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Running examples in 'ggcoverage-Ex.R' failed
The error most likely occurred in:

> ### Name: geom_base
> ### Title: Add Base and Amino Acid Annotation to Coverage Plot.
> ### Aliases: geom_base
> 
> ### ** Examples
> 
> library(ggcoverage)
> library("BSgenome.Hsapiens.UCSC.hg19")
Error in library("BSgenome.Hsapiens.UCSC.hg19") : 
  there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
Execution halted
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':::' call which should be '::': 'scales:::censor'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'productplots:::bound'
  See the note in ?`:::` about the use of this operator.
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Problems with news in 'NEWS.md':
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    * Changes all data options to .data to decrease possibility of column naming overlap
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GNU make is a SystemRequirements.
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installed size is  6.6Mb
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Unknown package 'gvcm.cat' in Rd xrefs
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GNU make is a SystemRequirements.
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accrualReport: multiple local function definitions for 'gg' with
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S3 methods shown with full name in documentation object 'groc.fit':
  'groc.fit'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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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 ?) ========
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.ga.breed' '.ga.fitness' '.ga.init' '.ga.mutate' '.ga.step'
  '.ga.weight'
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S3 methods shown with full name in documentation object 'defunct':
  'anova.mean' 'print.glht.mmc.multicomp' 'coef.arima.HH' 'glht.mmc'
  'plot.odds.ratio' 'persp.plane' 'persp.floor' 'persp.back.wall.x'
  'persp.back.wall.y' 'persp.setup' 'plot.hov' 'plot.hov.bf'
  'plot.matchMMC' 'seqplot.forecast'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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html_describe_con: multiple local function definitions for 'g' with
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Error(s) in re-building vignettes:
--- re-building 'hSDM.Rmd' using rmarkdown
--- finished re-building 'hSDM.Rmd'

--- re-building 'publications.Rmd' using rmarkdown
Error reading bibliography file bib/biblio-publications.bib:
(line 50, column 3):
unexpected '%'
expecting white space
Error: processing vignette 'publications.Rmd' failed with diagnostics:
pandoc document conversion failed with error 25
--- failed re-building 'publications.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    2.1Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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   5.5Mb
    libs      1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SparkR'
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'icd'
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
S3 methods shown with full name in documentation object 'orlm':
  'orlm.forboot.fixed' 'orlm.forboot'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) pulmonary.Rd:13: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rggobi'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object 'internals':
  'plot.page'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   1.4Mb
    libs   6.2Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         1.4Mb
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:  198.13 622.23 826.55 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.2Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     10.1Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Package suggested but not available for checking: 'cmdstanr'
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'surveyspec'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'iotools/libs/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
Specified C++11: please drop specification unless essential
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object 'print.Item':
  'print.Item'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.3Mb
    libs   2.8Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Package suggested but not available for checking: 'locClass'
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          10.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    i18n   4.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: 'remMap'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
apparently using $(BLAS_LIBS) without following $(FLIBS) in 'src/Makevars'
S3 methods shown with full name in documentation object 'bw.abram.temp':
  'bw.abram.temp'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor Changes
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: wml_animals
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> keyToEnglish(1:5, word_list=wml_animals)
Warning in keyToEnglish(1:5, word_list = wml_animals) :
  Converting input to character
[1] "GargantuanYellowFishOfAmbition"      "MinisculeLimeBatOfForgetfulness"    
[3] "GargantuanPinkMooseOfWarfare"        "BigBeigeHoneybadgerOfCuddles"       
[5] "AstronomicalVermillionDragonOfOrder"
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.11 0.11 1.21 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
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'unlist.constr':
  'unlist.constr'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'VARSEDIG'
Unknown package 'VARSEDIG' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'stat.functions':
  'kappa.cor'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   1.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'ergm.userterms'
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package 'ergm.userterms' in Rd xrefs
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'akmedoids', 'clusterCrit'
Unknown packages 'clusterCrit', 'akmedoids' in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
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
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
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.4Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'gpclib'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'rsyslog'
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.7Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
'LazyData' is specified without a 'data' directory
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S3 methods shown with full name in documentation object 'BIC.threshold.ggm':
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The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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S3 methods shown with full name in documentation object 'set.scale':
  'scale.dm' 'scale.par'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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qr.X: no visible binding for global variable 'R'
Undefined global functions or variables:
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Found the following significant warnings:
  datablock.h:124:42: warning: pointer used after 'void operator delete(void*)' [-Wuse-after-free]
See 'd:/Rcompile/CRANpkg/local/4.3/MCMCpack.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
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S3 methods shown with full name in documentation object 'complete.miceadds':
  'complete.mids.nmi' 'complete.mids.1chain'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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Running examples in 'migraph-Ex.R' failed
The error most likely occurred in:

> ### Name: core-periphery
> ### Title: Core-periphery clustering algorithms
> ### Aliases: core-periphery node_core
> 
> ### ** Examples
> 
> mpn_elite_usa_advice %>% as_tidygraph %>% 
+   mutate(corep = node_core(mpn_elite_usa_advice)) %>% 
+   autographr(node_color = "corep")
The Rgraphviz package is required to run this function. Would you like to install Rgraphviz from BioConductor? (Yes/no/cancel) 
The BiocManager package is required to run this function. Would you like to install BiocManager from CRAN? (Yes/no/cancel) 
Installing package into 'D:/temp/Rtmp881K6u/RLIBS_20f9827a3a90'
(as 'lib' is unspecified)
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Calls: %>% ... thisRequiresBio -> thisRequires -> <Anonymous> -> contrib.url
Execution halted
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':::' call which should be '::': 'parallel:::detectCores'
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    Bug Fix
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    Function Optimizing
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    Optimization
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    Update Description Files
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Packages which this enhances but not available for checking:
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Packages suggested but not available for checking:
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  'BSgenome.Hsapiens.UCSC.hg19'
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    * efourier with default norm=TRUE now messages about how wrong it may be
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S3 methods shown with full name in documentation object 'pca.plot.wrap':
  'lda.plot.wrap.1'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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Running examples in 'multipanelfigure-Ex.R' failed
The error most likely occurred in:

> ### Name: images
> ### Title: Images
> ### Aliases: images rhino unicorn
> 
> ### ** Examples
> 
> figure <- multi_panel_figure(
+   width = c(60, 40, 40), height = c(40, 40, 40)
+ )
> image_files <- system.file("extdata", package = "multipanelfigure") %>%
+   dir(full.names = TRUE) %>%
+   setNames(basename(.))
> figure %>%
+   fill_panel(image_files["farouq.tiff"]) %>%
+   fill_panel(image_files["unicorn.svg"], column = 2:3) %>%
+   fill_panel(image_files["rhino.jpg"], row = 2:3) %>%
+   fill_panel(image_files["Rlogo.png"], column = 2:3, row = 2:3)
Setting row to 1
Setting column to 1
Warning in warn_about_file.access_under_windows() :
  This function depends on file.access, which can give unexpected results under Windows.
Setting row to 1
Warning in warn_about_file.access_under_windows() :
  This function depends on file.access, which can give unexpected results under Windows.
Error: Rterm.exe: FailedToExecuteCommand `"inkscape" "D:/temp/RtmpoR0Kqb/magick-OiTE4g9oEFOOgaq1qO4fSpPgM7lXdcNF" --export-png="D:/temp/RtmpoR0Kqb/magick-YNM0YqLZGZeiaMZfLzsMdgGsTY7xgBz9.png" --export-dpi="300" --export-background="rgb(100%,100%,100%)" --export-background-opacity="1" > "D:/temp/RtmpoR0Kqb/magick-vomrXfoG8ojbu4zTDfs4AWfa3wPzM17Y" 2>&1' (-1) @ error/delegate.c/ExternalDelegateCommand/514
Execution halted
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    Version (2018-01-22)
    Version  (2017-08-22)
    Version
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Package which this enhances but not available for checking: 'jpndistrict'
Malformed Description field: should contain one or more complete sentences.
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    libs   2.6Mb
    mods   3.3Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/OpenCL.Rcheck/00install.out' for details.
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S3 methods shown with full name in documentation object 'unary_ops':
  'log10.ProcessNode' 'log10.ProcessGraphParameter'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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Running 'testthat.R' [63s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(optimall)
  > 
  > test_check("optimall")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 205 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-optimall_shiny.R:37:3'): App runs ──────────────────────────────
  <webdriver_error/error/condition>
  Error in `session_makeRequest(self, private, endpoint, data, params, headers)`: Unable to find input binding for element with id strata
  Backtrace:
      ▆
   1. └─app$setInputs(...) at test-optimall_shiny.R:37:2
   2.   └─shinytest:::sd_setInputs(...)
   3.     └─private$flushInputs(wait_, timeout_)
   4.       └─shinytest:::sd_flushInputs(self, private, wait, timeout)
   5.         └─private$web$executeScriptAsync(...)
   6.           └─webdriver:::session_executeScriptAsync(...)
   7.             └─private$makeRequest(...)
   8.               └─webdriver:::session_makeRequest(...)
   9.                 └─webdriver:::report_error(response)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 205 ]
  Error: Test failures
  Execution halted
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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S3 methods shown with full name in documentation object 'pamr-internal':
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The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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S3 methods shown with full name in documentation object 'vec_cast.partial_time':
  'vec_cast.partial_time'

S3 methods shown with full name in documentation object 'vec_cast.timespan':
  'vec_cast.timespan'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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S3 methods shown with full name in documentation object 'ped':
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The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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S3 methods shown with full name in documentation object 'format.relation':
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The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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--- re-building 'intro-to-penppml.Rmd' using rmarkdown

Quitting from lines 140-155 [plot regularization path] (intro-to-penppml.Rmd)
Error: processing vignette 'intro-to-penppml.Rmd' failed with diagnostics:
object 'last.bumpup' not found
--- failed re-building 'intro-to-penppml.Rmd'

SUMMARY: processing the following file failed:
  'intro-to-penppml.Rmd'

Error: Vignette re-building failed.
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The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    extdata   9.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinyApp   5.4Mb
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'INLA'
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Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'rcbc'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.3Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    4.7Mb
    libs   1.6Mb
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'LazyData' is specified without a 'data' directory
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installed size is 11.5Mb
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    doc           8.8Mb
    htmlwidgets   2.5Mb
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checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
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Package suggested but not available for checking: 'ProFit'
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    libs      1.2Mb
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installed size is 14.3Mb
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Package suggested but not available for checking: 'cmdstanr'
installed size is  8.0Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
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Found the following significant warnings:
  arch/windows/process_handles.h:100:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  arch/windows/process_handles.c:23:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/ps.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
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    doc        4.0Mb
    examples   2.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
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installed size is  7.3Mb
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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
installed size is  6.2Mb
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    gui          1.6Mb
    staticdocs   3.3Mb
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S3 methods shown with full name in documentation object 'internals':
  'format.perc'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 26.2Mb
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    libs  25.5Mb
'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:
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Package suggested but not available for checking: 'spDataLarge'
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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.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object 'internals':
  'plot.piqr2'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'internals':
  'predict.iqrL.internal'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
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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  7.2Mb
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    extdata   3.3Mb
    libs      2.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.0Mb
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installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    data   3.8Mb
    libs   1.4Mb
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Package suggested but not available for checking: 'fastshp'
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    shiny_app   1.4Mb
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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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installed size is  5.1Mb
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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  7.3Mb
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    htmlwidgets   1.8Mb
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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
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets  10.0Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Problems with news in 'NEWS.md':
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Package suggested but not available for checking: 'googlesheets'
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Package suggested but not available for checking: 'gurobi'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
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'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is  9.5Mb
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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  6.5Mb
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    data   3.9Mb
    libs   1.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> 
> ### ** 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 ?) ========
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installed size is  6.7Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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S3 methods shown with full name in documentation object 'export.default':
  'export.default'

