: \& \$
'LazyData' is specified without a 'data' directory
File ‘MediaK/libs/MediaK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘patchwork’ ‘tidyverse’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘vroom’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  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:
  pspp-system-for-R.c:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  pspp-system-for-R.c:1291:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/memisc.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Error(s) in re-building vignettes:
--- re-building ‘memor.Rmd’ using rmarkdown
! Missing = inserted for \ifnum.
<to be read again> 
                   v
l.126 \usepackage
                 {array} 

Error: processing vignette 'memor.Rmd' failed with diagnostics:
LaTeX failed to compile /data/gannet/ripley/R/packages/tests-devel/memor.Rcheck/vign_test/memor/vignettes/memor.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See memor.log for more info.
--- failed re-building ‘memor.Rmd’

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
Found the following significant warnings:
  meminfo/src/meminfo.h:61:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrappers.c:48:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrappers.c:71:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrappers.c:93:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrappers.c:129:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  memuse_native.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  memuse_native.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  memuse_native.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  memuse_native.c:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/memuse.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
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: found 37 marked UTF-8 strings
Package suggested but not available for checking: ‘genuMet’
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘gbm’ ‘ggplot2’ ‘graphics’ ‘randomForest’
  All declared Imports should be used.
File ‘MetaheuristicFPA/libs/MetaheuristicFPA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
Suggests orphaned package: ‘udunits2’
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmerTest’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘guide.Rnw’ using knitr
Error: processing vignette 'guide.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'guide.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.138 \hldef
            {}\hldef{\ \ }\hldef{blastx\ }\hlkwb{{-}db\ }\hldef{referenceDB\...

? 
! Emergency stop.
l.138 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘guide.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ade4’ ‘dendextend’ ‘ggforce’ ‘ggrepel’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
checkRd: (-1) dslp.Rd:11: Escaped LaTeX specials: \&
File ‘MEtest/libs/MEtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Note: found 1 marked UTF-8 string
Found the following significant warnings:
  init.c:37:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/mets.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    mev v.1.9x
    mev v.1.8x
Found the following significant warnings:
  SplineFunc.h:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  SplineFunc.h:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  SplineFunc.h:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  SplineFunc.c:84:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  SplineFunc.c:212:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  SplineFunc.c:248:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/mexhaz.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    First release of mfe:
Namespace in Imports field not imported from: ‘ECoL’
  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: ‘fs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘mgarchBEKK/libs/mgarchBEKK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘boot’ ‘energy’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  mgcv.c:66:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/mgcv.Rcheck/00install.out’ for details.
checkRd: (-1) gam.fit3.Rd:4: Escaped LaTeX specials: \&
File ‘MGL/libs/MGL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘ProteoMM’
Package unavailable to check Rd xrefs: ‘DAPAR’
checkRd: (-1) IPDNa.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) fdgs.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) mice.impute.cart.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) mice.impute.rf.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) pmm.match.Rd:41: Escaped LaTeX specials: \&
Note: found 9345 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  do_nothing.h:4:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  do_nothing.c:11:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotimer.c:88:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/microbenchmark.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘curl’ ‘jsonlite’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
'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
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:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘gmp’ ‘jpeg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘markdown’ ‘metafor’
  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:
  ‘pracma’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘MiSPU/libs/MiSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
checkRd: (-1) AKMCS.Rd:215: Escaped LaTeX specials: \&
checkRd: (-1) BMP.Rd:164: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:151: Escaped LaTeX specials: \&
checkRd: (-1) MP.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) MetropolisHastings.Rd:58: Escaped LaTeX specials: \&
checkRd: (-1) SubsetSimulation.Rd:152: Escaped LaTeX specials: \&
checkRd: (-1) oscillator_d6.Rd:14: Escaped LaTeX specials: \&
Packages suggested but not available for checking:
  'karyoploteR', 'regioneR'
Found the following files/directories:
  ‘par-7269706c6579’
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/mixedClust.Rcheck/00install.out’ for details.
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
File ‘mixexp/libs/mixexp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘AnalyzeFMRI’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) mixmeta.ml.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mixRasch’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  libCEigen.c:84:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/MixSim.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RTdata2.Rd:3: Escaped LaTeX specials: \#
checkRd: (-1) boot.comp.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) boot.se.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) compCDF.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) hmeEM.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) logisregmixEM.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) multmixEM.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) mvnormalmixEM.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) normalmixEM.Rd:133: Escaped LaTeX specials: \&
checkRd: (-1) normalmixEM2comp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) poisregmixEM.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) regmixEM.Rd:67: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ashr’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) qboxplot.Rd:127: Escaped LaTeX specials: \&
checkRd: (-1) qboxplot.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) qbxp.stats.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) mi.t.test.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) qboxplot.Rd:127: Escaped LaTeX specials: \&
checkRd: (-1) qboxplot.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) qbxp.stats.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) ssize.propCI.Rd:38: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
Found the following significant warnings:
  waveform.c:31:4: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  waveform.c:44:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/mlbench.Rcheck/00install.out’ for details.
checkRd: (-1) BreastCancer.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) Ionosphere.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) Ionosphere.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) PimaIndiansDiabetes.Rd:19: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘ConfusionTableR’ ‘OddsPlotty’ ‘caret’ ‘dplyr’ ‘ggplot2’ ‘parsnip’
  ‘ranger’ ‘recipes’ ‘rsample’ ‘varhandle’ ‘workflows’
  All declared Imports should be used.
checkRd: (-1) AutumnLab.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) gp.list.Rd:16: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘mlmc/libs/mlmc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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
File ‘mlmmm/libs/mlmmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘ClusterR’ ‘MASS’ ‘Rdpack’ ‘multiwave’ ‘ranger’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘randomForest’
  All declared Imports should be used.
Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘e1071’ ‘mlr3’ ‘mlr3learners’ ‘mlr3measures’ ‘plyr’
  ‘purrr’ ‘ranger’ ‘readxl’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stats’ ‘stringr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  mmap.h:104:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mmap.h:108:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mmap.h:117:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mmap.c:74:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mmap.c:286:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  types.c:4:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/mmap.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘DT’ ‘XML’ ‘caTools’ ‘data.table’ ‘dplyr’ ‘ggplot2’
  ‘htmltools’ ‘leaflet’ ‘lubridate’ ‘plotly’ ‘shinyjs’ ‘stringr’ ‘xts’
  ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘doParallel’ ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Flury’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘alstructure’

Packages which this enhances but not available for checking:
  'miraculix', 'MoBPSmaps'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 313 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lattice’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 18 marked Latin-1 strings
Namespace in Imports field not imported from: ‘parsnip’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 5238 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) polypes.Rd:17: Escaped LaTeX specials: \&
Note: found 20578 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.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * efourier with default norm=TRUE now messages about how wrong it may be
Note: found 16 marked UTF-8 strings
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Found the following significant warnings:
  client.c:5:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mongoc/mongoc-generation-map-private.h:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mongoc/mongoc-async-private.h:59:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mongoc/mongoc-async.c:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mongoc/mongoc-stream-tls-openssl-bio-private.h:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mongoc/mongoc-stream-tls-openssl-bio.c:87:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ./mongoc/mongoc-generation-map-private.h:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ./mongoc/mongoc-async-private.h:59:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mongoc/mongoc-generation-map.c:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mongoc/mongoc-generation-map.c:57:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mongoc/mongoc-timeout-private.h:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mongoc/mongoc-timeout.c:56:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  kms/kms_crypto.h:38:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  kms/kms_crypto.h:41:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  kms/kms_crypto_libcrypto.c:42:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  kms/kms_crypto_libcrypto.c:48:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  kms/kms_request_str.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/mongolite.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ordsampler.c:59:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:113:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:124:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:386:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:544:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:560:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:710:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:1102:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sampler.c:52:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sampler.c:149:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sampler.c:158:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sampler.c:729:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/monoreg.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Note: found 13 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 56 marked UTF-8 strings
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘NlcOptim’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
checkRd: (-1) Context.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) psyfun.boot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) psyfun.boot.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
File ‘mpmi/libs/mpmi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) F.huggins.estim.Rd:199: Escaped LaTeX specials: \$ \$
checkRd: (-1) F.huggins.estim.Rd:205: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:206: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:207: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:208: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:209: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:210: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:212: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:213: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:214: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:215: Escaped LaTeX specials: \$
checkRd: (-1) lines.cjs.Rd:15: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  combination.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  combination.c:63:21: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  product.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  product.c:62:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/mrfse.Rcheck/00install.out’ for details.
File ‘mrfse/libs/mrfse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 75 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘MSGLasso/libs/MSGLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.txt’
File ‘msgps/libs/msgps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘tidyselect’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘markdown’ ‘methods’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
Note: found 2632 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Found the following significant warnings:
  muhaz.c:1367:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/mudens.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gtools’ ‘patchwork’ ‘plyr’ ‘tidyverse’
  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: ‘shape’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘polycor’
  All declared Imports should be used.
checkRd: (-1) MultBiplotR-package.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) MultBiplotR-package.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) print.multcompLetters.Rd:20: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘MultiBD/libs/MultiBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Rdpack’
  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: ‘cowsay’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ez’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plsgenomics’
  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
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘stats’ ‘tidyverse’
  All declared Imports should be used.
Note: found 15 marked UTF-8 strings
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘fields’ ‘optmatch’ ‘rcbalance’ ‘utils’
  All declared Imports should be used.
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘multispatialCCM/libs/multispatialCCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘poweRlaw’ ‘rmutil’
  All declared Imports should be used.
Note: found 6 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: ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
Packages suggested but not available for checking: 'BioNet', 'DLBCL'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 50 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Kendall’ ‘perm’
  All declared Imports should be used.
Note: found 63 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘mlr3learners’ ‘rpart’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘asreml’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    PREVIOUS (Incomplete below)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
Found the following significant warnings:
  namespace.c:4:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/namespace.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
File ‘namespace/libs/namespace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 47936 marked UTF-8 strings
File ‘nanop/libs/nanop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘spatialClust’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Found the following files/directories:
  ‘Crashpad’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
Package suggested but not available for checking: ‘gurobi’
Note: found 5 marked Latin-1 strings
  Note: found 7187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
Note: found 140 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘rrpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘sSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
File ‘nbpMatching/libs/nbpMatching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Note: found 7332 marked UTF-8 strings
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
checkRd: (-1) netCoin-package.Rd:38: Escaped LaTeX specials: \&
Note: found 21 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’
  All declared Imports should be used.
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_ \_
checkRd: (-1) makeNetwork.Rd:31: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fastshp’
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘NetPreProc/libs/NetPreProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 2 marked Latin-1 strings
Running examples in ‘neurobase-Ex.R’ failed
The error most likely occurred in:

> ### Name: boxplot.nifti
> ### Title: Boxplot of Values in an Image
> ### Aliases: boxplot.nifti boxplot.anlz
> 
> ### ** Examples
> 
> img = nifti(array(rnorm(10^3), dim = rep(10, 3)))
> mask = img > 0
> boxplot(img)
> boxplot(img, mask = mask)
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars$yaxs) : 
  need finite 'ylim' values
Calls: boxplot ... boxplot.default -> do.call -> <Anonymous> -> plot.window
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘neurobase.Rmd’ using rmarkdown
Quitting from lines 459-460 (neurobase.Rmd) 
Error: processing vignette 'neurobase.Rmd' failed with diagnostics:
need at least 2 points to select a bandwidth automatically
--- failed re-building ‘neurobase.Rmd’

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

--- re-building ‘simple_io.Rmd’ using rmarkdown
trying URL 'https://johnmuschelli.com/open_ms_data/cross_sectional/raw/patient01/T1W.nii.gz'
Content type 'application/gzip' length 21807043 bytes (20.8 MB)
==================================================
downloaded 20.8 MB

--- finished re-building ‘simple_io.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
File ‘neuroim/libs/neuroim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Note: found 318 marked UTF-8 strings
Note: found 4894 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘curl’ ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nflfastR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  getseed.c:41:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  getseed.c:60:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  getseed.c:81:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  getseed.c:83:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ngram_native.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ngram.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
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHSRdatasets’ ‘grid’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘nice/libs/nice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
Note: found 170 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nleqslv.c:4:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nwout.c:49:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/nleqslv.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘nlraa’
  All declared Imports should be used.
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) nltm.control.Rd:29: Escaped LaTeX specials: \$
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocManager’
  All declared Imports should be used.
checkRd: (-1) Frobenius-nmf.Rd:141: Escaped LaTeX specials: \#
checkRd: (-1) KL-nmf.Rd:158: Escaped LaTeX specials: \#
checkRd: (-1) NMFStrategyIterative-class.Rd:69: Escaped LaTeX specials: \#
checkRd: (-1) NMFstd-class.Rd:179: Escaped LaTeX specials: \#
checkRd: (-1) nmf.Rd:755: Escaped LaTeX specials: \#
checkRd: (-1) nmf_update_KL.Rd:87: Escaped LaTeX specials: \#
checkRd: (-1) nmf_update_euclidean.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) offset-nmf.Rd:144: Escaped LaTeX specials: \#
Running examples in ‘NMF-Ex.R’ failed
The error most likely occurred in:

> ### Name: profplot
> ### Title: Plotting Expression Profiles
> ### Aliases: profplot profplot.default
> ### Keywords: aplot
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # create a random target matrix
> v <- rmatrix(35, 10)
> 
> # fit a single NMF model
> res <- nmf(v, 3)
> profplot(res)
> 
> # fit a multi-run NMF model
> res2 <- nmf(v, 3, nrun=2)
# NOTE - CRAN check detected: limiting maximum number of cores [2/24]
> # ordering according to first profile
> profplot(res2, Colv=1) # increasing
> 
> # draw a profile correlation plot: this show how the basis components are
> # returned in an unpredictable order
> profplot(res, res2)
Error in col["alpha", ] <- as.character(as.hexmode(alpha)) : 
  incorrect number of subscripts on matrix
Calls: profplot ... <Anonymous> -> .set.list.defaults -> expand_list -> alphacol
Execution halted
'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:
  veclib.h:302:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/nncc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  geodesic.c:57:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/nngeo.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Other ideas
File ‘nnls/libs/nnls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’ ‘forcats’
  ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘digest’ ‘hash’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulatePop.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘noncompliance/libs/noncompliance.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
'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:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    norgeo (development version)
Namespaces in Imports field not imported from:
  ‘progressr’ ‘vcr’
  All declared Imports should be used.
File ‘norm2/libs/norm2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/norm.Rcheck/00install.out’ for details.
'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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Running ‘testthat.R’ [63s/74s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #' Copyright(c) 2017-2020 R. Mark Sharp
  > #' This file is part of nprcgenekeepr
  > library(testthat)
  > library(nprcgenekeepr)
  > test_check("nprcgenekeepr")
  15 15 
  15 15 
  [ FAIL 1 | WARN 3 | SKIP 19 | PASS 747 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  • Sys.info()[names(Sys.info()) == "user"] == "msharp" is not TRUE (18)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_getDatedFilename.R:12'): getDatedFilename form correctly dated file name ──
  stri_sub(getDatedFilename("testName"), 21) not equal to "testName".
  1/1 mismatches
  x[1]: "719999_testName"
  y[1]: "testName"
  