S3 methods shown with full name in documentation object 'export.listpoly':
  'export.listpoly'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
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installed size is 24.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
S3 methods shown with full name in documentation object 'editDataset.design':
  'editDataset.design'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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Package suggested but not available for checking: 'ROpenOffice'
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  8.8Mb
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    doc   4.5Mb
    po    2.4Mb
installed size is  7.5Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rcplex.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
installed size is  8.6Mb
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    libs      1.2Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
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Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.2Mb
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.1Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      1.3Mb
installed size is  8.0Mb
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    include        2.0Mb
    jsonexamples   3.8Mb
    libs           2.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
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':
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'devAll'
'LazyData' is specified without a 'data' directory
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installed size is  5.9Mb
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    libs   2.2Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'DIDmultiplegt'
installed size is  6.5Mb
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    R      4.0Mb
    data   1.5Mb
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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
'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':
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is 10.3Mb
  sub-directories of 1Mb or more:
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installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.1Mb
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installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.0Mb
'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
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installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      1.3Mb
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) calc.relimp.Rd:41: Escaped LaTeX specials: \~
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Package which this enhances but not available for checking: 'Rcplex'
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in 'reReg-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.reReg
> ### Title: Plot the Baseline Cumulative Rate Function and the Baseline
> ###   Cumulative Hazard Function
> ### Aliases: plot.reReg
> ### Keywords: Plots
> 
> ### ** Examples
> 
> data(simDat)
> fm <- Recur(t.start %to% t.stop, id, event, status) ~ x1 + x2
> 
> fit <- reReg(fm, data = simDat, B = 0)
> plot(fit)
> plot(fit, xlab = "Time (days)", smooth = TRUE)
> 
> ## Predicted cumulative rate and hazard given covariates
> newdata <- expand.grid(x1 = 0:1, x2 = mean(simDat$x2))
> plot(fit, newdata = newdata, showName = TRUE)
Error in get(method[[1]]) : object 'last.bumpup' not found
Calls: <Anonymous> ... drawDetails -> drawDetails.dlgrob -> apply.method -> get
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs      1.6Mb
    models    1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
39 8  1    g
40 1  2    j
41 1  1    r
42 4  3    t
43 2  7    g
44 1  6    s
45 6 10    f
46 6  2    a
47 2  4    e
48 7 24    c
49 8  1    g
50 1  2    j
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  9.4 0.36 10 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) CardioRiskFactors.Rd:35: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
installed size is 100.0Mb
  sub-directories of 1Mb or more:
    doc        3.3Mb
    gdal       2.9Mb
    libs      81.6Mb
    pictures   1.3Mb
    proj       8.3Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
'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
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs    2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Specified C++11: please drop specification unless essential
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    lib    3.3Mb
    libs   4.1Mb
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File 'rJava/R/import.R':
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File 'rJava/R/jinit.R':
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    include   2.9Mb
    libs      2.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    extdata  23.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
GNU make is a SystemRequirements.
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    hdf5     16.0Mb
    include   6.5Mb
    lib       2.6Mb
    libs      8.2Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object 'fitted.values.margint':
  'fitted.values.margint'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
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:
+ })
ERROR: Detected objects with duplicated names (A). Only the last occurance of each duplicated object will be available in MATLAB if completed: writeMat.default(filename, A = A, B = B, A = C) 
> 
> 
> ## Not run: 
> ##D # When writing to a stream connection the receiver needs to know on
> ##D # beforehand how many bytes are available. This can be done by using
> ##D # the 'onWrite' argument.
> ##D onWrite <- function(x)
> ##D   writeBin(x$length, con = x$con, size = 4, endian = "little")
> ##D   writeMat(con, A = A, B = B, onWrite = onWrite)
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  171.51 586.36 761.12 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  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs       1.0Mb
    minizinc   2.3Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following significant warnings:
  common_stub.c:74:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/rmumps.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'g++.exe (GCC) 12.2.0'
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
Package suggested but not available for checking: 'rnaturalearthhires'
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\emmintrin.h:131:24: warning: array subscript '__m128d_u[0]' is partly outside array bounds of 'Eigen::internal::plain_matrix_type<Eigen::Product<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>, Eigen::Transpose<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false> >, 0>, Eigen::Dense>::type [1]' {aka 'Eigen::Matrix<double, 1, 1, 0, 1, 1> [1]'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.3/RobustGaSP.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'g++.exe (GCC) 12.2.0'
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              1.3Mb
    simulationStudy   1.6Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/ROracle.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs   1.5Mb
Package suggested but not available for checking: 'RandomFields'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  vendor/boost/intrusive/detail/slist_node.hpp:56:16: warning: pointer used after 'void operator delete(void*, std::size_t)' [-Wuse-after-free]
  vendor/boost/intrusive/detail/hook_traits.hpp:77:10: warning: pointer used after 'void operator delete(void*, std::size_t)' [-Wuse-after-free]
See 'd:/Rcompile/CRANpkg/local/4.3/RPostgres.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'g++.exe (GCC) 12.2.0'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  websockets.c:21:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  standalone.c:160:301: warning: format '%ld' expects argument of type 'long int', but argument 16 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:3788:97: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4133:62: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4435:118: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4804:106: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4824:147: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4836:114: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4864:121: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  Rserv.c:4870:139: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  qap_encode.c:142:17: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'rlen_t' {aka 'long long int'} [-Wformat=]
  websockets.c:513:119: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.3/Rserve.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
GNU make is a SystemRequirements.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
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Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'INLA'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.4Mb
    help   1.4Mb
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.8Mb
    libs   9.5Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    lib    2.0Mb
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is 40.0Mb
  sub-directories of 1Mb or more:
    libs    1.1Mb
    swipl  38.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R           1.4Mb
    bootstrap   1.6Mb
    doc         1.4Mb
    help        2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    rmarkdown   9.4Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object 'printHTML.trackInfo':
  'printHTML.trackInfo'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package which this enhances but not available for checking: 'glmmADMB'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs      5.2Mb
Problems with news in 'NEWS.md':
No news entries found.
S3 methods shown with full name in documentation object 'matmult':
  '%*%.rv'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rWCVPdata'
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) mapBubbles.Rd:62: Escaped LaTeX specials: \$
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
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Package suggested but not available for checking: 'unix'
Specified C++14: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  6.5Mb
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    libs   5.4Mb
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
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No news entries found.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
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checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  13.4Mb
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installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   1.3Mb
Package suggested but not available for checking: 'networkTomography'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'santoku-cast':
  'santoku_cast_common.default' 'santoku_cast_common.double'
  'santoku_cast_common.Date' 'santoku_cast_common.POSIXct'
  'santoku_cast_common.ts' 'santoku_cast_common.zoo'
  'santoku_cast_common.integer64' 'santoku_cast_common.hexmode'
  'santoku_cast_common.octmode'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'FitARMA'
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checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
'library' or 'require' call to 'progress' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin   5.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'DuoClustering2018'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'ssvd'
Unexported object imported by a ':::' call: 'simplifyEnrichment:::is_GO_id'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'plot':
  'plot.discretization'

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

S3 methods shown with full name in documentation object 'summary':
  'summary.discretization'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: 'INLA'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Package unavailable to check Rd xrefs: 'INLA'
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   2.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spgrass6'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'min.abs':
  'min.abs'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) fahst.rd:39: Escaped LaTeX specials: \^
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GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Aliases: contrast-theory Intensity Luminance
> 
> ### ** Examples
> 
> Intensity(color = c('black', 'white', '#E76BF3'))
  black   white #E76BF3 
   0.00  255.00  159.58 
> 
> Luminance(color = c('black', 'white', '#E76BF3'))
    black     white   #E76BF3 
0.0000000 1.0000000 0.3397538 
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  78.77 1.51 80.29 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
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'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown

Quitting from lines 44-48 [unnamed-chunk-3] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `loadNamespace()`:
! there is no package called 'prettymapr'
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
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    doc      1.7Mb
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    libs    83.1Mb
    proj     8.3Mb
    sqlite   1.5Mb
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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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    doc   5.0Mb
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installed size is  9.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
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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
Problems with news in 'NEWS.md':
No news entries found.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    www   8.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/SIGN.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
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No news entries found.
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GNU make is a SystemRequirements.
Package suggested but not available for checking: 'BSgenome.Hsapiens.UCSC.hg38'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'fg_step_tab_pp'
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Version (Date)
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No news entries found.
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'LazyData' is specified without a 'data' directory
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Package which this enhances but not available for checking: 'kmndirs'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
installed size is  5.5Mb
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Package suggested but not available for checking: 'gurobi'
GNU make is a SystemRequirements.
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Unknown package 'InformationValue' in Rd xrefs
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'lseq'
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.solveEnv'
installed size is  5.5Mb
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S3 methods shown with full name in documentation object 'plot.predictions':
  'plot.predictions'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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installed size is  6.2Mb
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Package suggested but not available for checking: 'NLMR'
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Unknown package 'sparsebn' in Rd xrefs
'LazyData' is specified without a 'data' directory
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No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
installed size is 14.5Mb
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    help   1.7Mb
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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:
 3 <split [11/2]> Fold03
 4 <split [17/2]> Fold04
 5 <split [17/2]> Fold05
 6 <split [10/2]> Fold06
 7 <split [11/2]> Fold07
 8 <split [14/2]> Fold08
 9 <split [11/2]> Fold09
10 <split [10/2]> Fold10
> data(ames, package = "modeldata")
> ames_sf <- sf::st_as_sf(ames, coords = c("Longitude", "Latitude"), crs = 4326)
> ames_neighborhoods <- spatial_leave_location_out_cv(ames_sf, Neighborhood)
> ## End(Don't show)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  9.2 0.61 9.82 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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Depends: includes the non-default packages:
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  'spatstat.model', 'spatstat.linnet', 'spatstat.data', 'spatstat',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'

Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package unavailable to check Rd xrefs: 'RandomFields'
Packages suggested but not available for checking:
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Package unavailable to check Rd xrefs: 'RandomFields'
Depends: includes the non-default packages:
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  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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installed size is  6.5Mb
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installed size is  8.5Mb
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    etc   1.4Mb
Problems with news in 'NEWS.md':
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    Roadmap of specklestar package
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Running examples in 'spinifex-Ex.R' failed
The error most likely occurred in:

> ### Name: wine
> ### Title: The wine dataset from the UCI Machine Learning Repository.
> ### Aliases: wine
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(spinifex)
> str(wine)
'data.frame':	178 obs. of  14 variables:
 $ Type           : Factor w/ 3 levels "1","2","3": 1 1 1 1 1 1 1 1 1 1 ...
 $ Alcohol        : num  14.2 13.2 13.2 14.4 13.2 ...
 $ Malic          : num  1.71 1.78 2.36 1.95 2.59 1.76 1.87 2.15 1.64 1.35 ...
 $ Ash            : num  2.43 2.14 2.67 2.5 2.87 2.45 2.45 2.61 2.17 2.27 ...
 $ Alcalinity     : num  15.6 11.2 18.6 16.8 21 15.2 14.6 17.6 14 16 ...
 $ Magnesium      : int  127 100 101 113 118 112 96 121 97 98 ...
 $ Phenols        : num  2.8 2.65 2.8 3.85 2.8 3.27 2.5 2.6 2.8 2.98 ...
 $ Flavanoids     : num  3.06 2.76 3.24 3.49 2.69 3.39 2.52 2.51 2.98 3.15 ...
 $ Nonflavanoids  : num  0.28 0.26 0.3 0.24 0.39 0.34 0.3 0.31 0.29 0.22 ...
 $ Proanthocyanins: num  2.29 1.28 2.81 2.18 1.82 1.97 1.98 1.25 1.98 1.85 ...
 $ Color          : num  5.64 4.38 5.68 7.8 4.32 6.75 5.25 5.05 5.2 7.22 ...
 $ Hue            : num  1.04 1.05 1.03 0.86 1.04 1.05 1.02 1.06 1.08 1.01 ...
 $ Dilution       : num  3.92 3.4 3.17 3.45 2.93 2.85 3.58 3.58 2.85 3.55 ...
 $ Proline        : int  1065 1050 1185 1480 735 1450 1290 1295 1045 1045 ...
> dat  <- scale_sd(wine[, 2:6])
> clas <- wine$Type
> 
> bas <- basis_pca(dat)
> mv  <- manip_var_of(bas)
> mt  <- manual_tour(bas, mv)
> 
> ggt <- ggtour(mt, dat, angle = .2) +
+   proto_default(aes_args = list(color = clas, shape = clas))
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  55.98 1.53 57.5 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
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Problems with news in 'NEWS.md':
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    Feature Changes
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installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
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  Cannot extract version info from the following section titles:
    updates of 10th May 2021
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
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installed size is  5.4Mb
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installed size is 16.3Mb
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installed size is  6.3Mb
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    libs   5.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
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GNU make is a SystemRequirements.
installed size is  5.7Mb
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    libs   4.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    To do
Package suggested but not available for checking: 'starsdata'
installed size is  6.3Mb
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checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
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installed size is  5.1Mb
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    libs   1.4Mb
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File 'statnet.common/R/control.utilities.R':
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: 'networksis'
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'INLA'
installed size is 14.5Mb
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Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: 'StrathE2E2examples'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
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installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'STRaitRazoR'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'size.penalize':
  'size.penalize'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.3Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'extraTrees'
Unknown package 'extraTrees' in Rd xrefs
Package suggested but not available for checking: 'extraTrees'
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surfaceSimulate : phytransform: no visible global function definition
  for 'rescale'
Undefined global functions or variables:
  rescale
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'INLA', 'gpclib'
installed size is  7.5Mb
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    doc    2.2Mb
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: 'distr6'
Unknown package 'distr6' in Rd xrefs
installed size is  8.1Mb
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    R      1.2Mb
    data   1.9Mb
    doc    3.9Mb
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installed size is 12.1Mb
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    data  12.0Mb
installed size is  6.0Mb
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    doc   5.5Mb
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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Error(s) in re-building vignettes:
--- re-building 'svHttp.Rmd' using rmarkdown
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installed size is  5.7Mb
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Package suggested but not available for checking: 'swephRdata'
Problems with news in 'NEWS.md':
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    Additional functions and data sets
    Amendments to functions
'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)
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Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
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installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
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installed size is  5.2Mb
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    extdata   3.1Mb
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installed size is  6.0Mb
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    libs   1.4Mb
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installed size is  6.1Mb
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No news entries found.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'designMatrices':
  'print.designMatrices'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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installed size is  6.2Mb
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installed size is  6.3Mb
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installed size is 22.1Mb
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    tessdata  14.0Mb
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Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
installed size is  5.2Mb
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installed size is  7.5Mb
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    data   2.6Mb
    doc    3.0Mb
    libs   1.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    data   5.6Mb
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Problems with news in 'NEWS.md':
No news entries found.
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Unknown package 'textreadr' in Rd xrefs
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
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    data   1.1Mb
    rda    7.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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    R      4.1Mb
    data   3.0Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes:
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
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    doc       1.9Mb
    extdata   4.5Mb
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Found the following significant warnings:
  common.c:36:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/tiff.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
installed size is 19.6Mb
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checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
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No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is  6.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
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    doc    1.9Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.8Mb
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    examples  12.6Mb
    include    3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
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'LazyData' is specified without a 'data' directory
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installed size is  7.7Mb
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    libs   7.5Mb
installed size is  6.4Mb
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    data-tables   1.4Mb
    doc           1.9Mb
    help          1.2Mb
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Package suggested but not available for checking: 'corpus.JSS.papers'
Packages suggested but not available for checking:
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installed size is  7.2Mb
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    data   7.2Mb
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    R         5.5Mb
    help      1.6Mb
    include   3.4Mb
    libs     17.9Mb
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Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'taxidata'
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installed size is 15.9Mb
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    libs  13.2Mb
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR'
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'TreeDistData'
installed size is  6.7Mb
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    libs   1.2Mb
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug fixes
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
installed size is  5.6Mb
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    doc        1.3Mb
    libs       1.1Mb
installed size is 17.6Mb
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    data      1.3Mb
    doc       1.3Mb
    extdata  14.8Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.2Mb
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    doc    3.9Mb
    libs   7.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'log2console'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'tsibble-vctrs':
  'vec_ptype2.tbl_ts' 'vec_cast.tbl_ts' 'vec_cast.yearmonth'
  'vec_ptype2.yearmonth' 'vec_cast.yearquarter'
  'vec_ptype2.yearquarter' 'vec_cast.yearweek' 'vec_ptype2.yearweek'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
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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
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
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'sl3'
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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.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  9.9Mb
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    doc     7.1Mb
    ubinc   2.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.0Mb
    libs   4.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
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    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.5Mb
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Aliases: variantQC
> 
> ### ** Examples
> 
> ## Not run: 
> ##D variantQC(snpQcFile=covid_example("sim_ukb_snp_qc.txt.gz"), 
> ##D mfiDir=covid_example("alleleFreqs"), 
> ##D mafFilt=0.001, 
> ##D infoFilt=0.5, 
> ##D outDir=covid_example("results"))
> ## End(Not run)
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3.14 0.2 3.36 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
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Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
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Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.4Mb
    libs  14.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'USA.state.boundaries.data'
installed size is  6.1Mb
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    data   6.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    doc   3.8Mb
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installed size is  7.0Mb
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Found the following significant warnings:
  randutils.c:60:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/uuid.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
installed size is 17.2Mb
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Problems with news in 'NEWS.md':
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Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
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installed size is 97.1Mb
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checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
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installed size is  8.5Mb
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'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'vdg.Rnw' using knitr

Quitting from lines 239-244 [spv-example] (vdg.Rnw)
Error: processing vignette 'vdg.Rnw' failed with diagnostics:
there is no package called 'tinytex'
--- failed re-building 'vdg.Rnw'

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

Error: Vignette re-building failed.
Execution halted
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S3 methods shown with full name in documentation object 'syntab':
  'print.syntab'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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'LazyData' is specified without a 'data' directory
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installed size is  5.2Mb
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installed size is  6.8Mb
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Problems with news in 'NEWS.md':
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    NEW FEATURES
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installed size is  6.6Mb
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GNU make is a SystemRequirements.
installed size is 10.7Mb
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installed size is  5.8Mb
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installed size is  6.0Mb
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installed size is  6.8Mb
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
installed size is 21.0Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
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
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checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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Running 'spelling.R' [0s]
  Running 'testthat.R' [42s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(vroom)
  
  Attaching package: 'vroom'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("vroom")
  Error in x$add_result(...) : attempt to apply non-function
  Calls: test_check ... <Anonymous> -> o_apply -> lapply -> FUN -> <Anonymous>
  Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'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     1.2Mb
    doc   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'prepr'
Problems with news in 'NEWS.md':
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'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
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Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'QIC.gee':
  'QIC.gee'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
Package suggested but not available for checking: 'anomalize'
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
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Specified C++11: please drop specification unless essential
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.6Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is 12.7Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is 11.2Mb
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installed size is 11.4Mb
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    data  11.3Mb
installed size is 11.2Mb
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    data  11.1Mb
Malformed Title field: should not end in a period.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    java  24.5Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) read.npc.vpc.results.Rd:16: Escaped LaTeX specials: \_
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'zdat'
Problems with news in 'NEWS.md':
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    NEW DEPENDENCIES
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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 31.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.4Mb
  sub-directories of 1Mb or more:
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    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 95.9Mb
  sub-directories of 1Mb or more:
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'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 11.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
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    libs   5.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
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Packages suggested but not available for checking:
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installed size is  5.0Mb
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Namespace in Imports field not imported from: ‘svglite’
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Namespace in Imports field not imported from: ‘tidyr’
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Packages required but not available:
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
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installed size is  8.4Mb
  sub-directories of 1Mb or more:
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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
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
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installed size is  5.8Mb
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installed size is  5.5Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data  10.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Package suggested but not available for checking: ‘HiTC’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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installed size is  6.3Mb
  sub-directories of 1Mb or more:
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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  6.2Mb
  sub-directories of 1Mb or more:
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'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:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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Namespaces in Imports field not imported from:
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  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  7.9Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package which this enhances but not available for checking: ‘asreml’
installed size is  9.0Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Note: found 53 marked UTF-8 strings
installed size is  8.0Mb
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'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 apparent S3 methods exported but not registered:
  print.amAlleleFreq print.amDataset summary.amCluster
  summary.amPairwise summary.amUnique
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
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'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
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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 31.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  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:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 36.1Mb
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Package suggested but not available for checking: ‘rhdf5’
installed size is  5.7Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 16.4Mb
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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:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.2Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
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installed size is  6.7Mb
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installed size is  5.8Mb
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Running ‘testthat.R’ [21s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-DT-tbl.R:6:3', 'test-color-signature.R:64:3',
    'test-fix-find-overlap.R:40:3', 'test-fix-find-overlap.R:89:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-mutate_profile.R:23:3'): transform & mutate_profile ──────────
  all(res$sumrelthickness == 1) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 1430 ]
  Error: Test failures
  Execution halted
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
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Namespace in Imports field not imported from: ‘sp’
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
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Packages unavailable to check Rd xrefs: ‘affxparser’, ‘oligo’, ‘oligoClasses’
Packages suggested but not available for checking:
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'LazyData' is specified without a 'data' directory
installed size is 97.1Mb
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installed size is  5.8Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
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'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
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Package which this enhances but not available for checking: ‘asreml’
installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘asteRiskData’
installed size is  5.6Mb
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GNU make is a SystemRequirements.
installed size is  6.5Mb
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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:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Note: found 552 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
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:
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'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
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Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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Namespace in Imports field not imported from: ‘openssl’
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Namespace in Imports field not imported from: ‘curl’
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Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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Namespace in Imports field not imported from: ‘R6’
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Package suggested but not available for checking: ‘lixoftConnectors’
Note: found 64209 marked UTF-8 strings
Note: found 133353 marked UTF-8 strings
installed size is  6.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
installed size is 91.9Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 87.9Mb
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GNU make is a SystemRequirements.
installed size is 59.5Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument>  \text 
                  {E}[s_i|\omega ,y_{ij}]=\exp ({f(y_{ij},\omega )}) 
l.307   }{}
           