  [ FAIL 1 | WARN 3 | SKIP 19 | PASS 747 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  vadr.h:55:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  promises.h:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dots.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  promises.c:93:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vadr.c:22:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/nseval.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
checkRd: (-1) Ardechedata.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) nsRFA-package.Rd:231: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
'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:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘argparse’ ‘tidyverse’ ‘vcfR’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘pedtools’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 6409 marked UTF-8 strings
Note: found 7284 marked UTF-8 strings
'LazyData' is specified without 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: ‘httr’
  All declared Imports should be used.
Note: found 7 marked UTF-8 strings
Packages suggested but not available for checking:
  'originr', 'parallelsugar'
Namespaces in Imports field not imported from:
  ‘rnaturalearthdata’ ‘spocc’ ‘tidyverse’
  All declared Imports should be used.
Note: found 1242 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.
Note: found 4 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’ ‘ggthemes’ ‘mlbench’ ‘rmarkdown’ ‘tidymodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
Package suggested but not available for checking: ‘morse’
Found the following significant warnings:
  gutsRedIT.c:34:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gutsRedIT.c:58:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gutsRedSD.c:36:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gutsRedSD.c:64:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  odeGUTS_init.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  odeGUTS_init.c:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/odeGUTS.Rcheck/00install.out’ for details.
'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
'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
'LazyData' is specified without a 'data' directory
File ‘olctools/libs/olctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Note: found 842 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘crayon’ ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘gdata’ ‘genefilter’ ‘maftools’ ‘readxl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘onlinePCA/libs/onlinePCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 32 marked UTF-8 strings
Note: found 34 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘glue’ ‘httpcode’ ‘httr’ ‘jsonlite’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2524 marked UTF-8 strings
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
possible bashism in configure line 52 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
Package suggested but not available for checking: ‘openNLPmodels.en’
Namespaces in Imports field not imported from:
  ‘formattable’ ‘rintrojs’ ‘shinyBS’ ‘shinyFeedback’ ‘shinyWidgets’
  ‘shinycssloaders’ ‘shinydashboard’ ‘shinydashboardPlus’ ‘shinyjs’
  ‘shinythemes’ ‘splines’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Note: found 167 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘hrbrthemes’ ‘magrittr’ ‘orthopolynom’ ‘plotly’ ‘shinyalert’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
File ‘OptGS/libs/OptGS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
File ‘OptHedging/libs/OptHedging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
checkRd: (-1) quad_3D.Rd:22: Escaped LaTeX specials: \&
'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
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
File ‘optpart/libs/optpart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
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.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Found the following significant warnings:
  utilityFuns.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:30:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:37:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:41:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:42:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:43:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ordinal.Rcheck/00install.out’ for details.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
Found the following significant warnings:
  zzz.h:4:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.h:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.c:22:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.c:58:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  onig/st.h:69:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  onig/st.h:70:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  onig/st.h:128:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  onig/st.h:129:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  onig/st.c:1483:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  onig/st.c:1567:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  enc/jis/props.kwd:106:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  onig/enc/unicode/name2ctype.h:33390:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ore.Rcheck/00install.out’ for details.
'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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  cleancall.h:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cleancall.c:40:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  keyring-macos.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  keyring-secret-service.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  keyring-wincred.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/oskeyring.Rcheck/00install.out’ for details.
Note: found 263 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../osqp_sources//lin_sys/direct/pardiso/pardiso_loader.h:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../osqp_sources//lin_sys/direct/pardiso/pardiso_interface.c:35:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../osqp_sources//lin_sys/direct/pardiso/pardiso_loader.c:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../osqp_sources//lin_sys/direct/pardiso/pardiso_loader.c:58:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../osqp_sources//lin_sys/direct/pardiso/pardiso_loader.c:90:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/osqp.Rcheck/00install.out’ for details.
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
Namespaces in Imports field not imported from:
  ‘R6’ ‘jsonlite’
  All declared Imports should be used.
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
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
Problems with news in ‘NEWS.md’:
No news entries found.
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: \$
Namespace in Imports field not imported from: ‘optparse’
  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: ‘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
Package which this enhances but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Imap’
'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.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
File ‘PAMA/libs/PAMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 34 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
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.
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.
Namespaces in Imports field not imported from:
  ‘caret’ ‘gstat’ ‘pryr’
  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 16 marked UTF-8 strings
Found the following significant warnings:
  socp.h:42:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  socp.h:43:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  socp.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  socp.h:45:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  socp.h:48:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  socp.h:49:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  socp.h:52:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  socp.h:55:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  socp.h:56:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/parma.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  mingw.c:24:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/parsedate.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘parallel’
  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:
  ‘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.
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 1 marked UTF-8 string
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.
Checking should be performed on sources prepared by ‘R CMD build’.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘Mfuzz’ ‘SelectBoost’ ‘gplots’ ‘grid’ ‘jetset’ ‘magic’
  ‘msgps’ ‘splines’ ‘stats4’ ‘survival’
  All declared Imports should be used.
checkRd: (-1) plot-methods.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) plot-methods.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) glue_search_tables.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_batch_get_item.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_delete_item.Rd:81: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_get_item.Rd:55: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_put_item.Rd:98: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_query.Rd:237: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_scan.Rd:174: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_update_item.Rd:177: Escaped LaTeX specials: \#
checkRd: (-1) elasticache_create_cache_cluster.Rd:291: Escaped LaTeX specials: \#
checkRd: (-1) elasticache_create_replication_group.Rd:329: Escaped LaTeX specials: \#
checkRd: (-1) cloudwatchlogs_create_log_group.Rd:30: Escaped LaTeX specials: \#
checkRd: (-1) licensemanager_create_license_configuration.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) licensemanager_create_license_configuration.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) opsworks_update_layer.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) opsworkscm_create_server.Rd:76: Escaped LaTeX specials: \#
checkRd: (-1) ssm_send_command.Rd:47: Escaped LaTeX specials: \$
checkRd: (-1) ssm_send_command.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) apigatewayv2_create_stage.Rd:34: Escaped LaTeX specials: \#
checkRd: (-1) apigatewayv2_update_stage.Rd:36: Escaped LaTeX specials: \#
checkRd: (-1) iam_update_account_password_policy.Rd:21: Escaped LaTeX specials: \#
Found the following significant warnings:
  pbatR_init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  pbatR_init.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/pbatR.Rcheck/00install.out’ for details.
---- unloading
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
Found the following significant warnings:
  R_zmq.h:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_zmq.h:30:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_zmq.h:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_zmq.h:52:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_zmq.h:59:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_zmq.h:60:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_zmq_context.c:7:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_zmq_utility.c:26:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_zmq_message.c:8:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_zmq_poll.c:39:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_zmq_poll.c:48:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/pbdZMQ.Rcheck/00install.out’ for details.
'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
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
Found the following significant warnings:
  PBSddesolve.c:149:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/PBSddesolve.Rcheck/00install.out’ for details.
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.
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
checkRd: (-1) l1pcastar.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) pcaL1-package.Rd:52: Escaped LaTeX specials: \&
'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.
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Dist.Rd:50: Escaped LaTeX specials: \&
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.
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
'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
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.
Found the following significant warnings:
  pearson.h:100:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  QuadDouble.c:497:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  QuadDouble.c:508:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/PearsonDS.Rcheck/00install.out’ for details.
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: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘georob’
Note: found 13918 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
GNU make is a SystemRequirements.
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: \_ \_
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
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.
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.
Problems with news in ‘NEWS.md’:
No news entries found.
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.
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.
Found the following files/directories:
  ‘permus_per_dist_4’ ‘permus_per_shape_bin_4_0’
  ‘permus_per_shape_bin_4_1’ ‘permus_per_shape_bin_4_2’
  ‘permus_per_shape_bin_4_3’
'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
'LazyData' is specified without 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.
'LazyData' is specified without a 'data' directory
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
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:
  ml.c:39:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/phangorn.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.pdf’
Note: found 114 marked UTF-8 strings
'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: \_ \_
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
checkRd: (-1) 11_d.EMControl.Rd:52: Escaped LaTeX specials: \_
checkRd: (-1) plotdots.Rd:33: Escaped LaTeX specials: \#
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) 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: \&
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: \$ \$
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
'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
'LazyData' is specified without a 'data' directory
Note: found 2048 marked UTF-8 strings
'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’
'LazyData' is specified without a 'data' directory
'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
Found the following significant warnings:
  init.c:17:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/pkgcache.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Running examples in ‘pkgmaker-Ex.R’ failed
The error most likely occurred in:

> ### Name: alphacol
> ### Title: Colour utilities
> ### Aliases: alphacol
> 
> ### ** Examples
> 
> 
> # Alphas
> alphacol('red') # do nothing
Error in apply(col, 2, function(x) paste("#", paste(x, collapse = ""),  : 
  dim(X) must have a positive length
Calls: alphacol -> apply
Execution halted
'LazyData' is specified without a 'data' directory
'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.
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:
  'harmony', 'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
'LazyData' is specified without a 'data' directory
'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’ ‘patchwork’
  All declared Imports should be used.
'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
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
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘gridExtra’
  All declared Imports should be used.
File ‘png/libs/png.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
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
Found the following significant warnings:
  rwrapper.c:274:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/poismf.Rcheck/00install.out’ for details.
'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
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’
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
Packages suggested but not available for checking:
  'BASIX', 'WhopGenome', 'BlockFeST'
Found the following significant warnings:
  tabix/khash.h:129:38: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  tabix/bgzf.c:138:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  tabix/bam_endian.h:6:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/PopGenome.Rcheck/00install.out’ for details.
checkRd: (-1) BayeScanR.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) MKT-methods.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘lfa’
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.
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.
Namespaces in Imports field not imported from:
  ‘areal’ ‘microbenchmark’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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: \$
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
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
checkRd: (-1) findRes.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) ppmlasso-package.Rd:42: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rpart’ ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'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.
Namespace in Imports field not imported from: ‘here’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    CalEquation function can calculate intercept in multiple regression model with interaction
    New arguments summarymode added to fit2newdata(), predict3d() and ggPredict()
    New arguments xlab, ylab and zlab added to predict3d()
    New function gg_color_hue() and theme_bw2() added
    Bug-fixed
    New function restoreData2(), restoreData3()  added
    New function add_lines() added
    New function ggPredict() and predict3d() added
    New function fit2newdata() added
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 71 marked UTF-8 strings
Namespace in Imports field not imported from: ‘badger’
  All declared Imports should be used.
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.
Note: found 93457 marked UTF-8 strings
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 165 marked UTF-8 strings
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.
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.
checkRd: (-1) prim.box.Rd:60: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gurobi', 'Rcplex'
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
Namespaces in Imports field not imported from:
  ‘DT’ ‘rio’ ‘shiny’ ‘shinyjs’ ‘utils’ ‘webp’
  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: ‘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
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
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  procmap.c:20:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/procmaps.Rcheck/00install.out’ for details.
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: \&
Package suggested but not available for checking: ‘BayesianTools’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProFit’
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.
'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
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘SDMTools’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Running ‘testthat.R’ [44s/54s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(propr)
  > 
  > test_check("propr")
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 197 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-aldex2propr.R:97'): iqlr matches ALDEx2 implementation ───────
  perb(marg.abs[, 1:50] + 0.5, ivar = "iqlr")@matrix not equal to perb(marg.abs[, 1:50] + 0.5, ivar = z)@matrix.
  2450/2500 mismatches (average diff: 0.0509)
  [2]   0.45221 -  0.3838 ==  0.06842
  [3]  -0.65122 - -0.7554 ==  0.10416
  [4]  -0.82028 - -0.8190 == -0.00130
  [5]   0.40911 -  0.3153 ==  0.09377
  [6]  -0.58339 - -0.6845 ==  0.10112
  [7]   0.51454 -  0.5107 ==  0.00379
  [8]  -0.57212 - -0.6929 ==  0.12082
  [9]  -0.00375 -  0.0136 == -0.01739
  [10]  0.59415 -  0.5631 ==  0.03102
  ...
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 197 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘cin’
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.
Found the following significant warnings:
  computeParentIonMass.c:59:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/protViz.Rcheck/00install.out’ for details.
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’
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.
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘miceadds’
  All declared Imports should be used.
'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
Note: found 140 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: \&
Error(s) in re-building vignettes:
--- re-building ‘scoring.Rnw’ using knitr
Error: processing vignette 'scoring.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'scoring.tex' failed.
LaTeX errors:
! Missing = inserted for \ifnum.
<to be read again> 
                   v
l.79 \usepackage
                {longtable}
! Emergency stop.
<to be read again> 
                   v
l.79 \usepackage
                {longtable}
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘scoring.Rnw’

--- re-building ‘intro.Rnw’ using Sweave
--- finished re-building ‘intro.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘lifecycle’ ‘patchwork’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 107 marked UTF-8 strings
Namespace in Imports field not imported from: ‘yaml’
  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.
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.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘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
'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: \&
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Found the following files/directories:
  ‘EWAS_QC_graph_effectsize.png’ ‘EWAS_QC_graph_precision.png’
  ‘EWAS_QC_legend.txt’ ‘sample1.txt.gz’ ‘sample2.txt.gz’
  ‘sample_map.txt.gz’ ‘sample_output.graph_M.png’
  ‘sample_output.graph_QQ.png’ ‘sample_output.graph_p.png’
  ‘sample_output.graph_volcano.png’ ‘sample_output.histo.png’
  ‘sample_output.txt’ ‘sample_output1.graph_M.png’
  ‘sample_output1.graph_QQ.png’ ‘sample_output1.graph_p.png’
  ‘sample_output1.graph_volcano.png’ ‘sample_output1.histo.png’
  ‘sample_output2.graph_M.png’ ‘sample_output2.graph_QQ.png’
  ‘sample_output2.graph_p.png’ ‘sample_output2.graph_volcano.png’
  ‘sample_output2.histo.png’ ‘translation_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
checkRd: (-1) CentAndClusfuns.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) EBICglasso.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) pathways.Rd:36: Escaped LaTeX specials: \&
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.
Note: found 76102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/qoi.Rcheck/00install.out’ for details.
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.
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.
Malformed Description field: should contain one or more complete sentences.
Note: found 6 marked UTF-8 strings
'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
Found the following significant warnings:
  ibsFn.c:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ibsFn.c:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ibsFn.c:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  idcoef.c:40:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  idcoef.c:41:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  idcoef.c:42:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  idcoef.c:43:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  idcoef.c:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  idcoef.c:45:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  idcoef.c:46:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  idcoef.c:47:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  idcoef.c:48:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  idcoef.c:49:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdat.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdat.c:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/QTLRel.Rcheck/00install.out’ for details.
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
'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.
Note: found 4 marked UTF-8 strings
Note: found 35707 marked UTF-8 strings
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
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.
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
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.
Package suggested but not available for checking: ‘BayesianTools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
Package required but not available: ‘harmony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Namespace in Imports field not imported from: ‘Rcompadre’
  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:
  ‘Biobase’ ‘CGHbase’
  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
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
Package suggested but not available for checking: ‘RandomFields’
Found the following significant warnings:
  win_linux_aux.h:40:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:46:2: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:47:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:64:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:66:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:67:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:68:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:72:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Utils.h:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  options.h:152:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  options.h:155:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz_RandomFieldsUtils.h:96:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz_RandomFieldsUtils.h:97:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz_RandomFieldsUtils.h:132:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/RandomFieldsUtils.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
    New Features
    Major Changes
    Minor changes
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ri’
'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.
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.
'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.
Found the following significant warnings:
  gsl_randist.h:73:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  discrete.c:539:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ranlip.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Rstrptime.h:1199:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/RApiDatetime.Rcheck/00install.out’ for details.
'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.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
'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
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  geodesic.c:50:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/raster.Rcheck/00install.out’ for details.
'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'
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
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
Found the following significant warnings:
  charsets.h:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bib2be.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bibtexdirectin.c:93:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  charsets.c:34614:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rbibutils.Rcheck/00install.out’ for details.
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:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
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
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
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
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.
'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.
'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.
'LazyData' is specified without a 'data' directory
Note: found 345 marked UTF-8 strings
Package suggested but not available for checking: ‘conics’
Found the following significant warnings:
  init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/RcppAnnoy.Rcheck/00install.out’ for details.
Found the following significant warnings:
  init.c:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/RcppBDT.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'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.
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
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/RcppEigen.Rcheck/00install.out’ for details.
‘configure’: /bin/bash is not portable
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:12:1: 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/RcppGSL.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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’
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/RcppRedis.Rcheck/00install.out’ for details.
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/RcppXts.Rcheck/00install.out’ for details.
'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
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
Namespaces in Imports field not imported from:
  ‘DeclareDesign’ ‘fabricatr’
  All declared Imports should be used.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
'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"
'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
'LazyData' is specified without a 'data' directory
Note: found 1036 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘readr’
  All declared Imports should be used.
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
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.
'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
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’ ‘scales’
  All declared Imports should be used.
'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
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
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.
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.
'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
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
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
Found the following significant warnings:
  dist.c:246:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dist.c:278:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/repeated.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) KitchenhamEtAl.CorrelationsAmongParticipants.Madeyski10.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) KitchenhamEtAl.CorrelationsAmongParticipants.Madeyski10.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 25 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘P.csv’ ‘correct_alpha.csv’ ‘correct_beta.csv’ ‘correct_gamma.csv’
  ‘correct_lambda.csv’ ‘correct_perm_list.csv’ ‘correct_psi.csv’
'LazyData' is specified without a 'data' directory
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: \&
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
Package suggested but not available for checking: ‘evdbayes’
Found the following significant warnings:
  init.c:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/revdbayes.Rcheck/00install.out’ for details.
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
Package suggested but not available for checking: ‘RevGadgets’
'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.
checkRd: (-1) boot.james.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) boot.student2.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) coljack.means.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) collognorm.mle.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) collognorm.mle.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) fipois.reg.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) halfcauchy.mle.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) halfcauchy.mle.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) jack.mean.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) lm.parboot.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) multivm.mle.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) ancova1.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) ancovas.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) boot.ttest2.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) colnormal.mle.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) colnormal.mle.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) colnormal.mle.Rd:77: Escaped LaTeX specials: \&
checkRd: (-1) colrint.regbx.Rd:58: Escaped LaTeX specials: \&
checkRd: (-1) colvarcomps.mom.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) colvarcomps.mom.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) ftest.Rd:90: Escaped LaTeX specials: \&
checkRd: (-1) ftests.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) gammamle.Rd:81: Escaped LaTeX specials: \&
checkRd: (-1) gammamle.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) gammamle.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) rint.regbx.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) rint.regs.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) twoway.anovas.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) varcomps.mom.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) varcomps.mom.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) vm.mle.Rd:60: 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: ‘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.
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
'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
Found the following significant warnings:
  /data/gannet/ripley/R/test-dev/sp/include/sp.h:95:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdal.h:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdal.h:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdal.h:130:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdal.h:134:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdal.h:135:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdal.h:136:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdal.h:138:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rgdal.Rcheck/00install.out’ for details.
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
Found the following significant warnings:
  IP2Loc_DBInterface.h:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IP2Loc_DBInterface.h:55:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IP2Location.h:186:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IP2Loc_DBInterface.c:242:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IP2Location.c:208:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IP2Location.c:275:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IP2Location.c:841:27: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rgeolocate.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-dev/sp/include/sp.h:95:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rgeos.Rcheck/00install.out’ for details.
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.
checkRd: (-1) Rglpk_read_file.Rd:6: Escaped LaTeX specials: \_
Found the following significant warnings:
  gl2ps.h:254:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gl2ps.c:6479:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rgl.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
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 significant warnings:
  qoma-hli.h:23:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.h:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.h:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.h:26:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.c:29:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.c:39:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.c:58:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.c:131:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rhli.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  filterhr.c:7:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/RHRV.Rcheck/00install.out’ for details.
'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.
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:
  'mockthat', 'mimic.demo', 'eicu.demo'
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: \&
'LazyData' is specified without 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’ [25s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("rim")
  Loading required package: rim
  Maxima successfully registered as knitr engine!
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 46 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-engine.R:18'): maxima knitr engine works ─────────────────────
  digest::digest\(readLines\(fo\), "sha256"\) does not match "b3e41ffd272cce65787f4846b298d889deba7fe80d98517c8a1a3e9ce776e86e".
  Actual value: "04961b317e7365f7f1582bd3a9b0a4d6032c4aea0d1fb3bb71a2950f68177bce"
  Backtrace:
      ▆
   1. └─testthat::expect_match(...) at test-engine.R:18:2
   2.   └─testthat:::expect_match_(...)
  ── Failure ('test-warnings.R:9'): warnings are forwarded ───────────────────────
  `maxima.get("bfloat(x);")` did not throw the expected warning.
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 46 ]
  Error: Test failures
  Execution halted
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.
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_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'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.
Package suggested but not available for checking: ‘ipw’
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
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Running examples in ‘RiverLoad-Ex.R’ failed
The error most likely occurred in:

> ### Name: CQregression
> ### Title: Relationship between concentration and flow
> ### Aliases: CQregression
> ### Keywords: regression
> 
> ### ** Examples
> 
> data("flow.data1","conc.data1")
> union<-db.union(flow.data1, conc.data1)
> reg.relationship<-CQregression(union, 2)
Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 
  0 (non-NA) cases
Calls: CQregression -> lm -> lm.fit
Execution halted
'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.
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.
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 ‘_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
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: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rlibjson.c:364:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/RJSONIO.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  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 ‘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: \$
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.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Previous version rmangal
Note: found 31 marked UTF-8 strings
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
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: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘blockcluster’
Package suggested but not available for checking: ‘blockcluster’
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
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.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Found the following significant warnings:
  dist.c:246:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dist.c:278:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:188:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:189:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:190:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:191:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:192:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:193:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:194:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:195:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:196:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:197:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:198:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rmutil.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
checkRd: (-1) wr.Rd:2: Escaped LaTeX specials: \&
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 7 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.
Found the following significant warnings:
  RNetCDF.h:149:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  udunits.c:385:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/RNetCDF.Rcheck/00install.out’ for details.
'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.
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
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) hybrid.filter.Rd:159: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
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.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘methods’ ‘utils’
  All declared Imports should be used.
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.
checkRd: (-1) aircraft.Rd:8: Escaped LaTeX specials: \$
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘textreadr’
Unknown package ‘textreadr’ in Rd xrefs
Running examples in ‘rock-Ex.R’ failed
The error most likely occurred in:

> ### Name: doc_to_txt
> ### Title: Convert a document (.docx, .pdf, etc) to a plain text file
> ### Aliases: doc_to_txt
> 
> ### ** Examples
> 
> print(
+   rock::doc_to_txt(
+     input = system.file(
+       "extdata/doc-to-test.docx", package="rock"
+     )
+   )
+ );
Error in loadNamespace(x) : there is no package called ‘textreadr’
Calls: print ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
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
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  graph_geodesic.c:9:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/common.h:84:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/common.h:85:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/BitVector.h:57:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/BitVector.h:58:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/BitVector.c:36:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/BitVector.c:46:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/common.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/common.c:110:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/common.c:133:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rogue.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 261 marked UTF-8 strings
GNU make is a SystemRequirements.
Found the following significant warnings:
  /data/gannet/ripley/R/packages/tests-devel/rolog/src/swipl-devel/src/os/pl-os.c:2159:26: warning: the comparison will always evaluate as ‘true’ for the address of ‘S__iob’ will never be NULL [-Waddress]
See ‘/data/gannet/ripley/R/packages/tests-devel/rolog.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘Rook/libs/Rook.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
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
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rpart.h:78:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rpart.h:79:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rpart.h:80:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rpart.h:81:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gini.c:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  func_table.h:50:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  func_table.h:51:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  func_table.h:52:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  func_table.h:53:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rpart.Rcheck/00install.out’ for details.
checkRd: (-1) post.rpart.Rd:45: Escaped LaTeX specials: \# \#
checkRd: (-1) post.rpart.Rd:46: Escaped LaTeX specials: \#
checkRd: (-1) text.rpart.Rd:52: Escaped LaTeX specials: \# \#
checkRd: (-1) text.rpart.Rd:53: Escaped LaTeX specials: \#
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘Rpdb.pdb’
'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.
'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:
  init.c:109:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:153:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/RProtoBuf.Rcheck/00install.out’ for details.
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
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
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'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
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
'LazyData' is specified without a 'data' directory
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.
'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.
Found the following significant warnings:
  cli.c:172:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cli.c:211:18: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cli.c:1152:9: warning: ‘RSA_size’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
  cli.c:1153:9: warning: ‘RSA_public_encrypt’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
  cli.c:1194:5: warning: ‘d2i_RSAPublicKey’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
  dummy.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dummy.c:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dummy.c:8:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/RSclient.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘rsdepth/libs/rsdepth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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
Running ‘rsolr_unit_tests.R’ [14m/90m]
Running the tests in ‘tests/rsolr_unit_tests.R’ failed.
Complete output:
  > rsolr:::.test()
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  Solr started at: http://localhost:8983/solr/techproducts
  
  Attaching package: 'BiocGenerics'
  
  The following objects are masked from 'package:stats':
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from 'package:base':
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
      tapply, union, unique, unsplit, which.max, which.min
  
  
  Attaching package: 'rsolr'
  
  The following object is masked from 'package:stats':
  
      ftable
  
  The following object is masked from 'package:base':
  
      grouping
  
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  Solr started at: http://localhost:8983/solr/Cars93
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  
  Timing stopped at: 772.2 20.17 5332
  Error in file() : cannot open the connection
  Calls: <Anonymous> -> <Anonymous> -> <Anonymous> -> portIsOpen -> file
  In addition: Warning message:
  In file() :
    cannot open file '/tmp/Rtmpii5BPj/working_dir/Rtmp7fIEHG/Rf178c8e7110506f': Too many open files
  Execution halted
  sh: error while loading shared libraries: libtinfo.so.6: cannot open shared object file: Error 24
Error(s) in re-building vignettes:
--- re-building ‘intro.Rnw’ using knitr
Quitting from lines 122-123 (intro.Rnw) 
Error: processing vignette 'intro.Rnw' failed with diagnostics:
Failed to retrieve schema.
rsolr requires schema via REST or as XML from admin module.
Error from REST: Error in h(simpleError(msg, call)): error in evaluating the argument 'X' in selecting a method for function 'lapply': Not Found


--- failed re-building ‘intro.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MatrixExtra’
  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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Note: found 117 marked UTF-8 strings
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.
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.
'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.
Note: found 9 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppProgress’
  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.
'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
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘plyr’ ‘terra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 2023 marked Latin-1 strings
  Note: found 17 marked UTF-8 strings
Package suggested but not available for checking: ‘cmdstanr’
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
GNU make is a SystemRequirements.
Found the following significant warnings:
  gig.c:111:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rugarch.Rcheck/00install.out’ for details.
checkRd: (-1) sp500ret.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) spyreal.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:60:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/rust.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: ‘glmmADMB’
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘withr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
'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
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
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
checkRd: (-1) Analyze.Rd:344: Escaped LaTeX specials: \&
checkRd: (-1) Analyze.Rd:337: Escaped LaTeX specials: \&
checkRd: (-1) AnalyzeWithExitPoll.Rd:285: Escaped LaTeX specials: \&
checkRd: (-1) AnalyzeWithExitPoll.Rd:278: Escaped LaTeX specials: \&
checkRd: (-1) RxCEcolInf-package.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) RxCEcolInf-package.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) Tune.Rd:206: Escaped LaTeX specials: \&
checkRd: (-1) Tune.Rd:203: Escaped LaTeX specials: \&
checkRd: (-1) TuneWithExitPoll.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) TuneWithExitPoll.Rd:220: Escaped LaTeX specials: \&
checkRd: (-1) gendata.ep.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) gendata.ep.Rd:289: Escaped LaTeX specials: \&
checkRd: (-1) gendata.ep.Rd:286: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) butterfat.df.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) butterfat.df.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) fire.df.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) fruitfly.df.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) fruitfly.df.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) house.df.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) house.df.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) incomes.df.Rd:8: Escaped LaTeX specials: \$
checkRd: (-1) skulls.df.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) skulls.df.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) technitron.df.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) zoo.df.Rd:13: Escaped LaTeX specials: \$
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.
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
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.
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.
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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Package suggested but not available for checking: ‘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
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’
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
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.
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
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'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.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘harmony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 1 marked UTF-8 string
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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
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.
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
Note: found 464 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocStyle’ ‘cowplot’ ‘easypackages’ ‘plyr’ ‘readr’ ‘stringr’
  ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'ssvd', 'conos', 'pagoda2'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocSingular’
  All declared Imports should be used.
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
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
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 51 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Found the following 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.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘fansi’
  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 ‘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: ‘parallel’
  All declared Imports should be used.
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
'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) sobol_indices.Rd:119: Escaped LaTeX specials: \&
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: \^
Note: found 836 marked UTF-8 strings
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
Note: found 3128 marked UTF-8 strings
'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
checkRd: (-1) aaindex.Rd:525: Escaped LaTeX specials: \_
checkRd: (-1) aaindex.Rd:526: Escaped LaTeX specials: \_
checkRd: (-1) acnucopen.Rd:38: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_
checkRd: (-1) acnucopen.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) read.alignment.Rd:47: Escaped LaTeX specials: \_ \_
checkRd: (-1) read.alignment.Rd:48: Escaped LaTeX specials: \_ \_
Found the following significant warnings:
  BGenFile.cpp:12:55: warning: member ‘BGenFile::N’ is used uninitialized [-Wuninitialized]
  bcf.h:173:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bam_endian.h:6:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  khash.h:129:38: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bcfutils.c:38:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bgzf.c:107:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  tabix_index.c:19:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/00install.out’ for details.
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
'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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘sfnetworks’
Unknown package ‘sfnetworks’ in Rd xrefs
Running examples in ‘sfdep-Ex.R’ failed
The error most likely occurred in:

> ### Name: st_as_graph
> ### Title: Create an sfnetwork
> ### Aliases: st_as_graph st_as_graph.sf st_as_graph.sfc
> 
> ### ** Examples
> 
> library(magrittr)
> 
> guerry_nb %>%
+   st_as_graph(nb, wt)
Error in `check_pkg_suggests()`:
! Missing packages: `sfnetworks`
Backtrace:
    ▆
 1. ├─guerry_nb %>% st_as_graph(nb, wt)
 2. ├─sfdep::st_as_graph(., nb, wt)
 3. └─sfdep:::st_as_graph.sf(., nb, wt)
 4.   └─sfdep:::check_pkg_suggests("sfnetworks")
 5.     └─cli::cli_abort("Missing packages: {paste(\"`\", x[missing_pkgs], \"`\", sep = \"\", collapse = \", \")}")
 6.       └─rlang::abort(...)
Execution halted
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: ‘geometries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  proj_conf_test.c:5:5: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/sf.Rcheck/00install.out’ for details.
checkRd: (-1) TA.plot.Rd:32: Escaped LaTeX specials: \~
checkRd: (-1) diagDA.Rd:51: Escaped LaTeX specials: \#
checkRd: (-1) hatMat.Rd:35: Escaped LaTeX specials: \&
'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
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
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘huge’
  All declared Imports should be used.
Package suggested but not available for checking: ‘hydromad’
Package suggested but not available for checking: ‘getCRUCLdata’
'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
'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
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
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
Namespace in Imports field not imported from: ‘htmltools’
  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
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’
Found the following files/directories:
  ‘Crashpad’
'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.
'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
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’
Note: found 1231 marked UTF-8 strings
Note: found 28 marked UTF-8 strings
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
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pedtools’ ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
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.
'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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  splines.cpp:227:51: warning: default argument specified for lambda parameter [-Wc++14-extensions]
See ‘/data/gannet/ripley/R/packages/tests-devel/SimSurvNMarker.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lubridate’ ‘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
Namespaces in Imports field not imported from:
  ‘CompQuadForm’ ‘boot’ ‘mvtnorm’
  All declared Imports should be used.
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.
GNU make is a SystemRequirements.
File ‘skm/libs/skm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘png’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
Note: found 23 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) roadwear.Rd:26: 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.
Found the following significant warnings:
  /data/gannet/ripley/R/test-dev/vctrs/include/vctrs.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:69:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:72:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  slider-vctrs-private.c:12:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/vctrs/include/vctrs.c:7:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  slider-vctrs-public.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  summary-core.h:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  summary-core.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/slider.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
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.
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
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘methods’ ‘rgeos’
  All declared Imports should be used.
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.
Found the following files/directories:
  ‘my_new_social_media_plot.png’
Unknown package ‘andrews’ 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
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
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.
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
Namespaces in Imports field not imported from:
  ‘devtools’ ‘stats’ ‘tidyverse’
  All declared Imports should be used.
Found the following significant warnings:
  SoDA_init.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  crc32.c:161:23: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  digest_C.c:180:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/SoDA.Rcheck/00install.out’ for details.
File ‘SoDA/libs/SoDA.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
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
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
'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
'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.
'LazyData' is specified without a 'data' directory
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.
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
File ‘sparcl/libs/sparcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gtable’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Unknown package ‘sparsebn’ in Rd xrefs
'LazyData' is specified without a 'data' directory
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.
'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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘spatstat.core’ ‘spatstat.linnet’
  All declared Imports should be used.
'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
Package suggested but not available for checking: ‘RandomFields’
checkRd: (-1) grid2latlong.Rd:22: Escaped LaTeX specials: \$
checkRd: (-1) latlong2grid.Rd:22: Escaped LaTeX specials: \$
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
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘pheatmap’ ‘stats’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
Unknown package ‘RandomFields’ in Rd xrefs
checkRd: (-1) ants.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) ants.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) ants.Rd:36: Escaped LaTeX specials: \& \&
checkRd: (-1) ants.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) ants.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) ants.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) ants.Rd:124: Escaped LaTeX specials: \&
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  '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.core', '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.core', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package suggested but not available for checking: ‘RandomFields’
Unknown package ‘RandomFields’ in Rd xrefs
Found the following significant warnings:
  linalg.c:36:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  linalg.c:68:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  linalg.c:103:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  linalg.c:137:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  linalg.c:175:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  linalg.c:210:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  linalg.c:253:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  linalg.c:263:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  linalg.c:278:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  linalg.c:288:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sparselinalg.c:18:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sparselinalg.c:23:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sparselinalg.c:30:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sparselinalg.c:35:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/spatstat.sparse.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘spatstat.model’
Package unavailable to check Rd xrefs: ‘spatstat.model’
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  allspc.c:850:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  allspc.c:1117:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/spc.Rcheck/00install.out’ for details.
checkRd: (-1) euklid.ewma.arl.Rd:23: Escaped LaTeX specials: \&
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘spDataLarge’
Note: found 56 marked UTF-8 strings
Note: found 34 marked UTF-8 strings
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
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’
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  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:
  ‘sf’ ‘spData’
  All declared Imports should be used.
Note: found 189 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
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’
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
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
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.
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.
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: ‘ggridges’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sampling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  maqmap.h:62:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  maqmap.c:15:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/spp.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘rgeoda’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘progress’
  All declared Imports should be used.
Found the following significant warnings:
  sp.h:95:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/sp.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Note: found 199 marked UTF-8 strings
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  mathematics.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mathematics.h:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/spTDyn.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mathematics.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mathematics.h:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/spTimer.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘spatstat’ ‘spatstat.data’ ‘spatstat.linnet’ ‘spatstat.sparse’
  ‘spatstat.utils’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘RSQLite’ ‘dbplyr’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘arm’ ‘brms’ ‘lme4’ ‘plotly’ ‘shinyMatrix’
  All declared Imports should be used.
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
GNU make is a SystemRequirements.
'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
Package suggested but not available for checking: ‘scanstatistics’
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: \&
Found the following significant warnings:
  include/misc/adaptiveRadixTree.h:54:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  misc_adaptiveRadixTree.c:195:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/stan4bart.Rcheck/00install.out’ for details.
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.
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’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
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
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Note: found 52 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.
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
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 15 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.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
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
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
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
'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
Found the following significant warnings:
  dist.h:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dist.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qgram.c:87:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qgram.c:132:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qgram.c:196:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/stringdist.Rcheck/00install.out’ for details.
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
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: \&
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
checkRd: (-1) is_shebang.Rd:14: Escaped LaTeX specials: \#
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.
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: ‘extraTrees’
Unknown package ‘extraTrees’ in Rd xrefs
Package suggested but not available for checking: ‘extraTrees’
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Namespaces in Imports field not imported from:
  ‘mixtools’ ‘parallel’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) estweights.Rd:42: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gurobi’
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘readr’ ‘rlang’ ‘survival’ ‘tidyverse’ ‘utils’
  All declared Imports should be used.
Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
Namespace in Imports field not imported from: ‘ggtree’
  All declared Imports should be used.
Found the following significant warnings:
  agsurv3.c:66:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  agsurv3.c:260:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chinv3.c:58:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cox_Rcallback.c:20:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  survreg6.c:67:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  survreg7.c:76:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  survregc1.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/survival.Rcheck/00install.out’ for details.
Found the following significant warnings:
  survivalROC.c:16:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/survivalROC.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
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.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Note: found 25 marked UTF-8 strings
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
DNF: multiple local function definitions for ‘mu_x’ with different
  formal arguments
DNF: multiple local function definitions for ‘mu_y’ with different
  formal arguments
DNF: multiple local function definitions for ‘sigma_x’ with different
  formal arguments
DNF: multiple local function definitions for ‘sigma_y’ with different
  formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘mu_x’ with
  different formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘mu_y’ with
  different formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘sigma_x’
  with different formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘sigma_y’
  with different formal arguments
modelSim: multiple local function definitions for ‘mu_x’ with different
  formal arguments
modelSim: multiple local function definitions for ‘mu_y’ with different
  formal arguments
modelSim: multiple local function definitions for ‘sigma_x’ with
  different formal arguments
modelSim: multiple local function definitions for ‘sigma_y’ with
  different formal arguments
'LazyData' is specified without a 'data' directory
checkRd: (-1) diabetes.Rd:18: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
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.
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
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cplexAPI’
Packages suggested but not available for checking: 'cplexAPI', 'clpAPI'
Found the following math rendering problems:
optObj-class.Rd:240: Undefined control sequence: \boldmath in \mbox{\boldmath$Sv$\unboldmath...
robAna.Rd:53-67: Undefined control sequence: \boldmath in ...       & \mbox{\boldmath$c$\unboldmath}...
setRhsZero-methods.Rd:18: Undefined control sequence: \boldmath in \mbox{\boldmath$Sv$\unboldmath...
sysBiolAlg_fba-class.Rd:114-126: Undefined control sequence: \boldmath in ...       & \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_fba-class.Rd:132-135: Undefined control sequence: \boldmath in 
        \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_fbaEasyConstraint-class.Rd:93-105: Undefined control sequence: \boldmath in ...       & \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_fbaEasyConstraint-class.Rd:111-114: Undefined control sequence: \boldmath in 
        \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_fv-class.Rd:139-152: Undefined control sequence: \boldmath in ...       & \mbox{\boldmath$Sv$\unboldmath...
sysBiolAlg_lmoma-class.Rd:145-165: No such environment: minipage in ...       & \begin{minipage}[b]{5em}
        ...
sysBiolAlg_lmoma-class.Rd:167-169: Undefined control sequence: \boldmath in 
      \mbox{\boldmath$v$\unboldmath}...
sysBiolAlg_lmoma-class.Rd:177-205: No such environment: minipage in ...       & \begin{minipage}[b]{5em}
        ...
sysBiolAlg_moma-class.Rd:131-148: No such environment: minipage in ...       & \begin{minipage}[b]{5em}
        ...
sysBiolAlg_moma-class.Rd:155-157: Undefined control sequence: \boldmath in 
      \mbox{\boldmath$v$\unboldmath}...
sysBiolAlg_mtf-class.Rd:160-179: No such environment: minipage in ...      &  \begin{minipage}[b]{2.5em}
      ...
sysBiolAlg_mtf-class.Rd:181-184: Undefined control sequence: \boldmath in 
        \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_room-class.Rd:157-177: No such environment: minipage in ...       & \begin{minipage}[b]{5em}
        ...
Found the following significant warnings:
  sylcount_native.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sylcount_nthreads.c:9:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sylcount_nthreads.c:31:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/sylcount.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
checkRd: (-1) HINoV.SDA.rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package required but not available: ‘harmony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  SymTS.c:22:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  SymTS.c:28:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/SymTS.Rcheck/00install.out’ for details.
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
'LazyData' is specified without 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’
Note: found 551 marked UTF-8 strings
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
Note: found 81 marked UTF-8 strings
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.
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: \&
Note: found 4 marked Latin-1 strings
  Note: found 1270 marked UTF-8 strings
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 50 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  tdt.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  tdt.c:191:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/tdthap.Rcheck/00install.out’ for details.
'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
'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
Found the following significant warnings:
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_state.h:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:380:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:381:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:382:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_wtstate.h:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:585:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:586:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  /data/gannet/ripley/R/test-dev/ergm/include/ergm_stubs.c:587:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/tergm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  proj_conf_test.c:5:5: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/terra.Rcheck/00install.out’ for details.
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
Problems with news in ‘inst/NEWS.Rd’:
No news entries found.
'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'
Note: found 3 marked UTF-8 strings
Note: found 35 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
'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
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 3 marked UTF-8 strings
Note: found 4 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
'LazyData' is specified without 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: ‘ggm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Found the following significant warnings:
  thor.h:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.h:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.h:23:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.h:106:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.c:9:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.c:23:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.c:35:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.c:748:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/thor.Rcheck/00install.out’ for details.
'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
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘knitr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘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 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
'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
'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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 113 marked UTF-8 strings
Note: found 34206 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
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.
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
Found the following significant warnings:
  parse.c:189:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/timechange.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
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
Note: found 2750 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Found the following significant warnings:
  ntr.c:65:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ntr.c:91:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/TIMP.Rcheck/00install.out’ for details.
checkRd: (-1) dat-class.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) dat-class.Rd:48: Escaped LaTeX specials: \_
checkRd: (-1) dat-class.Rd:49: Escaped LaTeX specials: \_
checkRd: (-1) dat-class.Rd:50: Escaped LaTeX specials: \_
Found the following files/directories:
  ‘_paramEst.txt’
'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:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
GNU make is a SystemRequirements.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  external_metis.c:102:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/TMB.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Note: found 134043 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'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.
'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.
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
Packages suggested but not available for checking:
  'lasso2', 'corpus.JSS.papers'
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Found the following significant warnings:
  topmodel.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:23:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:26:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/topmodel.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘stringr’ ‘torch’ ‘torchvision’ ‘zip’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
'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.
Package which this enhances but not available for checking: ‘p3state.msm’
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.
Running examples in ‘TrafficBDE-Ex.R’ failed
The error most likely occurred in:

> ### Name: PreProcessingLink
> ### Title: PreProcessing second model
> ### Aliases: PreProcessingLink
> 
> ### ** Examples
> 
> SpecLink <- loadDataSpecLink("163204843","1", X163204843_1)
> x <- fillMissingValues(SpecLink)
> datetime <- "2017-01-27 14:00:00" 
> newData <- fillMissingDates (x, datetime)
Error in seq.int(0, to0 - from, by) : 'to' must be a finite number
Calls: fillMissingDates -> seq.POSIXt
Execution halted
'LazyData' is specified without a 'data' directory
Note: found 2 marked Latin-1 strings
  Note: found 701 marked UTF-8 strings
Package suggested but not available for checking: ‘taxidata’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/TraMineR.Rcheck/00install.out’ for details.
Note: found 827 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  aha.c:482:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  shortsimplex.c:170:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  revsimplex.c:150:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  transport_init.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  transport_init.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  transport_init.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  transport_init.c:35:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/transport.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
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’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug fixes
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
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.
'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.
checkRd: (-1) ltriangle.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) triangle.Rd:70: Escaped LaTeX specials: \&
'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:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'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
checkRd: (-1) sepIdGaps.Rd:18: Escaped LaTeX specials: \_ \_
'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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
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
Namespaces in Imports field not imported from:
  ‘DT’ ‘ez’ ‘forcats’ ‘ggplot2’
  All declared Imports should be used.
Note: found 118 marked UTF-8 strings
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.
Namespace in Imports field not imported from: ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  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’ ‘crosstalk’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
checkRd: (-1) lindner.Rd:44: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 34 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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.
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
'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
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
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.
Note: found 3347 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lavaan’ ‘lifecycle’ ‘patchwork’ ‘ragg’ ‘scales’ ‘simstandard’
  All declared Imports should be used.
Note: found 7872 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: ‘xml2’
  All declared Imports should be used.
Note: found 488 marked UTF-8 strings
Found the following significant warnings:
  ursa.c:3714:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/ursa.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘USAboundariesData’
Package suggested but not available for checking: ‘USA.state.boundaries.data’
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) Glass.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:22: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:28: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Found the following HTML validation problems:
RequestHandlerCrul.html:50:6 (RequestHandlerCrul.Rd:78): Warning: missing </span> before <p>
RequestHandlerCrul.html:50:92 (RequestHandlerCrul.Rd:78): Warning: inserting implicit <span>
RequestHandlerCrul.html:53:6 (RequestHandlerCrul.Rd:79): Warning: missing </span> before <p>
RequestHandlerCrul.html:53:96 (RequestHandlerCrul.Rd:79): Warning: inserting implicit <span>
RequestHandlerHttr.html:53:6 (RequestHandlerHttr.Rd:55): Warning: missing </span> before <p>
RequestHandlerHttr.html:53:92 (RequestHandlerHttr.Rd:55): Warning: inserting implicit <span>
lightswitch.html:113:79 (lightswitch.Rd:67): Warning: inserting implicit <p>
lightswitch.html:150:58 (lightswitch.Rd:102): Warning: inserting implicit <p>
lightswitch.html:181:33 (lightswitch.Rd:131): Warning: inserting implicit <p>
lightswitch.html:202:42 (lightswitch.Rd:150): Warning: inserting implicit <p>
request-matching.html:83:57 (request-matching.Rd:49): Warning: inserting implicit <p>
'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.
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.
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: ‘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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) huse.Rd:61: Escaped LaTeX specials: \&
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
Found the following significant warnings:
  ./vic/vic_run/include/vic_run.h:230:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ./vic/vic_run/include/vic_run.h:324:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vic/vic_run/src/CalcBlowingSnow.c:282:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vic/vic_run/src/CalcBlowingSnow.c:376:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ./vic/drivers/shared_all/include/vic_driver_shared_all.h:615:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ./vic/drivers/shared_all/include/vic_driver_shared_all.h:617:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ./vic/drivers/shared_all/include/vic_driver_shared_all.h:718:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vic/drivers/shared_all/src/history_metadata.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vic/drivers/shared_all/src/timing.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vic/drivers/shared_all/src/timing.c:46:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/VIC5.Rcheck/00install.out’ for details.
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
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.
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.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    NEWS UPDATES:
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘colorspace’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
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
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.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘dismo’ ‘dplyr’ ‘ecospat’ ‘jsonlite’
  ‘leaflet.extras’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’ ‘sp’
  ‘spThin’ ‘spocc’ ‘zip’
  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’ ‘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: ‘stringi’
  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.
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:
  ‘rgdal’ ‘vctrs’
  All declared Imports should be used.
Found the following significant warnings:
  functions.c:75:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  functions.c:101:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  functions.c:189:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  functions.c:220:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  functions.c:221:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  functions.c:295:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrow.c:34:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrow.c:54:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrow.c:134:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrow.c:157:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrow.c:219:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/waveband.Rcheck/00install.out’ for details.
'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’
'LazyData' is specified without a 'data' directory
Note: found 3133 marked UTF-8 strings
Note: found 4413 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1668 marked UTF-8 strings
Found the following significant warnings:
  init.c:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/wdnet.Rcheck/00install.out’ for details.
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
Found the following significant warnings:
  cleancall.h:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cleancall.c:38:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rweb.c:153:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rweb.c:214:22: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/webfakes.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
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
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
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.
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
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  corFunctions.c:59:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  networkFunctions.c:182:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/WGCNA.Rcheck/00install.out’ for details.
checkRd: (-1) rgcolors.func.Rd:27: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
'LazyData' is specified without a 'data' directory
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.
Found the following significant warnings:
  trace_back_unwind.c:15:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/winch.Rcheck/00install.out’ for details.
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.
Note: found 3984 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.
'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.
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 933 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Note: found 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.
Found the following significant warnings:
  wrassp.h:197:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  types.c:10:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  types.c:38:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  types.c:65:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrassp_init.c:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrassp_init.c:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrassp_init.c:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/wrassp.Rcheck/00install.out’ for details.
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
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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’
Found the following significant warnings:
  init.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/xgboost.Rcheck/00install.out’ for details.
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.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  DocParse.c:58:2: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  NodeGC.c:424:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/XML.Rcheck/00install.out’ for details.
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: \_
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
'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
'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.
'LazyData' is specified without 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: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
Found the following significant warnings:
  miniz.h:743:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  miniz.h:796:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  miniz.c:2149:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  miniz.c:2884:21: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  tools/../miniz.h:743:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  tools/../miniz.h:796:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-devel/zip.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘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’
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
Running examples in 'activAnalyzer-Ex.R' failed
The error most likely occurred in:

> ### Name: average_results
> ### Title: Average results over valid days
> ### Aliases: average_results
> 
> ### ** Examples
> 
> file <- system.file("extdata", "acc.agd", package = "activAnalyzer")
> mydata <- prepare_dataset(data = file)
> mydata_with_wear_marks <- mark_wear_time(
+     dataset = mydata, 
+     TS = "TimeStamp", 
+     to_epoch = 60,
+     cts  = "vm",
+     frame = 90, 
+     allowanceFrame = 2, 
+     streamFrame = 30
+     )
Warning: Expected 2 pieces. Missing pieces filled with `NA` in 5 rows [1081, 2521, 3961, 5401, 6841].
frame is 90
streamFrame is 30
allowanceFrame is 2
Error in as.POSIXlt.character(x, tz, ...) : 
  character string is not in a standard unambiguous format
Calls: mark_wear_time ... as.POSIXct.default -> as.POSIXct -> as.POSIXlt -> as.POSIXlt.character
Execution halted
Error(s) in re-building vignettes:
--- re-building 'activAnalyzer.Rmd' using rmarkdown
Quitting from lines 53-67 (activAnalyzer.Rmd) 
Error: processing vignette 'activAnalyzer.Rmd' failed with diagnostics:
character string is not in a standard unambiguous format
--- failed re-building 'activAnalyzer.Rmd'

SUMMARY: processing the following file failed:
  'activAnalyzer.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
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.9Mb
    pictures   2.1Mb
checkRd: (-1) chickenk.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) multispati.Rd:54: Escaped LaTeX specials: \$
checkRd: (-1) randboot.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) kernelUD.Rd:210: Escaped LaTeX specials: \&
checkRd: (-1) orthobasis.Rd:106: Escaped LaTeX specials: \&
checkRd: (-1) orthobasis.Rd:110: Escaped LaTeX specials: \&
checkRd: (-1) treePart.Rd:33: Escaped LaTeX specials: \$
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(adobeanalyticsr)
  > 
  > test_check("adobeanalyticsr")
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 94 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-date_utilities.R:22:3): make_timeframe works as expected ──────
  `date_result` not equal to `datetime_result`.
  1/1 mismatches
  x[1]: "2021-01-01T00:00:00/2021-01-10T23:59:59"
  y[1]: "2021-01-01/2021-01-10 23:59:59"
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 94 ]
  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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'
Problems with news in 'NEWS.md':
No news entries found.
'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: \&
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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: \&
Running examples in 'agroclim-Ex.R' failed
The error most likely occurred in:

> ### Name: ehe
> ### Title: Extreme Heat Exposure (EHE)
> ### Aliases: ehe
> 
> ### ** Examples
> 
> 
>             ehe(mx = daily_tmax,
+             dates = seq.Date(as.Date('1981-01-01'),
+                     as.Date('2010-12-31'), by ='day'),
+             op = 'first')
Warning in as.character.POSIXt(as.POSIXlt(x), ...) :
  as.character(td, ..) no longer obeys a 'format' argument; use format(td, ..) ?
Warning in as.character.POSIXt(as.POSIXlt(x), ...) :
  as.character(td, ..) no longer obeys a 'format' argument; use format(td, ..) ?
Error in wini:wend : argument of length 0
Calls: ehe -> ff -> rle
Execution halted
checkRd: (-1) adapt.Rd:41: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
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checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'metaboliteIDmapping'
checkRd: (-1) varrob.Rd:44: Escaped LaTeX specials: \^
'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
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Problems with news in 'NEWS.md':
No news entries found.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) 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: \_ \_
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    test_v8    2.0Mb
    testdata   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'aoristic-Ex.R' failed
The error most likely occurred in:

> ### Name: aoristic.df
> ### Title: Calculate aoristic weights
> ### Aliases: aoristic.df
> 
> ### ** Examples
> 
> df <- aoristic.df(dcburglaries, 'X', 'Y', 'StartDateTime', 'EndDateTime')
Warning:  32 failed to parse.
Warning:  6 failed to parse.
Error in if (time.span >= 10080) { : 
  missing value where TRUE/FALSE needed
Calls: aoristic.df
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
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
checkRd: (-1) AQuadtree-package.Rd:11: Escaped LaTeX specials: \$
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is 40.2Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs  35.0Mb
Package which this enhances but not available for checking: 'ARTP'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.0Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    bin   11.8Mb
    misc   2.1Mb
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'asteRiskData'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.1Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R Under development (unstable) (2022-10-07 r83044 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   1.2Mb
'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   4.9Mb
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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
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
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Earlier versions
checkRd: (-1) bas.lm.Rd:425: Escaped LaTeX specials: \&
Packages which this enhances but not available for checking:
  'doMC', 'rPython'
'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   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
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checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
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checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.7Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
GNU make is a SystemRequirements.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
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.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    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     1.8Mb
    doc   3.8Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GNU make is a SystemRequirements.
Found the following significant warnings:
  arms.cpp:917:30: warning: format '%x' expects argument of type 'unsigned int', but argument 4 has type 'POINT*' {aka 'point*'} [-Wformat=]
  arms.cpp:927:26: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'POINT*' {aka 'point*'} [-Wformat=]
  arms.cpp:927:38: warning: format '%x' expects argument of type 'unsigned int', but argument 4 has type 'point*' [-Wformat=]
  arms.cpp:927:51: warning: format '%x' expects argument of type 'unsigned int', but argument 5 has type 'point*' [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.3/bayesSurv.Rcheck/00install.out' for details.
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
checkRd: (-1) create_ThetaMatrix.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) create_ThetaMatrix.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
checkRd: (-1) tlsce.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:93: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.5Mb
'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
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.9Mb
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
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) scrHpd.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    help   1.1Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
installed size is 146.7Mb
  sub-directories of 1Mb or more:
    include  145.7Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'INLA'
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bigrquery)
  > 
  > test_check("bigrquery")
  [ FAIL 1 | WARN 1 | SKIP 65 | PASS 129 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Authentication not available (8)
  • No BigQuery access credentials available (55)
  • On CRAN (1)
  • bq_authable() is not TRUE (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-bq-parse.R:37:3): can parse date/times ──────────────────────────
  Error in `round(x$sec[n0], digits)`: non-numeric argument to mathematical function
  Backtrace:
      ▆
   1. ├─testthat::expect_identical(...) at test-bq-parse.R:37:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─bigrquery:::bq_parse_single(...)
   5. │ └─jsonlite::toJSON(value, auto_unbox = TRUE)
   6. │   └─base::force(x)
   7. ├─base::as.character(dt, "%Y-%m-%dT%H:%M:%S")
   8. └─base::as.character.POSIXt(dt, "%Y-%m-%dT%H:%M:%S")
  