! Undefined control sequence.
<argument> ...athcal {N}(\boldsymbol {\mu }^\text 
                                                  {T}\boldsymbol {K},\sigma ...
l.609   }{}
           
! Undefined control sequence.
<argument> P(\text 
                   {\textbf {error}})=2\Phi (-\left |\boldsymbol {\mu }_{\bo...
l.615 ...dot\boldsymbol{\tau}_{\boldsymbol{D}})}{}
                                                  
! Undefined control sequence.
<argument> \alpha \sim \text 
                             {Half-Cauchy}(25)
l.707 \deqn{\alpha\sim\text{Half-Cauchy}(25)}{}
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
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installed size is  5.7Mb
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Package suggested but not available for checking: ‘fdpbandsdata’
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
Note: found 148 marked UTF-8 strings
Package suggested but not available for checking: ‘ArrayExpress’
'LazyData' is specified without a 'data' directory
installed size is 19.6Mb
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installed size is  9.4Mb
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installed size is  8.3Mb
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installed size is 13.6Mb
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Namespace in Imports field not imported from: ‘splines’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Namespace in Imports field not imported from: ‘vtable’
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installed size is 66.2Mb
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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
installed size is 41.5Mb
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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installed size is 97.8Mb
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
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installed size is  5.4Mb
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Namespaces in Imports field not imported from:
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Package suggested but not available for checking: ‘INLA’
installed size is 12.2Mb
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installed size is 70.3Mb
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
installed size is 53.9Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
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installed size is  8.7Mb
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GNU make is a SystemRequirements.
installed size is 11.4Mb
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installed size is 16.9Mb
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Namespace in Imports field not imported from: ‘FastGP’
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installed size is 27.2Mb
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installed size is  8.1Mb
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Note: found 1924 marked UTF-8 strings
installed size is 86.3Mb
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
installed size is 16.7Mb
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Namespace in Imports field not imported from: ‘dplyr’
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
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'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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Error(s) in re-building vignettes:
--- re-building ‘article.Rnw’ using Sweave
Setting levels: control = No, case = Yes
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-7
Setting levels: control = No, case = Yes
Setting levels: control = No, case = Yes
Loading required package: Biostrings
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated,
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    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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand, unname

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

    I, expand.grid, unname

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

Attaching package: 'Biostrings'

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

    strsplit

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

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

Error: Vignette re-building failed.
Execution halted
installed size is 34.1Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Namespaces in Imports field not imported from:
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installed size is  5.4Mb
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Package suggested but not available for checking: ‘BRugs’
Namespaces in Imports field not imported from:
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Package suggested but not available for checking: ‘webshot2’
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Note: found 72 marked UTF-8 strings
Namespace in Imports field not imported from: ‘DT’
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installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘flowCore’
installed size is 96.7Mb
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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installed size is  7.8Mb
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'LazyData' is specified without a 'data' directory
installed size is 48.1Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 15.3Mb
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'LazyData' is specified without a 'data' directory
installed size is 42.6Mb
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Namespace in Imports field not imported from: ‘rstantools’
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.8Mb
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GNU make is a SystemRequirements.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \text 
                      
l.267 \eqn{\text{logit}^{-1}(p) \sim N(2,5)}{}
                                               which produces a mean reporti...
installed size is 51.9Mb
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GNU make is a SystemRequirements.
installed size is 27.9Mb
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Namespace in Imports field not imported from: ‘BiDAG’
  All declared Imports should be used.
installed size is 60.6Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
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'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
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Note: found 582 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is 163.8Mb
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installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
installed size is  9.8Mb
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Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
installed size is  5.6Mb
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Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
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installed size is  6.3Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
installed size is  7.2Mb
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installed size is  9.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
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installed size is 12.0Mb
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Namespace in Imports field not imported from: ‘rmio’
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Namespace in Imports field not imported from: ‘survival’
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Namespace in Imports field not imported from: ‘tibble’
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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  5.9Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 92.3Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘msa’
installed size is  6.3Mb
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installed size is  6.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
Package required but not available: ‘MEIGOR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
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installed size is  8.2Mb
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Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  6.1Mb
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Note: found 46 marked UTF-8 strings
Package listed in more than one of Depends, Imports, Suggests, Enhances:
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A package should be listed in only one of these fields.
Packages in Depends field not imported from:
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  These packages need to be imported from (in the NAMESPACE file)
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  6.5Mb
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installed size is 38.6Mb
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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Package suggested but not available for checking: ‘cmdstanr’
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  8.6Mb
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'LazyData' is specified without a 'data' directory
installed size is 36.4Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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installed size is 14.1Mb
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Namespace in Imports field not imported from: ‘shiny’
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
installed size is 139.5Mb
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GNU make is a SystemRequirements.
installed size is 95.2Mb
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
installed size is 48.3Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 92.6Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  7.0Mb
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Namespace in Imports field not imported from: ‘dplyr’
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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Package suggested but not available for checking: ‘sangerseqR’
installed size is 13.1Mb
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installed size is 373.3Mb
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GNU make is a SystemRequirements.
installed size is 99.6Mb
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Namespace in Imports field not imported from: ‘sna’
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Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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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
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
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Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.1Mb
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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
installed size is  8.0Mb
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installed size is  5.4Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘cmdstanr’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘glmmADMB’
Package required but not available: ‘DiffBind’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 11.5Mb
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GNU make is a SystemRequirements.
installed size is 33.5Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 117.7Mb
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installed size is  8.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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'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:
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installed size is  6.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
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installed size is 22.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘doMPI’
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 53.9Mb
  sub-directories of 1Mb or more:
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installed size is 43.2Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  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
'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.
installed size is 62.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Note: found 58 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘org.Dr.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
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Note: found 287 marked UTF-8 strings
Package required but not available: ‘bluster’

Package suggested but not available for checking: ‘scran’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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installed size is 11.1Mb
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Note: found 1 marked UTF-8 string
installed size is  7.8Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
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installed size is 37.8Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  5.8Mb
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...}} \lbrace \xi _{i,j} w_{i,j} \text 
                                                  {exp}(\eta ' A_{i,j}) A_{i...
l.272 ...A_{i,j}) A_{i,j} - A_{i,j} \rbrace = 0}{}
                                                  ,
! Undefined control sequence.
<argument> w_{i,j} \text 
                         {exp}(\hat \eta ' A_{i,j})
l.279 ...w_{i,j} \text{exp}(\hat \eta' A_{i,j})}{}
                                                  , and
! Undefined control sequence.
<argument> ...}} \lbrace \xi _{i,j} w_{i,j} \text 
                                                  {exp}(\hat \eta ' A_{i,j})...
l.281 ...p}(\hat \eta' A_{i,j}) A_{i,j} \rbrace}{}
                                                  
! Undefined control sequence.
<argument> ...}} \lbrace \xi _{i,j} V_{i,j} \text 
                                                  {exp}( \gamma ' B_{i,j}) B...
l.1093 ...i,j} - \xi_{i,j} B_{i,j} \rbrace = 0,}{}
                                                  
! Undefined control sequence.
<recently read> \text 
                      
l.1100 ...\eqn{\text{exp}(\hat \gamma' B_{i,j})}{}
                                                  ,
! Undefined control sequence.
<argument> ...^{n^{(j)}} \xi _{i,j} V_{i,j} \text 
                                                  {exp}(\hat \gamma ' B_{i,j...
l.1101 ...xt{exp}(\hat \gamma' B_{i,j}) B_{i,j}}{}
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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installed size is 38.0Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  7.6Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
installed size is 40.0Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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installed size is  6.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 163.3Mb
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GNU make is a SystemRequirements.
Running examples in ‘cbsodataR-Ex.R’ failed
The error most likely occurred in:

> ### Name: cbs_get_catalogs
> ### Title: Retrieves the possible catalog values that can be used for
> ###   retrieving data
> ### Aliases: cbs_get_catalogs
> 
> ### ** Examples
> 
> catalogs <- cbs_get_catalogs()
Warning in readBin(3L, raw(0), 32768L) :
  URL 'https://opendata.cbs.nl/ODataCatalog/Tables?$format=json': Timeout of 60 seconds was reached
Warning: Failing: http://opendata.cbs.nl/ODataCatalog/Tables?$format=json
Retrying...
Warning in readBin(3L, raw(0), 32768L) :
  URL 'https://opendata.cbs.nl/ODataCatalog/Tables?$format=json': Timeout of 60 seconds was reached
Error in readBin(3L, raw(0), 32768L) : cannot read from connection
Calls: cbs_get_catalogs ... parse_and_simplify -> parseJSON -> parse_con -> readBin
Execution halted
installed size is 18.4Mb
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Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 22.4Mb
  sub-directories of 1Mb or more:
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.1Mb
    libs  10.2Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
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Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘batchtools’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘htmltools’
  ‘jsonlite’ ‘magrittr’ ‘methods’ ‘plotly’ ‘reshape’ ‘rlang’ ‘shiny’
  ‘shinyWidgets’ ‘shinyjqui’ ‘shinyjs’ ‘shinymaterial’ ‘sortable’ ‘ssh’
  ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.9Mb
  sub-directories of 1Mb or more:
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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bench’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'GenomicInteractions', 'GenomicRanges', 'Gviz', 'countreg'
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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installed size is 18.0Mb
  sub-directories of 1Mb or more:
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'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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R         2.8Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Packages required but not available:
  'ChIPseeker', 'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 28982 marked UTF-8 strings
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘networkD3’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.5Mb
    libs   1.2Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...{C}=c\mathbf {U}\cdot \operatorname 
                                                  {diag}(\mathbf {s}) + \mat...
l.149 \mathbf{1}\,\mathbf{o}^T}{}
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Package required but not available: ‘IsoGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Namespaces in Imports field not imported from:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
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
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FNN’ ‘R.utils’ ‘SearchTrees’ ‘colorspace’ ‘colourpicker’
  ‘data.table’ ‘fields’ ‘mapproj’ ‘maps’ ‘maptools’ ‘ncdf4’ ‘raster’
  ‘rworldxtra’ ‘shinyFiles’ ‘shinyWidgets’ ‘shinyjs’ ‘shinythemes’ ‘sp’
  ‘tcltk’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.9Mb
  sub-directories of 1Mb or more:
    libs  34.6Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package required but not available: ‘GenomicInteractions’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   3.9Mb
Package suggested but not available for checking: ‘disttree’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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’
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
Note: found 4186 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 742 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘colorspace-Ex.R’ failed
The error most likely occurred in:

> ### Name: scale_colour_binned_diverging
> ### Title: HCL-Based Binned Diverging Color Scales for ggplot2
> ### Aliases: scale_colour_binned_diverging scale_color_binned_diverging
> ###   scale_fill_binned_diverging
> 
> ### ** Examples
> 
> # adapted from stackoverflow: https://stackoverflow.com/a/20127706/4975218
> 
> library("ggplot2")
Error: package or namespace load failed for ‘ggplot2’:
 .onAttach failed in attachNamespace() for 'ggplot2', details:
  call: loadNamespace(x)
  error: there is no package called ‘withr’
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  15.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘CAM’
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  28.4Mb
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Note: found 92 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘lwgeom’ ‘s2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
installed size is 62.6Mb
  sub-directories of 1Mb or more:
    libs  61.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   2.6Mb
    libs   3.3Mb
Packages required and available but unsuitable versions:
  'stats', 'grDevices'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘cec2005benchmark’
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs          2.8Mb
    sample_data   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> \log _2 \dfrac 
                          {f_1 + \frac 12}{n_1 + \frac 12} - \log _2 \dfrac ...
l.1526           }{}
                    
! Undefined control sequence.
<argument> ...2}{n_1 + \frac 12} - \log _2 \dfrac 
                                                  {f_2 + \frac 12}{n_2 + \fr...
l.1526           }{}
                    
! Undefined control sequence.
<argument>  \dfrac 
                   {10^6 \cdot \frac {f_1}{n_1} + \lambda }{10^6 \cdot \frac...
l.1554           }{}
                    
! Undefined control sequence.
<argument> z := \dfrac 
                       {k - np}{\sqrt {n p (1-p)}} 
l.2597 ... := \dfrac{k - np}{\sqrt{n p (1-p)}} }{}
'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:
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProData’
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
Note: found 59 marked UTF-8 strings
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.2Mb
    doc    1.3Mb
    help   2.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.7Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘colourpicker’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Note: found 1934235 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Aux_info_data.Rmd’ using rmarkdown
--- finished re-building ‘Aux_info_data.Rmd’

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

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

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

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

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

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

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

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

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

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

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

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

Quitting from lines 68-97 [using offset] (time_series_offset.Rmd)
Error: processing vignette 'time_series_offset.Rmd' failed with diagnostics:
Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `as.Date.numeric()`:
! 'origin' must be supplied
--- failed re-building ‘time_series_offset.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
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
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘SeqArray’

Package suggested but not available for checking: ‘GENESIS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cplm.Rnw’ using Sweave
Loading required package: coda
Loading required package: Matrix
Loading required package: splines
Error: processing vignette 'cplm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cplm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cplm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.2Mb
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer3’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 500 marked UTF-8 strings
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    libs  26.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
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
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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1350 marked UTF-8 strings
installed size is 154.4Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    data    1.5Mb
    libs  149.6Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘IRanges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘pbdMPI’
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'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: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    doc    1.2Mb
    help   1.0Mb
    libs   4.8Mb
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  23.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    docs          1.0Mb
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘plyr’ ‘simpleboot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 109157 marked UTF-8 strings
Note: found 2020 marked UTF-8 strings
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 212 marked Latin-1 strings
  Note: found 12719 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   4.1Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 8 marked Latin-1 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs    1.4Mb
    tests   1.5Mb
Package suggested but not available for checking: ‘msa’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
'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
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
Package required and available but unsuitable version: ‘methods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dblog’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘RedeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘lubridate’ ‘tseries’
  All declared Imports should be used.
Note: found 122 marked UTF-8 strings
Package suggested but not available for checking: ‘BRugs’
Package suggested but not available for checking: ‘INLA’
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    libs  51.7Mb
Note: found 38 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \operatorname 
                              
l.514 \eqn{\operatorname{supp} D = \{0,1\}}{}
                                             , \eqn{E[U\vert D, X] = 0}{}, and
! Undefined control sequence.
<recently read> \operatorname 
                              
l.914 ...p} D = \operatorname{supp} Z = \{0,1\}}{}
                                                  ,
! Undefined control sequence.
<argument> \operatorname {supp} D = \operatorname 
                                                  {supp} Z = \{0,1\}
l.914 ...p} D = \operatorname{supp} Z = \{0,1\}}{}
                                                  ,
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...ilon _t(i) \right )= \left ( \dfrac 
                                                  {1}{\sqrt {p}}\sqrt {\sum ...
l.551     }{}
             
! Undefined control sequence.
<argument> ...}\sqrt {\sum _{j=1}^p \left (\dfrac 
                                                  {\left [\hat {\mathbf {x}}...
l.551     }{}
             
! Undefined control sequence.
<argument> ...sigma }_j^{(x)}}\right )^2}, \dfrac 
                                                  {1}{\sqrt {R}}\sqrt {\sum ...
l.551     }{}
             
! Undefined control sequence.
<argument> ...}\sqrt {\sum _{r=1}^R \left (\dfrac 
                                                  {\hat {{t}}_i^{(r)}} {\hat...
l.551     }{}
             
! Undefined control sequence.
<argument>  \hat {\mathbf {x}}_i = \dfrac 
                                          {1}{R}(\mathbf {x}_i-\hat {\boldsy...
l.561     }{}
             
! Undefined control sequence.
<argument> \hat {\sigma }_r^2=\dfrac 
                                     {1}{n}\sum _{j=1}^n\left ((\mathbf {x}_...
l.566     \mathbf{u}_r\right)^2}{}
                                   is thus the estimated empirical variance of
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  35.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 5764 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.8Mb
    help   1.6Mb
    libs   3.2Mb
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'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.2Mb
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.7Mb
GNU make is a SystemRequirements.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  14.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Note: found 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
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘zinbwave’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
installed size is 58.3Mb
  sub-directories of 1Mb or more:
    libs  57.5Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:158:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  
  [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
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
Namespaces in Imports field not imported from:
  ‘ggmulti’ ‘loon’ ‘loon.data’ ‘loon.ggplot’ ‘loon.shiny’ ‘loon.tourr’
  ‘stats’ ‘zenplots’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Package suggested but not available for checking: ‘BOLTSSIRR’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    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 19.8Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs  12.7Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
Note: found 100 marked UTF-8 strings
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘doMPI’
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘parallel’ ‘rgdal’ ‘sp’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’
  All declared Imports should be used.
installed size is 65.8Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  64.2Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> f:\mathbb 
                     {R}^K -> \mathbb {R}^L, (x_{n1},x_{n2},...,x_{nK}) -> f...
l.2519 ..._{nK}) -> f(x_{n1},x_{n2},...,x_{nK})}{}
                                                   be differentiable up to o...
! Undefined control sequence.
<argument> f:\mathbb {R}^K -> \mathbb 
                                      {R}^L, (x_{n1},x_{n2},...,x_{nK}) -> f...
l.2519 ..._{nK}) -> f(x_{n1},x_{n2},...,x_{nK})}{}
                                                   be differentiable up to o...
Package suggested but not available for checking: ‘dsBaseClient’
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.4Mb
'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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.7Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.3Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.0Mb
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 309.0Mb
  sub-directories of 1Mb or more:
    libs  308.3Mb
'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: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    R      3.3Mb
    data   8.5Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
Namespaces in Imports field not imported from:
  ‘NatureSounds’ ‘av’ ‘magrittr’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   3.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   8.5Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘eaf/libs/eaf.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘eaf/io.o’, ‘mo-tools/hv.o’
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘eaf/io.o’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AnnotationDbi', 'org.Hs.eg.db', 'qvalue'
Package unavailable to check Rd xrefs: ‘AnnotationDbi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qcr’
  All declared Imports should be used.
'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
Error: package or namespace load failed for ‘echarty’:
 .onLoad failed in loadNamespace() for 'echarty', details:
  call: loadNamespace(x)
  error: there is no package called ‘shiny’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
installed size is 107.8Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘opGMMassessment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 27.2Mb
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'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
Package suggested but not available for checking: ‘eggCountsExtra’
installed size is 91.4Mb
  sub-directories of 1Mb or more:
    libs  90.7Mb
GNU make is a SystemRequirements.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(EGRETci)
  > test_check("EGRETci")
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (10)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('tests_boot_tests.R:112:3'): paVector ──────────────────────────────
  `paIndexWinter` not equal to 11:13.
  Lengths differ: 4 is not 3
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  Error: Test failures
  Execution halted
installed size is 11.5Mb
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'LazyData' is specified without a 'data' directory
installed size is 142.4Mb
  sub-directories of 1Mb or more:
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installed size is 47.2Mb
  sub-directories of 1Mb or more:
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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
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
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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
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 60.4Mb
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Note: found 155 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
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installed size is 19.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
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installed size is  7.0Mb
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Note: found 16919 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 23639 marked Latin-1 strings
Namespace in Imports field not imported from: ‘BBmisc’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  6.1Mb
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Package suggested but not available for checking: ‘epidict’
installed size is 128.7Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 11.4Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mzR’
installed size is  5.6Mb
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installed size is  8.3Mb
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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 13.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.6Mb
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'LazyData' is specified without a 'data' directory
Packages required and available but unsuitable versions: 'stats', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
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installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
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Package suggested but not available for checking: ‘ExactData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 342 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is 14.1Mb
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'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.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 90.4Mb
  sub-directories of 1Mb or more:
    libs  88.2Mb
GNU make is a SystemRequirements.
installed size is  5.0Mb
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    images   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘exuberdata’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
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Error(s) in re-building vignettes:
--- re-building ‘jss.Rmd’ using rmarkdown
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
Error: processing vignette 'jss.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.2/fairadapt.Rcheck/vign_test/fairadapt/vignettes/jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
--- failed re-building ‘jss.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  6.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.1Mb
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Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

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

Probably some imports need to be declared in the NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
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installed size is 10.3Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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installed size is 47.4Mb
  sub-directories of 1Mb or more:
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
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installed size is 40.0Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘coxKM’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
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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  9.3Mb
  sub-directories of 1Mb or more:
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installed size is 17.8Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
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.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
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installed size is  7.5Mb
  sub-directories of 1Mb or more:
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    libs   5.5Mb
Package suggested but not available for checking: ‘NNLM’
installed size is 11.0Mb
  sub-directories of 1Mb or more:
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    libs   5.1Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is 14.2Mb
  sub-directories of 1Mb or more:
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Unexported objects imported by ':::' calls:
  ‘fdapace:::GCVLwls1D1’ ‘fdapace:::GetSmoothedMeanCurve’
  ‘fdapace:::HandleNumericsAndNAN’ ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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installed size is 40.2Mb
  sub-directories of 1Mb or more:
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installed size is 11.5Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
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Note: found 76 marked UTF-8 strings
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘panelView’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
'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
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.8Mb
    libs      1.3Mb
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MicrobeDS’
installed size is 39.8Mb
  sub-directories of 1Mb or more:
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installed size is  6.2Mb
  sub-directories of 1Mb or more:
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installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R         5.0Mb
    doc       2.1Mb
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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
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.6Mb
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installed size is  8.2Mb
  sub-directories of 1Mb or more:
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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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      2.4Mb
    extdata   2.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is 34.2Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 30.2Mb
  sub-directories of 1Mb or more:
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    libs  19.5Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Misplaced alignment tab character &.
<argument> ...} \pi + \frac {(1-\pi )}{\zeta (s)}&
                                                  ,k=0, \\ \frac {(1-\pi )k^...
l.512 }{}
         