  [ FAIL 1 | WARN 1 | SKIP 65 | PASS 129 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BinaryEPPM.Rd:159: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
checkRd: (-1) core.find.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) core.find.Rd:87: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:89: Escaped LaTeX specials: \^
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checkRd: (-1) core.find.Rd:97: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'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
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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) NOS.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) specieslevel.Rd:156: Escaped LaTeX specials: \&
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
checkRd: (-1) FighterAircraft.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BivRec)
  > 
  > test_check("BivRec")
  [1] "Fitting model with covariates: a1, a2"
  [1] "Estimating standard errors"
         Estimates       SE       z Pr(>|z|)   
  xij a1   0.16852  0.19315  0.8725  0.19147   
  xij a2   0.95427  0.34793  2.7427  0.00305 **
  yij a1  -0.18927  0.25172 -0.7519  0.22605   
  yij a2  -0.40401  0.56355 -0.7169  0.23672   
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  [1] "Estimating joint CDF and marginal survival"
  [1] "Estimating joint CDF and marginal survival"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 15 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test.all_one_episode.R:37:3): np check 2 ─────────────────────────────
  Error in `if (max(x.grid$rounded - x.grid$rounded[nrow(x.grid)]) < 0.1) {
      print("Cannot estimate conditional cdf, given.interval is too narrow")
      stop()
  }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─BivRec::bivrecNP(...) at test.all_one_episode.R:37:2
   2.   └─BivRec:::nonparam_conditional(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 15 ]
  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
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  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.2Mb
'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:
    extdata   7.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
GNU make is a SystemRequirements.
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
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'INLA'
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   4.2Mb
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
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
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.
installed size is 38.8Mb
  sub-directories of 1Mb or more:
    include   9.0Mb
    lib      29.3Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    modules 0.x
'LazyData' is specified without a 'data' directory
checkRd: (-1) bpca.Rd:85: Escaped LaTeX specials: \&
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) R2txtJG.Rd:90: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Encountered the following conversion/validation errors:
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: 'glmmADMB'
checkRd: (-1) brr-package.Rd:33: Escaped LaTeX specials: \&
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/BRugs.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Brundle.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    help   1.3Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    fonts   3.1Mb
    lib     4.5Mb
GNU make is a SystemRequirements.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
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    doc        2.1Mb
    pictures   4.1Mb
checkRd: (-1) caic-class.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) caic-class.Rd:15: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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    doc   5.7Mb
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot-methods.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) plot-methods.Rd:96: Escaped LaTeX specials: \_
installed size is  6.5Mb
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    doc   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'GAMBoost'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.9Mb
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    doc  37.7Mb
checkRd: (-1) belt.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) bipf.Rd:78: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
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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 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    News about the ccdf R package
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    duckdb   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.4Mb
    libs   1.7Mb
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'
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major refactoring of the code
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    include  38.4Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hyptis.Rd:31: Escaped LaTeX specials: \&
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Package suggested but not available for checking: 'countreg'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
Problems with news in 'NEWS.md':
No news entries found.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'entab'
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
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Package suggested but not available for checking: 'userfriendlyscience'
'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:
    doc   7.2Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warnings in file 'R/currency.R':
  unable to translate '<U+20AC>' to native encoding
  unable to translate '<U+00A5>' to native encoding
  unable to translate '<U+00A3>' to native encoding
'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:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
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    clhs_0.1-0
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checkRd: (-1) diagwl.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) diagwl.Rd:5: Escaped LaTeX specials: \&
installed size is  5.9Mb
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    doc   4.2Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    clinfun (development version)
checkRd: (-1) coxphCPE.Rd:2: Escaped LaTeX specials: \&
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installed size is  6.7Mb
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checkRd: (-1) dataADaMCDISCP01.Rd:48: Escaped LaTeX specials: \&
Running 'testthat.R' [21s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clinUtils)
  > 
  > test_check("clinUtils")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 300 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_loadDataADaMSDTM.R:172:2): An error is generated if the specified object to convert to date is not a date ──
  `convertToDateTime(c(1, 2))` did not throw an error.
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 300 ]
  Error: Test failures
  Execution halted
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
installed size is  6.1Mb
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Problems with news in 'NEWS.md':
No news entries found.
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Problems with news in 'NEWS.md':
No news entries found.
Running examples in 'cmsafops-Ex.R' failed
The error most likely occurred in:

> ### Name: hourmean
> ### Title: Determine hourly means
> ### Aliases: hourmean
> 
> ### ** Examples
> 
> ## Create an example NetCDF file with a similar structure as used by CM
> ## SAF. The file is created with the ncdf4 package.  Alternatively
> ## example data can be freely downloaded here: <https://wui.cmsaf.eu/>
> 
> library(ncdf4)
> 
> ## create some (non-realistic) example data
> 
> lon <- seq(5, 15, 0.5)
> lat <- seq(45, 55, 0.5)
> 
> time <- seq(ISOdate(2000, 1, 1), ISOdate(2000, 1, 2), "mins")
> origin <- as.Date("1983-01-01 00:00:00")
> time <- as.numeric(difftime(time, origin, units = "min"))
> data <- array(250:350, dim = c(21, 21, 1441))
> ## create example NetCDF
> 
> x <- ncdim_def(name = "lon", units = "degrees_east", vals = lon)
> y <- ncdim_def(name = "lat", units = "degrees_north", vals = lat)
> t <- ncdim_def(name = "time", units = "minutes since 1983-01-01 00:00:00",
+               vals = time, unlim = TRUE)
> var1 <- ncvar_def("SIS", "W m-2", list(x, y, t), -1, prec = "short")
> vars <- list(var1)
> ncnew <- nc_create(file.path(tempdir(),"CMSAF_example_file.nc"), vars)
> ncvar_put(ncnew, var1, data)
> ncatt_put(ncnew, "lon", "standard_name", "longitude", prec = "text")
> ncatt_put(ncnew, "lat", "standard_name", "latitude", prec = "text")
> nc_close(ncnew)
> 
> ## Determine the hourly means of the example CM SAF NetCDF file
> ## and write the output to a new file.
> hourmean(var = "SIS", infile = file.path(tempdir(),"CMSAF_example_file.nc"), 
+  outfile = file.path(tempdir(),"CMSAF_example_file_hourmean.nc"))
Error in hourx_wrapper(1, var, infile, outfile, nc34, overwrite, verbose,  : 
  The time steps must be available at least every hour. Please try daysum for diurnal aggregation. 
Calls: hourmean -> hourx_wrapper
Execution halted
Running 'spelling.R' [0s]
  Comparing 'spelling.Rout' to 'spelling.Rout.save' ...6c6
< NULL
---
> All Done!
  Running 'testthat.R' [148s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(cmsafops)
  > 
  > test_check("cmsafops")
  149016292920292920149016149016149016149028149016[ FAIL 3 | WARN 0 | SKIP 0 | PASS 9082 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_hourmean.R:8:1): (code run outside of `test_that()`) ────────────
  Error in `hourx_wrapper(1, var, infile, outfile, nc34, overwrite, verbose, 
      nc = nc)`: The time steps must be available at least every hour. Please try daysum for diurnal aggregation. 
  Backtrace:
      ▆
   1. └─cmsafops::hourmean(...) at test_hourmean.R:8:0
   2.   └─cmsafops:::hourx_wrapper(...)
  ── Error (test_hoursum.R:8:1): (code run outside of `test_that()`) ─────────────
  Error in `hourx_wrapper(2, var, infile, outfile, nc34, overwrite, verbose, 
      nc = nc)`: The time steps must be available at least every hour. Please try daysum for diurnal aggregation. 
  Backtrace:
      ▆
   1. └─cmsafops::hoursum(...) at test_hoursum.R:8:0
   2.   └─cmsafops:::hourx_wrapper(...)
  ── Error (test_mondaymean.R:8:1): (code run outside of `test_that()`) ──────────
  Error in `mondaymean("SIS", file.path(data_dir, "ex_mondaymean.nc"), file_out)`: The time steps must be available every 15min (at least 12 days per month), 30min (at least 6 days per month) or 1h (at least 3 days per month). One or more time steps do not meet the requirements. The result of these time steps is NA. 
  Backtrace:
      ▆
   1. └─cmsafops::mondaymean(...) at test_mondaymean.R:8:0
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 9082 ]
  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
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
checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
Package which this enhances but not available for checking: 'rkward'
Package suggested but not available for checking: 'userfriendlyscience'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   2.0Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
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
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(commonsMath)
  > 
  > test_check("commonsMath")
  
  Searching the system for Java.
    Failure with rscala home directory.
    Failure with JAVACMD environment variable.
    Failure with JAVA_HOME environment variable.
    Success with PATH environment variable.
    ... querying Java specifics.
  
  Searching the system for Scala.
    Failure with rscala home directory.
    Failure with SCALACMD environment variable.
    Failure with SCALA_HOME environment variable.
    Failure with PATH environment variable.
    Success with rscala package directory.
    ... querying Scala specifics.
  
  Searching the system for SBT.
    Failure with rscala home directory.
    Failure with SBTCMD environment variable.
    Failure with SBT_HOME environment variable.
    Failure with PATH environment variable.
    Failure with rscala package directory.
    Failure with rscala temporary directory.
  
  
  Starting instance. ********************************
  Error in gsub("^FreePhysicalMemory=", "", outTemp) : 
    input string 3 is invalid
  Calls: test_check ... FUN -> eval -> eval -> scala -> getHeapMaximum -> gsub
  In addition: Warning messages:
  1: In system2("wmic", c("/locale:ms_409", "OS", "get", "FreePhysicalMemory",  :
    running command '"wmic" /locale:ms_409 OS get FreePhysicalMemory /VALUE' had status 4112
  2: In gsub("^FreePhysicalMemory=", "", outTemp) :
    unable to translate 'Beschreibung = Ung<81>ltige Klasse
  ' to a wide string
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'commonsMath.Rmd' using rmarkdown
Quitting from lines 33-38 (commonsMath.Rmd) 
Error: processing vignette 'commonsMath.Rmd' failed with diagnostics:
input string 3 is invalid
--- failed re-building 'commonsMath.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'CAM'
checkRd: (-1) compareGroups-package.Rd:52: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
checkRd: (-1) HouseholdExp.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) HouseholdExp.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) mix2compositions.Rd:28: Escaped LaTeX specials: \$
checkRd: (-1) mixRead.Rd:30: Escaped LaTeX specials: \$ \$
checkRd: (-1) mixRead.Rd:31: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Deprecation
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
checkRd: (-1) plotMCC.Rd:19: Escaped LaTeX specials: \_
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
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
'LazyData' is specified without 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
Package suggested but not available for checking: 'cec2005benchmark'
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) poss_local.Rd:21: Escaped LaTeX specials: \~
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checkRd: (-1) BrownLOBPassives.Rd:14: Escaped LaTeX specials: \&
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checkRd: (-1) BrownStats.Rd:14: Escaped LaTeX specials: \&
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checkRd: (-1) KrennPPV.Rd:74: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  stemmer.c:171:26: warning: pointer targets in passing argument 1 of 'strlen' differ in signedness [-Wpointer-sign]
See 'd:/Rcompile/CRANpkg/local/4.3/corpus.Rcheck/00install.out' for details.
checkRd: (-1) sgt.Rd:16: Escaped LaTeX specials: \&
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checkRd: (-1) egde.Rd:26: Escaped LaTeX specials: \&
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installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Non-visible changes:
'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   5.1Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'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:
    doc   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Encountered the following conversion/validation errors:
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Encountered the following conversion/validation errors:
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major features
    Minor features
checkRd: (-1) handmovement.Rd:9: Escaped LaTeX specials: \_ \_
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Aliases: xtal_mat02
> 
> ### ** Examples
> 
> # Fractional coordinates
> Xf = c(0.1,0.4,0.8)
> 
> # Orthorombic unit cell
> M = xtal_mat02(10,40,20,90,90,90)
> 
> # Cartesian coordinates
> Xc = M%*%Xf
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  15 0.52 15.66 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
    data   7.5Mb
'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
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.6Mb
    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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.7Mb
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [151s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(cvms)
  > 
  > test_check("cvms")
  [ FAIL 1 | WARN 0 | SKIP 70 | PASS 3622 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Fails in check - IMPROVE THESE TESTS (1)
  • On CRAN (58)
  • Skipping check for CRAN release due to r_hub failure (1)
  • Skipping parallel tests (3)
  • empty test (1)
  • keras and tensorflow take too long and have too many dependencies (1)
  • mac and ubuntu give different warnings (4)
  • tidymodels have too many dependencies (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_cross_validate.R:3481:5): varying number of folds in repeated cv with cross_validate() ──
  CV$Coefficients not equal to list(...).
  Component 1: Attributes: < Names: 12 string mismatches >
  Component 1: Attributes: < Length mismatch: comparison on first 36 components >
  Component 1: Attributes: < Component 26: Modes: character, logical >
  Component 1: Attributes: < Component 26: Lengths: 2, 1 >
  Component 1: Attributes: < Component 26: names for target but not for current >
  Component 1: Attributes: < Component 26: target is character, current is logical >
  Component 1: Attributes: < Component 27: Modes: logical, numeric >
  Component 1: Attributes: < Component 27: target is logical, current is numeric >
  Component 1: Attributes: < Component 28: Modes: numeric, logical >
  ...
  
  [ FAIL 1 | WARN 0 | SKIP 70 | PASS 3622 ]
  Error: Test failures
  Execution halted
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'robustbase'
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    help   1.0Mb
    libs   1.2Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    CVXR pre-0.94-4
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dspg.Rd:29: Escaped LaTeX specials: \^ \^
checkRd: (-1) dspgd2015.Rd:31: Escaped LaTeX specials: \^ \^
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    deps  10.5Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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:
> ### * update.dev.pkg
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: update.dev.pkg
> ### Title: Perform update of development version of a package
> ### Aliases: update update.dev.pkg
> ### Keywords: data
> 
> ### ** Examples
> 
>   # data.table::update.dev.pkg()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  7.75 0.19 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 ?) ========
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.0Mb
'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
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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:11912 (sockconn)
Execution halted
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'doMC'
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'
'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
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lifetable.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Running examples in 'dendRoAnalyst-Ex.R' failed
The error most likely occurred in:

> ### Name: daily.data
> ### Title: Calculation of daily statistics for dendrometer data
> ### Aliases: daily.data
> 
> ### ** Examples
> 
> library(dendRoAnalyst)
> data(nepa17)
> daily_stats<-daily.data(df=nepa17, TreeNum=1)
Error in daily.data(df = nepa17, TreeNum = 1) : 
  Date not in the right format
Execution halted
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'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'
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'Rdonlp2'
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
checkRd: (-1) geom_axis.Rd:10: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: 'doMC'
checkRd: (-1) phihat.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) anova.dglm.Rd:41: Escaped LaTeX specials: \&
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
'LazyData' is specified without 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
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANWIN2.fb05.statistik.uni-dortmund.de:11977 (sockconn)
	<-CRANWIN2.fb05.statistik.uni-dortmund.de:11977 (sockconn)
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
Running examples in 'digiRhythm-Ex.R' failed
The error most likely occurred in:

> ### Name: resample_dgm
> ### Title: Change the sampling of a digiRhythm friendly dataset
> ### Aliases: resample_dgm
> 
> ### ** Examples
> 
> data("df516b_2", package = "digiRhythm")
> df <- df516b_2
> df <- remove_activity_outliers(df)
> new_sampling <- 30
> new_dgm <- resample_dgm(df, new_sampling)
Error in if ((new_sampling%%original_sampling) != 0) { : 
  missing value where TRUE/FALSE needed
Calls: resample_dgm
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Actgram_diurnality_avg_activity.Rmd' using rmarkdown
Quitting from lines 30-36 (Actgram_diurnality_avg_activity.Rmd) 
Error: processing vignette 'Actgram_diurnality_avg_activity.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building 'Actgram_diurnality_avg_activity.Rmd'

--- re-building 'DFC_and_HP_and_changing_plots.Rmd' using rmarkdown
Quitting from lines 20-26 (DFC_and_HP_and_changing_plots.Rmd) 
Error: processing vignette 'DFC_and_HP_and_changing_plots.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building 'DFC_and_HP_and_changing_plots.Rmd'

--- re-building 'Loading_and_preprocessing_data_in_DigiRhythm.Rmd' using rmarkdown
trying URL 'https://raw.githubusercontent.com/nasserdr/digiRhythm_sample_datasets/main/516b_2.csv'
Content type 'text/plain; charset=utf-8' length 2655404 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

Quitting from lines 118-120 (Loading_and_preprocessing_data_in_DigiRhythm.Rmd) 
Error: processing vignette 'Loading_and_preprocessing_data_in_DigiRhythm.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building 'Loading_and_preprocessing_data_in_DigiRhythm.Rmd'

SUMMARY: processing the following files failed:
  'Actgram_diurnality_avg_activity.Rmd'
  'DFC_and_HP_and_changing_plots.Rmd'
  'Loading_and_preprocessing_data_in_DigiRhythm.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dint)
  > 
  > test_check("dint")
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 1258 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (1)
  • not yet (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_date_xx.R:39:3): date_xx coercion to POSIXt works ─────────────
  as.POSIXlt(make_date_xx(2012)) not identical to as.POSIXlt(as.Date("2012-01-01")).
  Attributes: < Component "tzone": 1 string mismatch >
  ── Failure (test_date_xx.R:40:3): date_xx coercion to POSIXt works ─────────────
  as.POSIXct(make_date_xx(2012)) not identical to as.POSIXct(as.Date("2012-01-01")).
  Attributes: < Component "tzone": 1 string mismatch >
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 1258 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'INLA'
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
GNU make is a SystemRequirements.
checkRd: (-1) sammy.Rd:51: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BOLTSSIRR'
Packages suggested but not available for checking: 'sendplot', 'HWxtest'
checkRd: (-1) fastDivPart.Rd:13: Escaped LaTeX specials: \_
checkRd: (-1) inCalc.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) inCalc.Rd:13: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
Found the following significant warnings:
  arms-R.c:811:30: warning: format '%x' expects argument of type 'unsigned int', but argument 4 has type 'POINT *' {aka 'struct point *'} [-Wformat=]
  arms-R.c:821:26: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'POINT *' {aka 'struct point *'} [-Wformat=]
  arms-R.c:821:38: warning: format '%x' expects argument of type 'unsigned int', but argument 4 has type 'struct point *' [-Wformat=]
  arms-R.c:821:51: warning: format '%x' expects argument of type 'unsigned int', but argument 5 has type 'struct point *' [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.3/dlm.Rcheck/00install.out' for details.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.1Mb
'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
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   1.6Mb
GNU make is a SystemRequirements.
checkRd: (-1) block.catlg.Rd:61: Escaped LaTeX specials: \^ \^
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    data      2.0Mb
    extdata   2.3Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New features
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'OpenMPController'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      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) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
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checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
'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
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.4Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running examples in 'dtwSat-Ex.R' failed
The error most likely occurred in:

> ### Name: plotCostMatrix
> ### Title: Plotting paths
> ### Aliases: plotCostMatrix
> 
> ### ** Examples
> 
> log_fun = logisticWeight(-0.1, 100)
> ts = twdtwTimeSeries(MOD13Q1.ts.list)
> patt = twdtwTimeSeries(MOD13Q1.patterns.list)
> mat1 = twdtwApply(x=ts, y=patt, weight.fun=log_fun, keep=TRUE)
> 
> plotCostMatrix(mat1, matrix.name="costMatrix")
Error in data.frame(y.breaks, y.labels = names(y.labels)) : 
  arguments imply differing number of rows: 5, 6
Calls: plotCostMatrix -> do.call -> lapply -> FUN -> data.frame
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
'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
'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:
    data   4.2Mb
    doc    1.7Mb
    libs   2.8Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dynaTree.Rd:265: Escaped LaTeX specials: \&
checkRd: (-1) dynaTree.Rd:270: Escaped LaTeX specials: \&
checkRd: (-1) relevance.dynaTree.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) sens.dynaTree.Rd:140: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
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checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  whv.c:62:18: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  whv.c:62:18: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.3/eaf.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    bin       3.5Mb
    extdata   1.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    20181118
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    breaking changes
    major changes
    minor changes
    Internal
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'eggCountsExtra'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running examples in 'EHR-Ex.R' failed
The error most likely occurred in:

> ### Name: run_Build_PK_Oral
> ### Title: Build-PK-Oral Module
> ### Aliases: run_Build_PK_Oral
> 
> ### ** Examples
> 
> ## Data Generating Function
> mkdat <- function() {
+   npat <- 3
+   visits <- floor(runif(npat, min=2, max=6))
+   id <- rep(1:npat, visits)
+   dt_samp <- as.Date(sort(sample(700, sum(visits))), origin = '2019-01-01')
+   tm_samp <- as.POSIXct(paste(dt_samp, '10:00:00'), tz = 'UTC')
+   dt <- tm_samp + rnorm(sum(visits), 0, 1*60*60)
+   dose_morn <- sample(c(2.5,5,7.5,10), sum(visits), replace = TRUE)
+   conc <- round(rnorm(sum(visits), 1.5*dose_morn, 1),1)
+   ld <- dt - sample(10:16, sum(visits), replace = TRUE) * 3600
+   ld[rnorm(sum(visits)) < .3] <- NA
+   age <- rep(sample(40:75, npat), visits)
+   gender <- rep(sample(0:1, npat, replace=TRUE), visits)
+   weight <- rep(round(rnorm(npat, 180, 20)),visits)
+   hgb <- rep(rnorm(npat, 10, 2), visits)
+   data.frame(id, dt, dose_morn, conc, ld, age, gender, weight, hgb)
+ }
> 
> # Make raw data
> set.seed(30)
> dat <- mkdat()
> 
> #Process data without last-dose times
> run_Build_PK_Oral(x = dat,
+                   idCol = "id",
+                   dtCol = "dt",
+                   doseCol = "dose_morn",
+                   concCol = "conc",
+                   ldCol = NULL,
+                   first_interval_hours = 336,
+                   imputeClosest = NULL)
Error in round(x$sec[n0], digits) : 
  non-numeric argument to mathematical function
Calls: run_Build_PK_Oral -> as.character -> as.character.POSIXt
Execution halted
Error(s) in re-building vignettes:
--- re-building 'ehr_vignette_01_mxr.Rmd' using rmarkdown
--- finished re-building 'ehr_vignette_01_mxr.Rmd'

--- re-building 'ehr_vignette_02_str.Rmd' using rmarkdown
--- finished re-building 'ehr_vignette_02_str.Rmd'

--- re-building 'ehr_vignette_03_DoseBuilding.Rmd' using rmarkdown
--- finished re-building 'ehr_vignette_03_DoseBuilding.Rmd'

--- re-building 'ehr_vignette_04_Build_PK_Oral.Rmd' using rmarkdown
Quitting from lines 85-95 (ehr_vignette_04_Build_PK_Oral.Rmd) 
Error: processing vignette 'ehr_vignette_04_Build_PK_Oral.Rmd' failed with diagnostics:
non-numeric argument to mathematical function
--- failed re-building 'ehr_vignette_04_Build_PK_Oral.Rmd'

SUMMARY: processing the following file failed:
  'ehr_vignette_04_Build_PK_Oral.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
'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) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
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checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
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checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
checkRd: (-1) freudenstein_roth_func.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) check_several.Rd:34: Escaped LaTeX specials: \#
checkRd: (-1) check_several.Rd:35: Escaped LaTeX specials: \#
'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: \&
checkRd: (-1) cdfCompareCensored.Rd:299: Escaped LaTeX specials: \&
checkRd: (-1) detectionLimitCalibrate.Rd:149: Escaped LaTeX specials: \&
checkRd: (-1) ecdfPlotCensored.Rd:169: Escaped LaTeX specials: \&
checkRd: (-1) egammaAltCensored.Rd:344: Escaped LaTeX specials: \&
checkRd: (-1) egammaCensored.Rd:340: Escaped LaTeX specials: \&
checkRd: (-1) elnormAltCensored.Rd:694: Escaped LaTeX specials: \&
checkRd: (-1) elnormCensored.Rd:270: Escaped LaTeX specials: \&
checkRd: (-1) enormCensored.Rd:852: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:343: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:358: Escaped LaTeX specials: \&
checkRd: (-1) epoisCensored.Rd:354: Escaped LaTeX specials: \&
checkRd: (-1) ppointsCensored.Rd:406: Escaped LaTeX specials: \&
checkRd: (-1) predIntGammaSimultaneous.Rd:170: Escaped LaTeX specials: \&
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checkRd: (-1) predIntNormSimultaneous.Rd:204: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneous.Rd:205: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:277: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:278: Escaped LaTeX specials: \&
checkRd: (-1) qqPlotCensored.Rd:261: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTest.Rd:276: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:324: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:331: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  report.c:1466:31: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 1 and 8 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.3/epanet2toolkit.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'epidict'
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.0Mb
'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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    java   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Encountered the following conversion/validation errors:
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
missing value where TRUE/FALSE needed
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 13.6Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
'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
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ExactData'
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
checkRd: (-1) exams2blackboard.Rd:152: Escaped LaTeX specials: \&
checkRd: (-1) exams2qti12.Rd:186: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  RCOMObject.cpp:125:12: warning: format '%p' expects argument of type 'void*', but argument 3 has type 'SEXP' {aka 'SEXPREC*'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.3/excel.link.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: 'INLA'
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    exiftool  14.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Running examples in 'expss-Ex.R' failed
The error most likely occurred in:

> ### Name: net
> ### Title: Add subtotal to a set of categories
> ### Aliases: net subtotal tab_net_cells tab_net_cols tab_net_rows
> ###   tab_subtotal_cells tab_subtotal_cols tab_subtotal_rows hide unhide
> 
> ### ** Examples
> 
> ol = c(1:7, 99)
> var_lab(ol) = "Liking"
> val_lab(ol)  = num_lab("
+                      1 Disgusting
+                      2 Very Poor
+                      3 Poor
+                      4 So-so
+                      5 Good
+                      6 Very good
+                      7 Excellent
+                      99 Hard to say
+                      ")
>                      
> cro(subtotal(ol, BOTTOM = 1:3, TOP = 6:7, position = "top"))
Error in set_val_lab.default(x, value, add = FALSE) : 
  'set_val_lab' - duplicated values in labels: 1 1 2 2 3 3 4 5 6 6 7 7 99
Calls: cro ... net.default -> val_lab<- -> set_val_lab -> set_val_lab.default
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
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'exuberdata'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Package suggested but not available for checking: 'doMC'
Problems with news in 'NEWS.md':
No news entries found.
'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
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    minor changes
'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'.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.0Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
    images   3.1Mb
    libs     1.3Mb
Package suggested but not available for checking: 'coxKM'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Scent.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) Traffic.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
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  6.2Mb
  sub-directories of 1Mb or more:
    Rcgi      3.1Mb
    cgi-bin   2.9Mb
.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
Package suggested but not available for checking: 'NNLM'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
GNU make is a SystemRequirements.
checkRd: (-1) summary.fdata.comp.Rd:44: Escaped LaTeX specials: \&
Found the following math rendering problems:
fregre.plm.Rd:86-87: Undefined control sequence: \emph in y =\emph{r(X)}+\sum_{j=...
metric.kl.Rd:45-46: Undefined control sequence: \- in \left|f_i(t)\-g_i(t) \right|\...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) 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: \#
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New Stuff
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dimnames.ff.rd:18: Escaped LaTeX specials: \_
checkRd: (-1) ff.rd:120: Escaped LaTeX specials: \_
checkRd: (-1) names.ff.rd:22: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  fgsg.h:96:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:202:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:347:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:460:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:516:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:636:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:717:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:852:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:996:41: 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.
Package suggested but not available for checking: 'MicrobeDS'
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R         4.3Mb
    doc       2.2Mb
    extdata   2.1Mb
'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
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    lib    3.0Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fivethirtyeightdata'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
Error(s) in re-building vignettes:
--- re-building 'spot-rate-curve-indexing.Rmd' using rmarkdown
Quitting from lines 134-135 (spot-rate-curve-indexing.Rmd) 
Error: processing vignette 'spot-rate-curve-indexing.Rmd' failed with diagnostics:
invalid class "SpotRateCurve" object: FALSE
--- failed re-building 'spot-rate-curve-indexing.Rmd'

--- re-building 'spot-rate-curve-interpolation.Rmd' using rmarkdown

Attaching package: 'dplyr'

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

    first, last

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building 'spot-rate-curve-interpolation.Rmd'

--- re-building 'spot-rate-curve-plotting.Rmd' using rmarkdown
Quitting from lines 83-86 (spot-rate-curve-plotting.Rmd) 
Error: processing vignette 'spot-rate-curve-plotting.Rmd' failed with diagnostics:
'to' must be a finite number
--- failed re-building 'spot-rate-curve-plotting.Rmd'

SUMMARY: processing the following files failed:
  'spot-rate-curve-indexing.Rmd' 'spot-rate-curve-plotting.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.6Mb
    libs   1.5Mb
checkRd: (-1) etable.Rd:494: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fk_regression.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) cclust.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) randIndex.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:28: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
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 10.6Mb
  sub-directories of 1Mb or more:
    doc    9.0Mb
    libs   1.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pseudoOptim.Rd:27: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) write.AFNI.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) write.AFNI.Rd:17: Escaped LaTeX specials: \_
checkRd: (-1) write.AFNI.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) write.AFNI.Rd:22: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
checkRd: (-1) forecTheta-package.Rd:11: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.4Mb
    libs   1.1Mb
'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
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
'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:
    R      1.2Mb
    help   2.2Mb
    libs   3.4Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
'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:
    R   5.7Mb
checkRd: (-1) CatalogueAccessors.Rd:249: Escaped LaTeX specials: \^ \^
checkRd: (-1) FrF2.Rd:574: Escaped LaTeX specials: \^
checkRd: (-1) FrF2.Rd:629: Escaped LaTeX specials: \^ \^
checkRd: (-1) IAPlot.Rd:87: Escaped LaTeX specials: \$
checkRd: (-1) block.Rd:121: Escaped LaTeX specials: \^
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 20.4Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.6Mb
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'foba', '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
checkRd: (-1) mean.fts.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) median.fts.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) plot.fm.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) residuals.fm.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) sd.fts.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) var.fts.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) meyer.Rd:11: Escaped LaTeX specials: \&
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
checkRd: (-1) mia.Rd:39: Escaped LaTeX specials: \#
installed size is 46.2Mb
  sub-directories of 1Mb or more:
    doc   44.4Mb
    libs   1.2Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
Package in Depends field not imported from: 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'tools:::.Rd_get_argument_names' 'tools:::RdTags' 'tools:::fetchRdDB'
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 63.5Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    gdal     2.2Mb
    libs    49.2Mb
    proj     8.7Mb
Running examples in 'gdata-Ex.R' failed
The error most likely occurred in:

> ### Name: read.xls
> ### Title: Read Excel files
> ### Aliases: read.xls xls2csv xls2tab xls2tsv xls2sep
> ### Keywords: file
> 
> ### ** Examples
> 
> 
>    # iris.xls is included in the gregmisc package for use as an example
>    xlsfile <- file.path(path.package('gdata'),'xls','iris.xls')
>    xlsfile
[1] "D:/RCompile/CRANpkg/lib/4.3/gdata/xls/iris.xls"
> 
>    iris <- read.xls(xlsfile) # defaults to csv format
Error in findPerl(perl, verbose = verbose) : 
  perl executable not found. Use perl= argument to specify the correct path.
Calls: read.xls -> xls2sep -> findPerl
Error in file.exists(tfn) : invalid 'file' argument
Calls: read.xls -> file.exists
Execution halted
Encountered the following conversion/validation errors:
missing value where TRUE/FALSE needed
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
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
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.2Mb
    libs      1.1Mb
checkRd: (-1) plot_summary.Rd:14: Escaped LaTeX specials: \_
'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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
Warnings in file 'R/utils.R':
  unable to translate '<U+00E9>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+2019>' to native encoding
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    1.9Mb
    libs   1.3Mb
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:
> ###   Decimal degrees.
> ### Aliases: sexagesimal
> 
> ### ** Examples
> 
> # Latitude
> g <- -33
> m <- 38
> s <- 30.123456
> value <- sexagesimal(g, m, s, digits = 4)
> print(value)
[1] -33.6417
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  23.34 0.9 24.33 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'geomarocdata'
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R         9.4Mb
    extdata   2.0Mb
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) getopt.Rd:60: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) gexp.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) estGF.Rd:106: Escaped LaTeX specials: \&
checkRd: (-1) estGF.Rd:107: 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:
    earlier versions
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       5.2Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  8.0Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
Encountered the following conversion/validation errors:
missing value where TRUE/FALSE needed
'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
checkRd: (-1) diamonds.Rd:10: Escaped LaTeX specials: \$ \$
Encountered the following conversion/validation errors:
missing value where TRUE/FALSE needed
'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:
    History
'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
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug fixes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial Release (0.1.0)
'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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
checkRd: (-1) starship.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) starship.adaptivegrid.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) starship.adaptivegrid.Rd:54: Escaped LaTeX specials: \&
checkRd: (-1) starship.adaptivegrid.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) starship.obj.Rd:25: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
checkRd: (-1) basal.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) basal.Rd:33: Escaped LaTeX specials: \_ \_ \_
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs           13.9Mb
    test_data       2.2Mb
    vignette_data   1.1Mb
'LazyData' is specified without a 'data' directory
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checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'cplexAPI'
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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) barleyHeights.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) barleyHeights.Rd:22: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R   6.2Mb
checkRd: (-1) rotations.Rd:103: Escaped LaTeX specials: \^
installed size is  5.6Mb
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    libs   4.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
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installed size is  5.5Mb
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    data   1.6Mb
    doc    3.5Mb
installed size is  5.4Mb
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    doc   5.3Mb
'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
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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
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checkRd: (-1) mlGraphicalVAR.Rd:79: Escaped LaTeX specials: \~
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'printCrudeAndAdjustedModel.Rmd' using rmarkdown
Loading required package: forestplot
Loading required package: grid
Loading required package: checkmate
Loading required package: abind
Loading required package: Gmisc
Loading required package: Rcpp
Loading required package: htmlTable
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

Quitting from lines 70-77 (printCrudeAndAdjustedModel.Rmd) 
Error: processing vignette 'printCrudeAndAdjustedModel.Rmd' failed with diagnostics:
could not find function "%>%"
--- failed re-building 'printCrudeAndAdjustedModel.Rmd'

--- re-building 'timeSplitter.Rmd' using rmarkdown

Attaching package: 'dplyr'

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

    src, summarize

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning in coxph(formula = Surv(Start_time, Stop_time, status == "Died from melanoma") ~  :
  a variable appears on both the left and right sides of the formula
Warning in coxph(formula = Surv(Start_time, Stop_time, status == "Died from melanoma") ~  :
  a variable appears on both the left and right sides of the formula
--- finished re-building 'timeSplitter.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Problems with news in 'NEWS.md':
No news entries found.
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
Package suggested but not available for checking: 'doMC'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   2.6Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/gRim.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
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:
+                        df_stats$sex,
+                        df_stats$measurement,
+                        TRUE)
> 
> # Calculate exponentially weighted moving average
> e_df <- ewma(df_stats$agedays, sd, ewma.exp = -1.5)
> 
> 
> 
> cleanEx()
> nameEx("ext_bmiz")
> ### * ext_bmiz
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ext_bmiz
> ### Title: Calculate extended BMI measures
> ### Aliases: ext_bmiz
> 
> ### ** Examples
> 
> # Run on a small subset of given data
> df <- as.data.frame(syngrowth)
> df <- df[df$subjid %in% unique(df[, "subjid"])[1:5], ]
> df <- cbind(df,
+             "gcr_result" = cleangrowth(df$subjid,
+                                        df$param,
+                                        df$agedays,
+                                        df$sex,
+                                        df$measurement))
======== End of example output (where/before crash/hang up occured ?) ========
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
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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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Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) gsym.point.Rd:143: Escaped LaTeX specials: \&
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checkRd: (-1) luzdat.Rd:21: Escaped LaTeX specials: \~
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Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 182.2Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    java  179.3Mb
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hablar)
  > test_check("hablar")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 416 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test.convert.R:118:3): from Date ───────────────────────────────────
  tibble(a = as.Date(c("1970-05-03", NA, "1987-04-20"))) %>% convert(dtm(a)) not equal to tibble(a = as.POSIXct(as.Date(c("1970-05-03", NA, "1987-04-20")))).
  Component "a": 'tzone' attributes are inconsistent ('Europe/London' and 'UTC')
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 416 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs    1.0Mb
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb
    doc     4.0Mb
checkRd: (-1) haplo.design.Rd:33: Escaped LaTeX specials: \$
checkRd: (-1) haplo.design.Rd:42: Escaped LaTeX specials: \$
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checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
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checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
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checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
Found the following significant warnings:
  harmony.cpp:211:80: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
See 'd:/Rcompile/CRANpkg/local/4.3/harmony.Rcheck/00install.out' for details.
Running examples in 'harmony-Ex.R' failed
The error most likely occurred in:

> ### Name: HarmonyMatrix
> ### Title: Main Harmony interface
> ### Aliases: HarmonyMatrix
> 
> ### ** Examples
> 
> 
> 
> ## By default, Harmony inputs a normalized gene expression matrix
> ## Not run: 
> ##D harmony_embeddings <- HarmonyMatrix(exprs_matrix, meta_data, 'dataset')
> ## End(Not run)
> 
> ## Harmony can also take a PCA embeddings matrix
> data(cell_lines_small)
> pca_matrix <- cell_lines_small$scaled_pcs
> meta_data <- cell_lines_small$meta_data
> harmony_embeddings <- HarmonyMatrix(pca_matrix, meta_data, 'dataset', 
+                                     do_pca=FALSE)
Harmony 1/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Error in harmonyObj$cluster_cpp() : 
  element-wise pow(): incompatible matrix dimensions: 10x3 and 3x1
Calls: HarmonyMatrix -> harmonize -> cluster -> <Anonymous> -> .External
Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(harmony)
  Loading required package: Rcpp
  > 
  > test_check("harmony")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Seurat V3 not available (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_integration.R:5:1): (code run outside of `test_that()`) ─────────
  <std::logic_error/C++Error/error/condition>
  Error in `harmonyObj$cluster_cpp()`: element-wise pow(): incompatible matrix dimensions: 50x3 and 3x1
  Backtrace:
      ▆
   1. └─harmony::HarmonyMatrix(...) at test_integration.R:5:0
   2.   └─harmony:::harmonize(harmonyObj, max.iter.harmony, verbose)
   3.     └─harmony:::cluster(harmonyObj)
   4.       └─harmonyObj$cluster_cpp()
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'quickstart.Rmd' using rmarkdown
Quitting from lines 148-152 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
element-wise pow(): incompatible matrix dimensions: 79x3 and 3x1
--- failed re-building 'quickstart.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) hash-accessors.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) hash-class.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) hash-class.Rd:45: Escaped LaTeX specials: \$
checkRd: (-1) hash-package.Rd:39: Escaped LaTeX specials: \#
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) prm09.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) prm09.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) schools.Rd:18: Escaped LaTeX specials: \&
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/HDMT.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    TODO:
    "GW", "OLO"
    seriate(cophenetic(dend), method = "OLO", control = list(hclust = as.hclust(dend)))
    the downside in using cophenetic is that seriate has to go through running hclust all over again
    but we'll just have to accept it...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'synbreed'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) erode.hexbin.Rd:43: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
    libs      2.0Mb
':::' 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'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  arms-R.c:811:30: warning: format '%x' expects argument of type 'unsigned int', but argument 4 has type 'POINT *' {aka 'struct point *'} [-Wformat=]
  arms-R.c:821:26: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'POINT *' {aka 'struct point *'} [-Wformat=]
  arms-R.c:821:38: warning: format '%x' expects argument of type 'unsigned int', but argument 4 has type 'struct point *' [-Wformat=]
  arms-R.c:821:51: warning: format '%x' expects argument of type 'unsigned int', but argument 5 has type 'struct point *' [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.3/HI.Rcheck/00install.out' for details.
checkRd: (-1) trans.dens.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) Snow.Rd:118: Escaped LaTeX specials: \&
checkRd: (-1) Snow.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) Yeast.Rd:56: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'FGN'
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
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
Error(s) in re-building vignettes:
--- re-building 'hockey-ref-scrapers.Rmd' using rmarkdown
Quitting from lines 35-38 (hockey-ref-scrapers.Rmd) 
Error: processing vignette 'hockey-ref-scrapers.Rmd' failed with diagnostics:
no applicable method for 'xml_find_first' applied to an object of class "NULL"
--- failed re-building 'hockey-ref-scrapers.Rmd'

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

SUMMARY: processing the following file failed:
  'hockey-ref-scrapers.Rmd'

Error: Vignette re-building failed.
Execution halted
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
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.5Mb
checkRd: (-1) attributes_speclib.Rd:73: Escaped LaTeX specials: \$
checkRd: (-1) get_reflectance.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
Running examples in 'httpRequest-Ex.R' failed
The error most likely occurred in:

> ### Name: simplePostToHost
> ### Title: Sends Simple Post Request to HTTP Server (host)
> ### Aliases: simplePostToHost
> 
> ### ** Examples
> 
> host <- "api.scb.se"
> path <- "/OV0104/v1/doris/en/ssd"
> data <- '{"format":"json"}'
> simplePostToHost(host, path, data, contenttype="text/json")
socket error: Eine vorhandene Verbindung wurde vom Remotehost geschlossen
Error in read.socket(fp, maxlen, loop = FALSE) : 
  Error reading data in Rsockread
Calls: simplePostToHost -> read.socket
Execution halted
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: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Trancura9414001.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) Trancura9414001.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) hydroPSO.Rd:390: Escaped LaTeX specials: \&
checkRd: (-1) hydroPSO.Rd:408: Escaped LaTeX specials: \&
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:7: Escaped LaTeX specials: \&
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    exdata   6.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SparkR'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: 'icd'
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dmahal.Rd:18: Escaped LaTeX specials: \~
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/ichimoku.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
checkRd: (-1) pulmonary.Rd:13: Escaped LaTeX specials: \_
'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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.2Mb
    libs   6.4Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.1Mb
    libs         1.4Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> flush(stderr()); flush(stdout())
> 
> ### Name: run_imagefluency
> ### Title: Run imagefluency app
> ### Aliases: run_imagefluency
> 
> ### ** Examples
> 
> ## Only run this example in interactive R sessions
> if (interactive()) {
+   run_imagefluency()
+ }
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  202.14 620.36 833.72 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.4Mb
    extdata   1.0Mb
    include   3.0Mb
    libs      9.8Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
'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
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.6Mb
'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
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
BugReports field should be the URL of a single webpage
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
'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:
    INSPECTumours (development version)
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    TODO for future releases:
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
checkRd: (-1) Intervals-class.Rd:109: Escaped LaTeX specials: \_
checkRd: (-1) Intervals-class.Rd:110: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:68: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:76: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:77: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:78: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:79: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:81: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:88: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:89: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) sgd.Rd:12: Escaped LaTeX specials: \_
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc   9.7Mb
'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
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'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:
    doc   5.2Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R  11.7Mb
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pine.Rd:20: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app    4.3Mb
    data   1.5Mb
'LazyData' is specified without 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: 'locClass'
checkRd: (-1) ivmodel.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) ivmodelFormula.Rd:79: Escaped LaTeX specials: \&
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           8.5Mb
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
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
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.0Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    i18n   4.0Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    joineR <1.1
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
checkRd: (-1) summ.rq.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) summ.rq.Rd:108: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
math_to_rd.html:81:2153 (math_to_rd.Rd:45): Warning: <svg> attribute "width" has invalid value "400em"
math_to_rd.html:81:2153 (math_to_rd.Rd:45): Warning: <svg> attribute "height" has invalid value "1.08em"
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ionosphere.Rd:22: Escaped LaTeX specials: \&
checkRd: (-1) ionosphere.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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pathFrechet.Rd:54: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) kstIO-package.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) read_kbase.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) read_kdata.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) read_kfamset.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) read_kspace.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) read_kstructure.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) read_surmiserelation.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) write_kbase.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) write_kdata.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) write_kspace.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) write_kstructure.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) write_surmiserelation.Rd:36: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) alphaOnly.Rd:25: Escaped LaTeX specials: \^
checkRd: (-1) alphaOnly.Rd:26: Escaped LaTeX specials: \$
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
checkRd: (-1) natlongsurv.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs             1.7Mb
    shiny-landsepi   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gof', 'lava.tobit'
checkRd: (-1) Col.Rd:17: Escaped LaTeX specials: \#
checkRd: (-1) regression-set.Rd:103: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) goodnessfit.Rd:105: Escaped LaTeX specials: \&
checkRd: (-1) lba.Rd:252: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:46: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    lcars.0.3.1
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  12.0Mb
'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
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
checkRd: (-1) leaps.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   4.3Mb
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
'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  8.2Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
Running 'spelling.R' [0s]
  Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("LexisNexisTools")
  LexisNexisTools Version 0.3.5
  > 
  > test_check("LexisNexisTools")
  
    |                                                  | 0 % ~calculating  
    |+++++                                             | 10% ~00s          
    |++++++++++                                        | 20% ~00s          
    |+++++++++++++++                                   | 30% ~00s          
    |++++++++++++++++++++                              | 40% ~00s          
    |+++++++++++++++++++++++++                         | 50% ~00s          
    |++++++++++++++++++++++++++++++                    | 60% ~00s          
    |+++++++++++++++++++++++++++++++++++               | 70% ~00s          
    |++++++++++++++++++++++++++++++++++++++++          | 80% ~00s          
    |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~00s          
    |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
    adding: sample.DOCX (deflated 45%)
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 99 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • !dir.exists("/home/johannes/Dropbox/LexisNexis_sample_files/") is TRUE (1)
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-lnt_convert.R:16:3): Convert LNToutput to rDNA ────────────────
  {
      ...
  } not equal to readRDS("../files/rDNA.RDS").
  Component "date": 'tzone' attributes are inconsistent ('UTC' and '')
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 99 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'doMC'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'rsyslog'
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
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installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.7Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2'
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.0Mb
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checkRd: (-1) solveLP.Rd:119: 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:
> 
> ### ** Examples
> 
> ## Not run: 
> ##D # use the default set of linters
> ##D lintr::use_lintr()
> ##D # or try all linters
> ##D lintr::use_lintr(type = "full")
> ##D 
> ##D # then
> ##D lintr::lint_dir()
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  7.67 2.17 10.6 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.0Mb
    libs       1.4Mb
    testdata   1.3Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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  Cannot extract version info from the following section titles:
    Author
    Maintainer
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Encountered the following conversion/validation errors:
missing value where TRUE/FALSE needed
'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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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    R      4.0Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Found the following significant warnings:
  lxb.c:62:25: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
  lxb.c:62:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 4 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.3/lxb.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
GNU make is a SystemRequirements.
Running 'testthat.R' [20s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(madrat)
  Loading required package: magclass
  > 
  > test_check("madrat")
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 386 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (6)
  • reshape2 cannot be loaded (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-config.R:3:3): cache folder can be set properly ───────────────
  getwd() not identical to getConfig("cachefolder").
  1/1 mismatches
  x[1]: "d:/Rcompile/CRANpkg/local/4.3/madrat.Rcheck/tests/testthat"
  y[1]: "D:/RCompile/CRANpkg/local/4.3/madrat.Rcheck/tests/testthat"
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 386 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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installed size is 42.5Mb
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    doc    6.6Mb
    libs  35.6Mb
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checkRd: (-1) cilleruelo.Rd:36: Escaped LaTeX specials: \#
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   1.3Mb
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Package unavailable to check Rd xrefs: 'INLA'
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installed size is  7.1Mb
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    doc   6.7Mb
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    data   1.2Mb
    doc    3.5Mb
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installed size is 33.5Mb
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    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs          3.2Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug Fixes
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
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    R      2.7Mb
    data   2.4Mb
    libs   1.3Mb
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Package suggested but not available for checking: 'scrubr'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    To do
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    examples   2.7Mb
    libs       1.3Mb
'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:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'flashr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
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    java   3.3Mb
    libs   1.7Mb
checkRd: (-1) GerberGreenImai.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) GerberGreenImai.Rd:31: Escaped LaTeX specials: \#
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'LazyData' is specified without a 'data' directory
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) maxControl.Rd:83: Escaped LaTeX specials: \&
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:  5.41 0.11 5.52 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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Checking should be performed on sources prepared by 'R CMD build'.
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  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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    mev v.1.8x
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Running examples in 'miic-Ex.R' failed
The error most likely occurred in:

> ### Name: discretizeMutual
> ### Title: Iterative dynamic programming for (conditional) mutual
> ###   information through optimized discretization.
> ### Aliases: discretizeMutual
> 
> ### ** Examples
> 
> library(miic)
> N <- 1000
> # Dependence, conditional independence : X <- Z -> Y
> Z <- runif(N)
> X <- Z * 2 + rnorm(N, sd = 0.2)
> Y <- Z * 2 + rnorm(N, sd = 0.2)
> res <- discretizeMutual(X, Y, plot = FALSE)
Package suggested but not available for checking: 'gurobi'
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GNU make is a SystemRequirements.
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Error(s) in re-building vignettes:
--- re-building 'README.Rmd' using rmarkdown
INFO - This is Biber 2.16
INFO - Logfile is 'README.blg'
INFO - Reading 'README.bcf'
ERROR - Error: Found biblatex control file version 3.9, expected version 3.7.
This means that your biber (2.16) and biblatex (3.18b) versions are incompatible.
See compat matrix in biblatex or biber PDF documentation.
INFO - ERRORS: 1
Warning: LaTeX Warning: Empty bibliography on input line 181.
Warning: LaTeX Warning: There were undefined references.
Warning: LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
Warning: Package rerunfilecheck Warning: File `README.out' has changed.
Warning: (rerunfilecheck)                Rerun to get outlines right
Warning: (rerunfilecheck)                or use package `bookmark'.
Warning: Package biblatex Warning: Please (re)run Biber on the file:
Warning: (biblatex)                README
Warning: (biblatex)                and rerun LaTeX afterwards.
Error: processing vignette 'README.Rmd' failed with diagnostics:
Failed to build the bibliography via biber
--- failed re-building 'README.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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Problems with news in 'NEWS.md':
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    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/mlrCPO.Rcheck/00install.out' for details.
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Packages which this enhances but not available for checking:
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    * efourier with default norm=TRUE now messages about how wrong it may be
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Running examples in 'move-Ex.R' failed
The error most likely occurred in:

> ### Name: thinTrackTime
> ### Title: Thinning trajectories to a specific time interval or distance.
> ### Aliases: thinTrackTime thinDistanceAlongTrack
> ###   thinTrackTime,.MoveTrackSingle-method
> ###   thinDistanceAlongTrack,.MoveTrackSingle-method
> 
> ### ** Examples
> 
> data("leroy")
> leroysub <- leroy[1:200]
> ### selecting those segments that have a time interval of 15mins pulsminus 5mins
> thintime <- thinTrackTime(leroysub, interval = as.difftime(15, units='mins'),
+                           tolerance = as.difftime(5, units='mins'))
Error in validityMethod(as(object, superClass)) : 
  Burst ids need to be one shorter than the number of coordinates since it is a segment property
Calls: thinTrackTime ... validObject -> anyStrings -> isTRUE -> validityMethod
Execution halted
Package suggested but not available for checking: 'corpus.useR.2008.abstracts'
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GNU make is a SystemRequirements.
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    data   4.1Mb
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Running examples in 'mskcc.oncotree-Ex.R' failed
The error most likely occurred in:

> ### Name: get_tumor_types
> ### Title: Get tumor types
> ### Aliases: get_tumor_types
> 
> ### ** Examples
> 
> get_tumor_types()
Error in `resp_abort()`:
! HTTP 504 Gateway Timeout.
Backtrace:
     ▆
  1. ├─mskcc.oncotree::get_tumor_types()
  2. │ ├─base::withVisible(eval(mc, parent.frame()))
  3. │ └─base::eval(mc, parent.frame())
  4. │   └─base::eval(mc, parent.frame())
  5. ├─mskcc.oncotree (local) `<fn>`()
  6. │ ├─mskcc.oncotree:::get("/tumorTypes", version = oncotree_version)
  7. │ │ ├─base::withVisible(eval(mc, parent.frame()))
  8. │ │ └─base::eval(mc, parent.frame())
  9. │ │   └─base::eval(mc, parent.frame())
 10. │ └─mskcc.oncotree (local) `<fn>`(resource = "/tumorTypes", version = oncotree_version)
 11. │   └─... %>% httr2::resp_body_string(encoding = "UTF-8")
 12. ├─httr2::resp_body_string(., encoding = "UTF-8")
 13. │ └─httr2:::check_response(resp)
 14. │   └─httr2:::is_response(req)
 15. └─httr2::req_perform(.)
 16.   └─httr2:::resp_abort(resp, error_body(req, resp))
 17.     └─rlang::abort(...)
Execution halted
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checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) MultBiplotR-package.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) MultBiplotR-package.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) print.multcompLetters.Rd:20: Escaped LaTeX specials: \$
'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
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   6.7Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    PREVIOUS (Incomplete below)
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 're2r'
Malformed Description field: should contain one or more complete sentences.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs     2.3Mb
    models   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spatialClust'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.7Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("nat.utils")
  Loading required package: nat.utils
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 73 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • touch only supported on unix platforms (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-fsutils.r:79:3): common_path works ────────────────────────────
  common_path(c("/a", "/b"), normalise = T) not equal to np("/").
  1/1 mismatches
  x[1]: "d:/"
  y[1]: "D:/"
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 73 ]
  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
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
'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  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 're2r'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Slightly modified tests
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) netCoin-package.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_ \_
checkRd: (-1) makeNetwork.Rd:31: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fastshp'
'LazyData' is specified without a 'data' directory
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
GNU make is a SystemRequirements.
Running examples in 'neurobase-Ex.R' failed
The error most likely occurred in:

> ### Name: boxplot.nifti
> ### Title: Boxplot of Values in an Image
> ### Aliases: boxplot.nifti boxplot.anlz
> 
> ### ** Examples
> 
> img = nifti(array(rnorm(10^3), dim = rep(10, 3)))
> mask = img > 0
> boxplot(img)
> boxplot(img, mask = mask)
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars$yaxs) : 
  need finite 'ylim' values
Calls: boxplot ... boxplot.default -> do.call -> <Anonymous> -> plot.window
Execution halted
Error(s) in re-building vignettes:
--- re-building 'neurobase.Rmd' using rmarkdown
Quitting from lines 459-460 (neurobase.Rmd) 
Error: processing vignette 'neurobase.Rmd' failed with diagnostics:
need at least 2 points to select a bandwidth automatically
--- failed re-building 'neurobase.Rmd'

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

--- re-building 'simple_io.Rmd' using rmarkdown
trying URL 'https://johnmuschelli.com/open_ms_data/cross_sectional/raw/patient01/T1W.nii.gz'
Content type 'application/gzip' length 21807043 bytes (20.8 MB)
==================================================
downloaded 20.8 MB

--- finished re-building 'simple_io.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
nBartlett.Rd:45-50: Undefined control sequence: \raise in ... }
      \over {{\raise0.7ex\hbox{$1$}...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    CppCode   1.7Mb
    R         6.3Mb
    include   5.8Mb
    libs      1.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Package which this enhances but not available for checking: 'jpndistrict'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) nltm.control.Rd:29: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
checkRd: (-1) Frobenius-nmf.Rd:141: Escaped LaTeX specials: \#
checkRd: (-1) KL-nmf.Rd:158: Escaped LaTeX specials: \#
checkRd: (-1) NMFStrategyIterative-class.Rd:69: Escaped LaTeX specials: \#
checkRd: (-1) NMFstd-class.Rd:179: Escaped LaTeX specials: \#
checkRd: (-1) nmf.Rd:755: Escaped LaTeX specials: \#
checkRd: (-1) nmf_update_KL.Rd:87: Escaped LaTeX specials: \#
checkRd: (-1) nmf_update_euclidean.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) offset-nmf.Rd:144: Escaped LaTeX specials: \#
Running examples in 'NMF-Ex.R' failed
The error most likely occurred in:

> ### Name: profplot
> ### Title: Plotting Expression Profiles
> ### Aliases: profplot profplot.default
> ### Keywords: aplot
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # create a random target matrix
> v <- rmatrix(35, 10)
> 
> # fit a single NMF model
> res <- nmf(v, 3)
> profplot(res)
> 
> # fit a multi-run NMF model
> res2 <- nmf(v, 3, nrun=2)
# NOTE - CRAN check detected: limiting maximum number of cores [2/56]
> # ordering according to first profile
> profplot(res2, Colv=1) # increasing
> 
> # draw a profile correlation plot: this show how the basis components are
> # returned in an unpredictable order
> profplot(res, res2)
Error in col["alpha", ] <- as.character(as.hexmode(alpha)) : 
  incorrect number of subscripts on matrix
Calls: profplot ... <Anonymous> -> .set.list.defaults -> expand_list -> alphacol
Execution halted
'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:
    Other ideas
'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
checkRd: (-1) simulatePop.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    norgeo (development version)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Running 'testthat.R' [49s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #' Copyright(c) 2017-2020 R. Mark Sharp
  > #' This file is part of nprcgenekeepr
  > library(testthat)
  > library(nprcgenekeepr)
  > test_check("nprcgenekeepr")
  15 15 
  15 15 
  [ FAIL 1 | WARN 3 | SKIP 19 | PASS 747 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  • Sys.info()[names(Sys.info()) == "user"] == "msharp" is not TRUE (18)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_getDatedFilename.R:12:3): getDatedFilename form correctly dated file name ──
  stri_sub(getDatedFilename("testName"), 21) not equal to "testName".
  1/1 mismatches
  x[1]: "872496_testName"
  y[1]: "testName"
  
  [ FAIL 1 | WARN 3 | SKIP 19 | PASS 747 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ardechedata.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) nsRFA-package.Rd:231: 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.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    doc       5.7Mb
    extdata   1.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.0Mb
    libs   1.3Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Package suggested but not available for checking: 'cmdstanr'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
  print_address.c:11:27: warning: format '%p' expects argument of type 'void *', but argument 4 has type 'SEXP' {aka 'struct SEXPREC *'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.3/oops.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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/OpenCL.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'unix'
GNU make is a SystemRequirements.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs   13.1Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    R        2.6Mb
    libs     4.8Mb
    models   4.8Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Older changes
    trunk
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Package suggested but not available for checking: 'openNLPmodels.en'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   1.3Mb
    libs      1.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      1.4Mb
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
checkRd: (-1) quad_3D.Rd:22: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    libs   1.3Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   7.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rcplex'
'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
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:
    Changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    library  19.4Mb
Package which this enhances but not available for checking: 'CorShrink'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(PAMmisc)
  > 
  > test_check("PAMmisc")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 76 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-pgDatabase.R:18:5): Test gps adding ─────────────────────────────
  Error: Not able to properly convert UTC to POSIXct format, check format argument.
  Backtrace:
      ▆
   1. └─PAMmisc::addPgGps(tmpDb, tmpFile, source = "csv", format = "%Y-%m-%d %H:%M:%S") at test-pgDatabase.R:18:4
   2.   └─PAMmisc:::fmtGps(gps, source, format, tz)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 76 ]
  Error: Test failures
  Execution halted
'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: \_
Encountered the following conversion/validation errors:
missing value where TRUE/FALSE needed
'LazyData' is specified without a 'data' directory
checkRd: (-1) pan.bd.Rd:65: Escaped LaTeX specials: \$
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
'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
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Checking should be performed on sources prepared by 'R CMD build'.
GNU make is a SystemRequirements.
checkRd: (-1) plot-methods.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) plot-methods.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) glue_search_tables.Rd:24: Escaped LaTeX specials: \#
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checkRd: (-1) iam_update_account_password_policy.Rd:21: Escaped LaTeX specials: \#
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lib    2.8Mb
    libs   2.3Mb
'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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) l1pcastar.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) pcaL1-package.Rd:52: Escaped LaTeX specials: \&
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Dist.Rd:50: Escaped LaTeX specials: \&
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   7.8Mb
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
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
Package suggested but not available for checking: 'PythonInR'
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs    6.9Mb
    share  12.8Mb
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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
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) pec.Rd:250: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   2.2Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
GNU make is a SystemRequirements.
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: \_ \_
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checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
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checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANWIN2.fb05.statistik.uni-dortmund.de:11619 (sockconn)
	<-CRANWIN2.fb05.statistik.uni-dortmund.de:11619 (sockconn)
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
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'
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Fixed issues
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'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    application   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
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installed size is  5.9Mb
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    doc       1.5Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
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    doc    3.2Mb
    help   1.1Mb
checkRd: (-1) 11_d.EMControl.Rd:52: Escaped LaTeX specials: \_
checkRd: (-1) plotdots.Rd:33: Escaped LaTeX specials: \#
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
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Package suggested but not available for checking: 'INLA'
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'LazyData' is specified without a 'data' directory
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(piecemaker)
  > 
  > test_check("piecemaker")
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 23 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-clean.R:33:3): Can validate UTF8 ────────────────────────────────
  <encoding_error/rlang_error/error/condition>
  Error in `FUN(X[[i]], ...)`: Unsupported string type in <fa><b4><bf><bf><9f>
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-clean.R:33:2
    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. └─piecemaker::validate_utf8(bad_character)
    8.   └─base::vapply(...)
    9.     └─piecemaker (local) FUN(X[[i]], ...)
   10.       └─rlang::abort(message = error_message, class = "encoding_error")
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 23 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  dns.c:230:43: warning: format '%u' expects argument of type 'unsigned int', but argument 6 has type 'DWORD' {aka 'long unsigned int'} [-Wformat=]
  dns.c:230:46: warning: format '%u' expects argument of type 'unsigned int', but argument 7 has type 'DWORD' {aka 'long unsigned int'} [-Wformat=]
  dns.c:230:49: warning: format '%u' expects argument of type 'unsigned int', but argument 8 has type 'DWORD' {aka 'long unsigned int'} [-Wformat=]
  dns.c:230:52: warning: format '%u' expects argument of type 'unsigned int', but argument 9 has type 'DWORD' {aka 'long unsigned int'} [-Wformat=]
  dns.c:230:55: warning: format '%u' expects argument of type 'unsigned int', but argument 10 has type 'DWORD' {aka 'long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.3/pingr.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
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'ggsubplot'
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'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.
Running examples in 'pkgmaker-Ex.R' failed
The error most likely occurred in:

> ### Name: alphacol
> ### Title: Colour utilities
> ### Aliases: alphacol
> 
> ### ** Examples
> 
> 
> # Alphas
> alphacol('red') # do nothing
Error in apply(col, 2, function(x) paste("#", paste(x, collapse = ""),  : 
  dim(X) must have a positive length
Calls: alphacol -> apply
Execution halted
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installed size is 11.1Mb
  sub-directories of 1Mb or more:
    bin   8.6Mb
    doc   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'monocle3', 'ProjecTILs', 'SeuratWrappers'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    tests   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.8Mb
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) PLS_beta_wvc.Rd:5: Escaped LaTeX specials: \_
checkRd: (-1) plsRbeta.Rd:104: Escaped LaTeX specials: \^
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checkRd: (-1) PLS_lm_wvc.Rd:5: Escaped LaTeX specials: \_
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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 math rendering problems:
1dpoilog.Rd:31: Undefined control sequence: \emph in \code{nu}\,\emph{y}
Running 'testthat.R' [46s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(pointblank)
  
  Attaching package: 'pointblank'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > library(dittodb)
  Loading required package: DBI
  > test_check("pointblank")
  [ FAIL 5 | WARN 0 | SKIP 26 | PASS 1104 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (26)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-create_agent.R:77:3): Creating a valid `agent` object is possible ──
  agent\$label does not match "^\\[[0-9]{4}-[0-9]{2}-[0-9]{2}\\|[0-9]{2}:[0-9]{2}:[0-9]{2}\\]$".
  Actual value: "\[2022-10-08\|19:05:39\.824522\]"
  Backtrace:
      ▆
   1. └─testthat::expect_match(agent$label, "^\\[[0-9]{4}-[0-9]{2}-[0-9]{2}\\|[0-9]{2}:[0-9]{2}:[0-9]{2}\\]$") at test-create_agent.R:77:2
   2.   └─testthat:::expect_match_(...)
  ── Failure (test-x_list.R:34:3): An x-list for a step is structurally correct ──
  grepl(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-x_list.R:112:3): An x-list for a step is structurally correct ──
  grepl(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-x_list.R:201:3): A complete x-list is structurally correct ────
  grepl(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-x_list.R:305:3): A complete x-list is structurally correct ────
  grepl(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 5 | WARN 0 | SKIP 26 | PASS 1104 ]
  Error: Test failures
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
'LazyData' is specified without a 'data' directory
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checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
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installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
    libs   1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      1.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
installed size is  5.4Mb
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Package suggested but not available for checking: 'WhopGenome'
checkRd: (-1) BayeScanR.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) MKT-methods.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) genetic_distance.Rd:106: Escaped LaTeX specials: \~
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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    java   5.1Mb
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: \$
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is 12.1Mb
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    doc  10.3Mb
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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:
    CalEquation function can calculate intercept in multiple regression model with interaction
    New arguments summarymode added to fit2newdata(), predict3d() and ggPredict()
    New arguments xlab, ylab and zlab added to predict3d()
    New function gg_color_hue() and theme_bw2() added
    Bug-fixed
    New function restoreData2(), restoreData3()  added
    New function add_lines() added
    New function ggPredict() and predict3d() added
    New function fit2newdata() added
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinyApp   5.3Mb
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installed size is  5.7Mb
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    libs   1.4Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    4.6Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is 11.5Mb
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    htmlwidgets   2.5Mb
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checkRd: (-1) prodlim.Rd:119: Escaped LaTeX specials: \&
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    extdata   1.2Mb
    libs      1.2Mb
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installed size is 12.2Mb
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Package suggested but not available for checking: 'cmdstanr'
installed size is  6.6Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Package suggested but not available for checking: 'SDMTools'
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
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Package suggested but not available for checking: 'rdt'
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Found the following significant warnings:
  api-windows.c:923:69: warning: format '%d' expects argument of type 'int', but argument 4 has type 'DWORD' {aka 'long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.3/ps.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) esa.Rd:15: Escaped LaTeX specials: \&
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installed size is  8.9Mb
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    R          1.2Mb
    doc        4.0Mb
    examples   2.5Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > print(Sys.getenv("NOT_CRAN"))
  [1] ""
  > testthat::test_check("pxweb")
  Loading required package: pxweb
  pxweb 0.16.1: R tools for the PX-WEB API.
  https://github.com/ropengov/pxweb
  
  [ FAIL 1 | WARN 0 | SKIP 33 | PASS 17 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (32)
  • on_github_actions() is not TRUE (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-pxweb_query.R:149:3): mandatory variables are included automatically ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Recv failure: Connection was reset
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(pxd <- pxweb_get(url, pxq4)) at test-pxweb_query.R:149:2
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─pxweb::pxweb_get(url, pxq4)
   10.   └─pxweb::pxweb_advanced_get(url = url, query = query, verbose = verbose)
   11.     └─pxweb::pxweb(url)
   12.       └─pxweb:::pxweb_add_config(obj)
   13.         └─httr::GET(cfg_url)
   14.           └─httr:::request_perform(req, hu$handle$handle)
   15.             ├─httr:::request_fetch(req$output, req$url, handle)
   16.             └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   17.               └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 33 | PASS 17 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'pxweb.Rmd' using rmarkdown
pxweb 0.16.1: R tools for the PX-WEB API.
https://github.com/ropengov/pxweb

Quitting from lines 127-130 (pxweb.Rmd) 
Error: processing vignette 'pxweb.Rmd' failed with diagnostics:
Recv failure: Connection was reset
--- failed re-building 'pxweb.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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installed size is  6.1Mb
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    gui          1.6Mb
    staticdocs   3.3Mb
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'LazyData' is specified without a 'data' directory
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installed size is 26.2Mb
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    libs  25.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  5.9Mb
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checkRd: (-1) CentAndClusfuns.Rd:70: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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    extdata   3.3Mb
    libs      2.5Mb
installed size is  5.0Mb
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    libs      1.0Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) GRI.Rd:3: Escaped LaTeX specials: \&
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
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checkRd: (-1) qwraps2.Rd:73: Escaped LaTeX specials: \&
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Package suggested but not available for checking: 'ReGenesees'
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Package suggested but not available for checking: 'RDCOMClient'
'library' or 'require' call to 'RDCOMClient' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'BRugs'
installed size is 11.5Mb
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installed size is  7.2Mb
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    htmlwidgets   1.8Mb
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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
installed size is 10.6Mb
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    doc    6.6Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    doc   5.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) fdepth.Rd:43: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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installed size is 10.9Mb
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installed size is 11.6Mb
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    htmlwidgets   6.8Mb
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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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug Fixes
    New Features
    Major Changes
    Minor changes
'LazyData' is specified without a 'data' directory
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Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'gurobi'
installed size is  7.2Mb
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    doc    1.5Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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    libs   1.4Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
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    etc    1.9Mb
    po     1.2Mb
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
installed size is  6.4Mb
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    libs   1.5Mb
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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:
> 
> ### ** Examples
> 
>     library(rbiom)
>     
>     infile <- system.file("extdata", "hmp50.bz2", package = "rbiom")
>     biom <- read.biom(infile)
>     
>     ntaxa(biom)
[1] 490
> 
> 
> 
> 
> cleanEx()
> nameEx("phylogeny")
> ### * phylogeny
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: phylogeny
> ### Title: Get the phylogenetic tree.
> ### Aliases: phylogeny
> 
> ### ** Examples
> 
>     library(rbiom)
>     
>     infile <- system.file("extdata", "hmp50.bz2", package = "rbiom")
>     biom <- read.biom(infile)
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
checkRd: (-1) mn4joint1condi.Rd:39: Escaped LaTeX specials: \$
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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'
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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
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Package suggested but not available for checking: 'ROpenOffice'
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
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    doc   3.2Mb
    po    2.4Mb
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installed size is  7.5Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rcplex.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      1.2Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    include  45.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.1Mb
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GNU make is a SystemRequirements.
installed size is 10.5Mb
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    doc       1.1Mb
    include   6.4Mb
    libs      1.3Mb
installed size is  7.5Mb
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    include        1.5Mb
    jsonexamples   3.8Mb
    libs           1.9Mb
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'LazyData' is specified without a 'data' directory
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcrypt)
  > 
  > test_check("rcrypt")
  gpg: decryption failed: Bad session key
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 18 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-decrypt.r:69:3): Decryption with passphrase passthrough and armor works ──
  Error in `file(con, "r")`: cannot open the connection
  Backtrace:
      ▆
   1. └─base::readLines("file2-decrypt.txt") at test-decrypt.r:69:2
   2.   └─base::file(con, "r")
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
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    libs   6.3Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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    libs   2.2Mb
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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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'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
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installed size is  5.4Mb
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    R      3.5Mb
    data   1.4Mb
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checkRd: (-1) re2_syntax.Rd:539: Escaped LaTeX specials: \_
Package suggested but not available for checking: 'dataui'
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'LazyData' is specified without a 'data' directory
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