! Misplaced alignment tab character &.
<argument> ...\ \frac {(1-\pi )k^{-s}}{\zeta (s)}&
                                                  ,k=1,2,\ldots \end {cases} 
l.512 }{}
installed size is  9.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Found the following apparent S3 methods exported but not registered:
  plot.fpp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
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'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:
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installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 300.6Mb
  sub-directories of 1Mb or more:
    libs  299.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘minet’
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘Rcpp’ ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without 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 31 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘LaplacesDemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
    libs   5.7Mb
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R   6.0Mb
Note: found 50 marked UTF-8 strings
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 81.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.7Mb
    libs  73.5Mb
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'foba', 'rrlda'
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 39 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 120 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘WGCNA’
Package suggested but not available for checking: ‘IRanges’
Package unavailable to check Rd xrefs: ‘IRanges’
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   4.2Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘cBioPortalData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 42.5Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
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
'LazyData' is specified without 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    2.3Mb
    libs   5.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Package which this enhances but not available for checking: ‘doMPI’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Environment aligned undefined.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Misplaced alignment tab character &.
<argument>  \begin {aligned} L &
                                 = m - z_\alpha s \cr U & = m + z_\alpha s \...
l.1068 }{}
          
! Misplaced \cr.
<argument> ... {aligned} L & = m - z_\alpha s \cr 
                                                  U & = m + z_\alpha s \end ...
l.1068 }{}
          
! Misplaced alignment tab character &.
<argument> ...ligned} L & = m - z_\alpha s \cr U &
                                                   = m + z_\alpha s \end {al...
l.1068 }{}
          
! LaTeX Error: \begin{list} on input line 1059 ended by \end{aligned}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Environment aligned undefined.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Misplaced alignment tab character &.
<argument>  \begin {aligned} m &
                                 = \frac {U + L}{2} \cr s & = \frac {U - L}{...
l.1075 }{}
          
! Misplaced \cr.
<argument> ...aligned} m & = \frac {U + L}{2} \cr 
                                                  s & = \frac {U - L}{2 z_\a...
l.1075 }{}
          
! Misplaced alignment tab character &.
<argument> ...gned} m & = \frac {U + L}{2} \cr s &
                                                   = \frac {U - L}{2 z_\alph...
l.1075 }{}
          
! LaTeX Error: \begin{list} on input line 1059 ended by \end{aligned}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...
installed size is 48.8Mb
  sub-directories of 1Mb or more:
    doc   44.3Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  10.1Mb
installed size is 84.8Mb
  sub-directories of 1Mb or more:
    libs  84.3Mb
GNU make is a SystemRequirements.
installed size is 65.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     61.4Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Package required and available but unsuitable version: ‘stars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.7Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
Package suggested but not available for checking: ‘gputools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 299.7Mb
  sub-directories of 1Mb or more:
    L8NY18    2.2Mb
    libs    296.3Mb
installed size is 249.0Mb
  sub-directories of 1Mb or more:
    extdata    1.0Mb
    libs     247.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    perl   3.9Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
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
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.4Mb
    libs      1.5Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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’
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
  ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   4.3Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
Note: found 58 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   3.0Mb
    libs      4.3Mb
Namespaces in Imports field not imported from:
  ‘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
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   4.5Mb
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    R        10.0Mb
    extdata   2.5Mb
    help      3.1Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 65.6Mb
  sub-directories of 1Mb or more:
    libs  64.0Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
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
Packages required and available but unsuitable versions:
  'biomaRt', 'grDevices', 'graphics', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pipeR’ ‘rlang’
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...s ,C_k)^\top = \mathbf {0}\,\,\text 
                                                  {and}\,\,\mathcal H_0: \ma...
l.238 ...H} (B_1,\ldots,B_k)^\top = \mathbf{0},}{}
                                                  
! Undefined control sequence.
<argument> ...\mathbf {C} = \mathbf {0}\,\, \text 
                                                  {or}\,\,\mathcal H_{0,\ell...
l.249 ...{B} = \mathbf{0}, \,\,\ell=1,\ldots,q,}{}
                                                  
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.251 ...s \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.252 \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                             , respectively, are calculated.
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.265 ...r \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.266 for \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                                 , the test statistics and c...
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘googlesheets4’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggmsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Package required but not available: ‘ggbio’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 2356 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  18.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘productplots’ ‘scales’
  All declared Imports should be used.
Packages required but not available: 'memes', 'universalmotif'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lefser', 'Maaslin2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lixoftConnectors’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.4Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   2.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Note: found 6242 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘nomogramFormula’ ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 138 marked UTF-8 strings
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   8.3Mb
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    Giac  17.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   2.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
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installed size is  7.1Mb
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installed size is 10.5Mb
  sub-directories of 1Mb or more:
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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 159.3Mb
  sub-directories of 1Mb or more:
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installed size is 18.3Mb
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Namespace in Imports field not imported from: ‘ordinal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 50.0Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
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installed size is 56.5Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 34.2Mb
  sub-directories of 1Mb or more:
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installed size is 28.9Mb
  sub-directories of 1Mb or more:
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Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 66.1Mb
  sub-directories of 1Mb or more:
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installed size is 32.9Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \mathbb 
                        
l.97 ...ong to a compact set of \eqn{\mathbb{R}}{}
                                                  .
! Undefined control sequence.
<recently read> \mathbb 
                        
l.161 ... to a compact set of \eqn{\mathbb{R}^2}{}
                                                  .
Namespace in Imports field not imported from: ‘rnaturalearthdata’
  All declared Imports should be used.
Note: found 1191 marked UTF-8 strings
installed size is 12.1Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘preprocessCore’
Packages suggested but not available for checking: 'graph', 'mutoss'
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package required but not available: ‘SeqArray’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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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
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.6Mb
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Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 1352 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.6Mb
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installed size is 30.2Mb
  sub-directories of 1Mb or more:
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installed size is 136.5Mb
  sub-directories of 1Mb or more:
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installed size is  8.1Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘monocle’
Package unavailable to check Rd xrefs: ‘monocle’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
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installed size is  7.7Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 11.5Mb
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installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Note: found 989 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 54.7Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for ‘gg’ with
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installed size is  5.6Mb
  sub-directories of 1Mb or more:
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installed size is 32.3Mb
  sub-directories of 1Mb or more:
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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
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
'LazyData' is specified without a 'data' directory
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument>  \min _{\boldsymbol \beta \in \mathbb 
                                                 {R}^p} L(\boldsymbol \beta ...
l.648 }{}
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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Package required but not available: ‘CelliD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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'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  5.6Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 269 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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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:
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  ‘tools’
  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
installed size is 259.7Mb
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    java  256.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
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    libs   5.0Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
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installed size is 149.3Mb
  sub-directories of 1Mb or more:
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    libs  147.5Mb
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         3.1Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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    htmlwidgets   2.8Mb
'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   7.1Mb
'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   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 21.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'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:
    libs   6.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    help      1.6Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
installed size is 22.8Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
  ...
--- re-building ‘hetGP_vignette.Rnw’ using knitr

Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
'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: ‘usethis’
  All declared Imports should be used.
installed size is  5.2Mb
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Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘fmrs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.7Mb
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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
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
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    libs        8.0Mb
Package suggested but not available for checking: ‘INLA’
installed size is 48.5Mb
  sub-directories of 1Mb or more:
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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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
installed size is 48.1Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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    libs   2.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
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    libs   4.3Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
html_describe_con: multiple local function definitions for ‘g’ with
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘HiddenMarkov’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 64.1Mb
  sub-directories of 1Mb or more:
    libs  63.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.3Mb
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installed size is 10.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Note: found 124 marked UTF-8 strings
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 60.9Mb
  sub-directories of 1Mb or more:
    libs  60.3Mb
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
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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installed size is 39.5Mb
  sub-directories of 1Mb or more:
    libs  38.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
'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:
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installed size is  7.7Mb
  sub-directories of 1Mb or more:
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    libs   5.2Mb
'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
installed size is 44.0Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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installed size is  5.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘webshot2’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
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installed size is  5.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 38558 marked UTF-8 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
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Note: found 1 marked UTF-8 string
Note: found 359 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: ‘SparkR’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
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'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: ‘LTRCtrees’
Package unavailable to check Rd xrefs: ‘LTRCtrees’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘icd’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is 16.4Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
  ‘digest’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 10 marked UTF-8 strings
'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:
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'LazyData' is specified without a 'data' directory
installed size is 31.1Mb
  sub-directories of 1Mb or more:
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    libs  29.3Mb
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: ‘Rdpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘IFCdata’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
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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  7.1Mb
  sub-directories of 1Mb or more:
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installed size is 14.2Mb
  sub-directories of 1Mb or more:
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    libs         4.3Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
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installed size is 22.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘rcccd’

See section ‘The DESCRIPTION file’ 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
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
'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
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘optimr’
  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’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘splines2’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
'LazyData' is specified without a 'data' directory
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
installed size is 32.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  31.4Mb
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
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.6Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘surveyspec’
Package suggested but not available for checking: ‘ComplexHeatmap’
Note: found 102 marked UTF-8 strings
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rhdf5’
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'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.
Note: found 46 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Package suggested but not available for checking: ‘Rmpi’
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘glmnet’
  All declared Imports should be used.
'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   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
Note: found 104 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: ‘rmarkdown’
  All declared Imports should be used.
installed size is 57.6Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.3Mb
    libs  52.4Mb
GNU make is a SystemRequirements.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  11.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Note: found 58 marked UTF-8 strings
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
'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
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          16.6Mb
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    docs   3.5Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.3Mb
Note: found 1984 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘mcmcplots’ ‘tidyverse’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/JavaGD.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.4Mb
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  41.4Mb
GNU make is a SystemRequirements.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.8Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘knitr’ ‘markdown’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  26.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.5Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    i18n   4.0Mb
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
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.2Mb
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.
Note: found 176 marked UTF-8 strings
Package required but not available: ‘scran’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  32.7Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    examples      2.8Mb
    htmlwidgets   1.1Mb
    www           2.7Mb
'LazyData' is specified without a 'data' directory
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
Running ‘tinytest.R’ [2s/3s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  test_fit.R....................    2 tests [0;32mOK[0m [0;36m49ms[0m
  
  test_mcd.R....................    4 tests [0;32mOK[0m [0;34m0.7s[0m
  
  test_seriation.R..............   12 tests [0;32mOK[0m [0;34m0.1s[0m
  ----- FAILED[data]: test_event.R<1--57>
   call| expect_equivalent_to_reference(boot, file = "_snaps/event_bootstrap.rds")
   diff| current does not match target read from _snaps/event_bootstrap.rds
   diff| Component 1: Mean relative difference: 0.005576492
   diff| Component 2: Mean relative difference: 0.003844346
   diff| Component 3: Mean relative difference: 0.004668564
   diff| Component 4: Mean relative difference: 0.005117474
   diff| Component 5: Mean relative difference: 0.004266483
  Error: 1 out of 32 tests failed
  Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gifski’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
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
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
'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
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘Rsamtools’ ‘rtracklayer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fitdistrplus’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 9 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.1Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.6Mb
'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:
    R      2.1Mb
    doc    1.7Mb
    help   1.1Mb
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘mixAK’
Package unavailable to check Rd xrefs: ‘mixAK’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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’ ‘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.
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:
  ‘devtools’ ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
Note: found 75 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
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
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 52.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  47.9Mb
GNU make is a SystemRequirements.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
installed size is  6.0Mb
  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
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.9Mb
installed size is 45.3Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘glue’ ‘stringr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘LFDREmpiricalBayes.Rnw’ using Sweave

Error: processing vignette 'LFDREmpiricalBayes.Rnw' failed with diagnostics:
 chunk 4 (label = generating artificial SNPs) 
Error in library(LFDR.MLE) : there is no package called ‘LFDR.MLE’

--- failed re-building ‘LFDREmpiricalBayes.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs  10.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 85.5Mb
  sub-directories of 1Mb or more:
    libs  84.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    libs  45.4Mb
'LazyData' is specified without a 'data' directory
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    doc       1.0Mb
    extdata   1.2Mb
    libs      9.2Mb
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
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.5Mb
installed size is 45.8Mb
  sub-directories of 1Mb or more:
    libs  45.2Mb
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs      20.0Mb
    testdata   1.3Mb
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    libs  55.7Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    doc-software   2.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 19.9Mb
  sub-directories of 1Mb or more:
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Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lestat’
  All declared Imports should be used.
installed size is 27.3Mb
  sub-directories of 1Mb or more:
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Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
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
'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
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'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
Package required but not available: ‘GeneticsPed’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Package suggested but not available for checking: ‘miceadds’
Note: found 55 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
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
'LazyData' is specified without a 'data' directory
installed size is 50.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  47.8Mb
'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
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpostgis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   1.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘orthogene’
Package unavailable to check Rd xrefs: ‘orthogene’
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.
Namespaces in Imports field not imported from:
  ‘rlang’ ‘torch’
  All declared Imports should be used.
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quitte’
Packages required but not available: 'SeqArray', 'GMMAT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 55.1Mb
  sub-directories of 1Mb or more:
    doc    6.2Mb
    libs  48.2Mb
'LazyData' is specified without a 'data' directory
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
Packages suggested but not available for checking: 'pdInfoBuilder', 'oligo'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocCheck’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.3Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Namespaces in Imports field not imported from:
  ‘cli’ ‘nomnoml’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
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
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
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
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Note: found 55 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
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
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs         16.7Mb
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   3.0Mb
    libs   4.8Mb
Namespace in Imports field not imported from: ‘pbmcapply’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.0Mb
Note: found 1 marked UTF-8 string
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
GNU make is a SystemRequirements.
Note: found 5210 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:
  ‘bookdown’ ‘kableExtra’ ‘knitr’
  All declared Imports should be used.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs      11.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘marssTMB’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.NCBI.GRCh38', 'wiggleplotr'
Package suggested but not available for checking: ‘flashier’
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  42.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.8Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘Matrix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
GNU make is a SystemRequirements.
qr.X: no visible binding for global variable ‘R’
Undefined global functions or variables:
  R
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 18 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.9Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lars’ ‘methods’ ‘parallel’ ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  13.2Mb
Namespace in Imports field not imported from: ‘boot.heterogeneity’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  34.9Mb
'LazyData' is specified without a 'data' directory
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
'LazyData' is specified without a 'data' directory
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'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: ‘psych’
  All declared Imports should be used.
'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:
    libs  10.7Mb
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
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 63.1Mb
  sub-directories of 1Mb or more:
    libs  61.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
'LazyData' is specified without a 'data' directory
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
ADPopSel: no visible global function definition for ‘%dorng%’
ADRand: no visible global function definition for ‘%dorng%’
ADSSMod: no visible global function definition for ‘%dorng%’
ADTreatSel: no visible global function definition for ‘%dorng%’
ClustRand: no visible global function definition for ‘%dorng%’
EventPred: no visible global function definition for ‘%dorng%’
FutRuleNCores: no visible global function definition for ‘%dorng%’
MultAdj1NCores: no visible global function definition for ‘%dorng%’
MultAdj2NCores: no visible global function definition for ‘%dorng%’
MultAdj3NCores: no visible global function definition for ‘%dorng%’
Undefined global functions or variables:
  %dorng%
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
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
'LazyData' is specified without a 'data' directory
installed size is 147.2Mb
  sub-directories of 1Mb or more:
    libs  145.8Mb
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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.1Mb
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
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
    libs      3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘merlin.Rmd’ using rmarkdown

Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.4Mb
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
installed size is 105.6Mb
  sub-directories of 1Mb or more:
    libs  104.9Mb
GNU make is a SystemRequirements.
Note: found 37 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:
  ‘e1071’ ‘gbm’ ‘ggplot2’ ‘graphics’ ‘randomForest’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'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.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
Packages suggested but not available for checking:
  'hgu133a.db', 'hgu95av2.db'
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.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
'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.
installed size is 58.9Mb
  sub-directories of 1Mb or more:
    libs  58.5Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Note: found 1 marked UTF-8 string
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.6Mb
    libs  20.9Mb
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Misplaced alignment tab character &.
<argument> \left (\begin {matrix} \cos (\rho ) &
                                                 \sin (\rho ) \\ - \sigma \s...
l.457 ... \sigma\cos(\rho) \end{matrix} \right)}{}
                                                  
! Misplaced alignment tab character &.
<argument> ...n (\rho ) \\ - \sigma \sin (\rho ) &
                                                   \sigma \cos (\rho ) \end ...
l.457 ... \sigma\cos(\rho) \end{matrix} \right)}{}
Package required but not available: ‘qusage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘boot’ ‘energy’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘webshot2’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \mathbb 
                        
l.268 ..., a random vector of \eqn{\mathbb{R}^p}{}
                                                   (\eqn{p > 1}{}) distribut...
! Undefined control sequence.
<recently read> \mathbb 
                        
l.270 ..., a random vector of \eqn{\mathbb{R}^p}{}
                                                   distributed according to ...
'LazyData' is specified without a 'data' directory
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  18.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'DAPAR', 'ProteoMM'
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dada2’
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’
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.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    lib    8.8Mb
    libs   4.4Mb
Found the following apparent S3 methods exported but not registered:
  plot.icss print.icss print.micss
See section ‘Registering S3 methods’ 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: ‘midfielddata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
'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
installed size is 116.7Mb
  sub-directories of 1Mb or more:
    libs  116.0Mb
Namespaces in Imports field not imported from:
  ‘pracma’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Package unavailable to check Rd xrefs: ‘mixAK’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   1.2Mb
    libs      1.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Packages suggested but not available for checking:
  'karyoploteR', 'regioneR'
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package which this enhances but not available for checking: ‘pbdMPI’
Package required but not available: ‘scran’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /opt/R/arm64/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
  #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/mixture.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
Namespaces in Imports field not imported from:
  ‘ashr’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ConfusionTableR’ ‘OddsPlotty’ ‘caret’ ‘dplyr’ ‘ggplot2’ ‘parsnip’
  ‘ranger’ ‘recipes’ ‘rsample’ ‘varhandle’ ‘workflows’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 236.6Mb
  sub-directories of 1Mb or more:
    include    9.6Mb
    libs     226.6Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘randomForest’
  All declared Imports should be used.
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
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:
  ‘datasets’ ‘doParallel’ ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  15.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 69.2Mb
  sub-directories of 1Mb or more:
    doc    5.9Mb
    libs  62.8Mb
'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
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
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
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...}, \frac {v}{2}, \frac {1}{2})\text 
                                                  {, if }x \geq 0\\ \frac {1...
l.1646 }{}
          
! Undefined control sequence.
<argument> ...}, \frac {v}{2}, \frac {1}{2})\text 
                                                  {, if }x < 0 \end {cases}, 
l.1646 }{}
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'doMPI', 'alstructure'

Package which this enhances but not available for checking: ‘MoBPSmaps’
Packages required but not available:
  'plyranges', 'RaggedExperiment', 'MultiAssayExperiment', 'ggbio',
  'OrganismDbi'

Packages suggested but not available for checking:
  'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 18 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 5238 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    libs   4.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.6Mb
Note: found 56 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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs     3.0Mb
    raster   2.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   2.0Mb
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Package suggested but not available for checking: ‘rhdf5’
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 68.9Mb
  sub-directories of 1Mb or more:
    libs  68.5Mb
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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> \gamma (s,t) = \sigma \text 
                                       {exp}\left (\frac {-(s-t)^2}{l}\right ),
l.342 ...t{exp}\left(\frac{-(s-t)^2}{l}\right),}{}
                                                  
! Undefined control sequence.
<argument> \gamma (s,t) = \sigma \text 
                                       {exp}\left (\frac {-|s-t|}{l}\right )
l.344 ...text{exp}\left(\frac{-|s-t|}{l}\right)}{}
                                                  
! Undefined control sequence.
<argument> \gamma (s,t) = \sigma ^2 \text 
                                          {exp}\left (\frac {-(s-t)^2}{2 l^2...
l.346 ...xp}\left(\frac{-(s-t)^2}{2 l^2}\right)}{}
                                                  .
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  12.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'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
Package suggested but not available for checking: ‘Biostrings’
Package unavailable to check Rd xrefs: ‘Biostrings’
'LazyData' is specified without a 'data' directory
Note: found 75 marked UTF-8 strings
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   4.5Mb
    libs   3.4Mb
installed size is 45.2Mb
  sub-directories of 1Mb or more:
    libs  44.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  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
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  17.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Namespaces in Imports field not imported from:
  ‘markdown’ ‘methods’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> j\text 
                  {th}
l.86 ...d \eqn{R_{j}^{2}}{} the \eqn{j\text{th}}{}
                                                   coefficient of determinat...
! Undefined control sequence.
<argument> j\text 
                  {th}
l.86 ...of determination of the \eqn{j\text{th}}{}
                                                   auxiliary regression.
'LazyData' is specified without 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:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘polycor’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.1Mb
Running examples in ‘multiblock-Ex.R’ failed
The error most likely occurred in:

> ### Name: basic
> ### Title: Single- and Two-Block Methods
> ### Aliases: basic
> 
> ### ** Examples
> 
> data(potato)
> X <- potato$Chemical
> y <- potato$Sensory[,1,drop=FALSE]
> 
> pca.pot  <- pca(X, ncomp = 2)
> pcr.pot  <- pcr(y ~ X, ncomp = 2)
> pls.pot  <- plsr(y ~ X, ncomp = 2)
> cca.pot  <- cca(potato[1:2])
> ifa.pot  <- ifa(potato[1:2])
Error in RGCCA::rgcca(blocks = X, connection = matrix(c(0, 1, 1, 0), 2,  : 
  unused arguments (blocks = X, connection = matrix(c(0, 1, 1, 0), 2, 2))
Calls: ifa
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vignette_A_data.Rmd’ using rmarkdown
--- finished re-building ‘vignette_A_data.Rmd’

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

Quitting from lines 66-79 [unnamed-chunk-3] (vignette_B_basic.Rmd)
Error: processing vignette 'vignette_B_basic.Rmd' failed with diagnostics:
unused arguments (blocks = X, connection = matrix(c(0, 1, 1, 0), 2, 2))
--- failed re-building ‘vignette_B_basic.Rmd’

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

Quitting from lines 82-97 [unnamed-chunk-3] (vignette_C_unsupervised.Rmd)
Error: processing vignette 'vignette_C_unsupervised.Rmd' failed with diagnostics:
unused arguments (blocks = X, connection = C)
--- failed re-building ‘vignette_C_unsupervised.Rmd’

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

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

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

SUMMARY: processing the following files failed:
  ‘vignette_B_basic.Rmd’ ‘vignette_C_unsupervised.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GFDmcv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Package suggested but not available for checking: ‘cmdstanr’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is 106.9Mb
  sub-directories of 1Mb or more:
    libs  106.6Mb
installed size is 137.5Mb
  sub-directories of 1Mb or more:
    doc     4.0Mb
    libs  132.0Mb
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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.
Package suggested but not available for checking: ‘ComplexHeatmap’
Package unavailable to check Rd xrefs: ‘ComplexHeatmap’
Error(s) in re-building vignettes:
--- re-building ‘multipol.Rnw’ using Sweave
Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

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

    deriv

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

    single

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘poweRlaw’ ‘rmutil’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘cias.Rnw’ using Sweave

Attaching package: ‘multivator’

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

    levels, rbind

--- finished re-building ‘cias.Rnw’

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
    libs   7.0Mb
'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: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'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:
    libs   6.0Mb
GNU make is a SystemRequirements.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
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’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    23.2Mb
    models   1.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
'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.
'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  6.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.7Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.5Mb
    libs   5.1Mb
GNU make is a SystemRequirements.
Note: found 140 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘rrpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘sSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.2Mb
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
installed size is  6.3Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rhdf5’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.8Mb
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installed size is 12.1Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ndexr’
installed size is 22.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
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    libs   5.5Mb
Packages required and available but unsuitable versions: 'stats', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 194.9Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
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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
Namespaces in Imports field not imported from:
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  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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
installed size is  7.0Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 40.0Mb
  sub-directories of 1Mb or more:
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installed size is  6.8Mb
  sub-directories of 1Mb or more:
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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.
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
installed size is  8.3Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
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installed size is  6.1Mb
  sub-directories of 1Mb or more:
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installed size is  6.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'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:
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Package suggested but not available for checking: ‘doMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'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:
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  ‘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
'LazyData' is specified without 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:
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  All declared Imports should be used.
installed size is 10.9Mb
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'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'treeio', 'ggtree'
Package unavailable to check Rd xrefs: ‘treeio’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
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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
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  7.3Mb
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘pedtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> x_i = a_i \, \mod 
                             \, m_i, \quad 1 \le i \le n 
l.562 ...i \, \mod \, m_i, \quad 1 \le i \le n }{}
                                                  
! Undefined control sequence.
<argument> a_i = a_j \, \mod 
                             \, \gcd (m_i, m_j)
l.566 \deqn{a_i = a_j \, \mod \, \gcd(m_i, m_j)}{}
installed size is 22.3Mb
  sub-directories of 1Mb or more:
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    libs  16.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 7 marked UTF-8 strings
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    doc       5.7Mb
    extdata   1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.3Mb
    libs   3.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   1.9Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 99.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> [0,\text 
                    {min}(p_1,p_2))
l.77 a number in \eqn{[0,\text{min}(p_1,p_2))}{}
                                                , indicating the cross-secti...
'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:
    data   5.1Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 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’
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  44.0Mb
GNU make is a SystemRequirements.
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  40.1Mb
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
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
'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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.7Mb
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
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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    exampledata   1.5Mb
    libs          3.6Mb
GNU make is a SystemRequirements.
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs   11.7Mb
    share  10.2Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   7.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Note: found 2524 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 212.7Mb
  sub-directories of 1Mb or more:
    R         3.1Mb
    data      1.4Mb
    libs    201.1Mb
    models    4.7Mb
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   2.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Note: found 167 marked UTF-8 strings
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   5.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      4.6Mb
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs     33.6Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.2Mb
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.
Package suggested but not available for checking: ‘gurobi’
'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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'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.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘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
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   6.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rcplex’
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Package required and available but unsuitable version: ‘utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘flexsurv’ ‘nlme’ ‘tibble’ ‘tidyverse’ ‘tm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Package required but not available: ‘genbankr’

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
Packages suggested but not available for checking: 'org.Dr.eg.db', 'scde'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
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
Namespaces in Imports field not imported from:
  ‘DT’ ‘dbplyr’ ‘downloadthis’ ‘ggExtra’ ‘htmlwidgets’ ‘methods’
  ‘rmarkdown’ ‘scales’
  All declared Imports should be used.
Note: found 34 marked UTF-8 strings
Namespace in Imports field not imported from: ‘smoothmest’
  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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘gstat’ ‘pryr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 16 marked UTF-8 strings
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is 47.5Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs  43.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.0Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
‘constparty.Rnw’... [3s/3s] OK
  ‘ctree.Rnw’ using ‘UTF-8’... [4s/4s] NOTE
differences from ‘ctree.Rout.save’
1409,1412d1408
< Deviance Residuals: 
<     Min       1Q   Median       3Q      Max  
< -45.801  -11.208   -1.049   10.903   53.615  
< 
  ‘mob.Rnw’... [5s/5s] OK
  ‘partykit.Rnw’... [1s/1s] OK
Package suggested but not available for checking: ‘MKmisc’
Package unavailable to check Rd xrefs: ‘MKmisc’
Running examples in ‘pastclim-Ex.R’ failed
The error most likely occurred in:

> ### Name: var_labels
> ### Title: Generate pretty variable labels for plotting
> ### Aliases: var_labels
> 
> ### ** Examples
> 
> var_labels("bio01", dataset = "Example")
expression("annual mean temperature (" * degree * C * ")")
> 
> # set the data_path for this example to run on CRAN
> # users don't need to run this line
> set_data_path_for_CRAN()
[1] TRUE
> 
> # for a SpatRaster
> climate_20k <- region_slice(
+ time_bp = -20000,
+ bio_variables = c("bio01", "bio10", "bio12"),
+ dataset = "Example"
+ )
> terra::plot(climate_20k, main = var_labels(climate_20k, dataset = "Example"))
Error in x$main != "" : comparison is not allowed for expressions
Calls: <Anonymous> ... plot -> plot -> .local -> .prep.plot.data -> .plotit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘a0_pastclim_overview.Rmd’ using rmarkdown

Quitting from lines 393-395 [unnamed-chunk-28] (a0_pastclim_overview.Rmd)
Error: processing vignette 'a0_pastclim_overview.Rmd' failed with diagnostics:
comparison is not allowed for expressions
--- failed re-building ‘a0_pastclim_overview.Rmd’

--- re-building ‘a1_available_datasets.Rmd’ using rmarkdown
--- finished re-building ‘a1_available_datasets.Rmd’

--- re-building ‘a2_custom_datasets.Rmd’ using rmarkdown
--- finished re-building ‘a2_custom_datasets.Rmd’

SUMMARY: processing the following file failed:
  ‘a0_pastclim_overview.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.5Mb
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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
GNU make is a SystemRequirements.
Package required but not available: ‘Mfuzz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.1Mb
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installed size is  6.9Mb
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installed size is  6.3Mb
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installed size is  6.6Mb
  sub-directories of 1Mb or more:
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installed size is  6.7Mb
  sub-directories of 1Mb or more:
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/pbdMPI.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

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  6.7Mb
  sub-directories of 1Mb or more:
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    doc    1.1Mb
    libs   1.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.4Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
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    libs   6.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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    help   1.4Mb
installed size is 126.3Mb
  sub-directories of 1Mb or more:
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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.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
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installed size is 34.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘PythonInR’
installed size is 20.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
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
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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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 18.2Mb
  sub-directories of 1Mb or more:
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    libs  14.0Mb
installed size is 134.4Mb
  sub-directories of 1Mb or more:
    libs  133.5Mb
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘jointseg’
Package suggested but not available for checking: ‘ptmixed’
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   7.7Mb
installed size is 56.2Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  32.7Mb
GNU make is a SystemRequirements.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
Note: found 114 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
installed size is 51.1Mb
  sub-directories of 1Mb or more:
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Package required but not available: ‘LBE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.5Mb
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 12.7Mb
  sub-directories of 1Mb or more:
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    libs  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggmsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 12.4Mb
  sub-directories of 1Mb or more:
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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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 23.4Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ggsubplot’
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.0Mb
'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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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    doc   1.2Mb
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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    libs         3.0Mb
    tmp_images   1.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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installed size is 12.9Mb
  sub-directories of 1Mb or more:
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    libs   9.5Mb
'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
installed size is  7.0Mb
  sub-directories of 1Mb or more:
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    htmlwidgets   4.0Mb
'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
'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:
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Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
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.
Namespaces in Imports field not imported from:
  ‘base’ ‘grDevices’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 62 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘argonDash’ ‘argonR’ ‘colourpicker’ ‘ggplot2’ ‘grid’ ‘hexSticker’
  ‘png’ ‘shinyWidgets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: ‘pollimetrydata’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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    extdata   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    R      7.0Mb
    data   5.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
    libs   1.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      2.9Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data      2.7Mb
    extdata   3.5Mb
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package required but not available: ‘EmpiricalBrownsMethod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.2Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> \hat d:=\underset 
                             {|d|<0.5}{\mathrm {argmin}}\bigg \{\sum _{h=s}^...
l.90 ...d)}h^{2d-1}\bigg|^r\bigg\}, \quad r > 0}{}
                                                  .
! Undefined control sequence.
<argument> K_1 = \iint 
                       _{I^2}\frac {1}{l_0(u)l_n(v)}\lim _{\theta \to a}\fra...
l.271 ...{\theta}(u,v)}{\partial\theta}\,dudv, }{}
                                                  
! Undefined control sequence.
<argument> \{F_n\}_{n\in \mathbb 
                                 {N}}
l.273 \eqn{\{F_n\}_{n\in\mathbb{N}}}{}
                                       is a sequence of absolutely continuou...
! Undefined control sequence.
<argument> K_1 = \iint 
                       _{I^2}\frac {1}{l_0(u)l_n(v)}\lim _{\theta \rightarro...
l.471 ...{\theta}(u,v)}{\partial\theta}\,dudv, }{}
                                                  
! Undefined control sequence.
<argument> \{F_n\}_{n\in \mathbb 
                                 {N}}
l.474 \eqn{\{F_n\}_{n\in\mathbb{N}}}{}
                                       is a sequence of absolutely continuou...
installed size is 12.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc  10.4Mb
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
'LazyData' is specified without a 'data' directory
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
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    libs   8.5Mb
Namespace in Imports field not imported from: ‘here’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata  11.6Mb
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    data   2.8Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...1}^{C+1} \hat {\sigma }^2_c}, \text 
                                                  { } \hat {\mu } + q^{calib...
l.965 ...m_{c=1}^{C+1} \hat{\sigma}^2_c} \Big].}{}
                                                  
! Undefined control sequence.
<argument> ...1}^{C+1} \hat {\sigma }^2_c}, \text 
                                                  { } \hat {\mu } + q^{calib...
l.1140 ..._{c=1}^{C+1} \hat{\sigma}^2_c} \Big].}{}
                                                  
! Undefined control sequence.
<argument> ...1}^{C+1} \hat {\sigma }^2_c}, \text 
                                                  { } \hat {\mu } + q^{calib...
l.1291 ..._{c=1}^{C+1} \hat{\sigma}^2_c} \Big].}{}
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
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
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    extdata   9.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinyApp   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 165 marked UTF-8 strings
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'rcbc'
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   5.7Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    4.7Mb
    libs  10.5Mb
'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
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘EBImage’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
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’
installed size is 115.3Mb
  sub-directories of 1Mb or more:
    libs  115.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  35.0Mb
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.1Mb
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’
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.0Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Note: found 26 marked Latin-1 strings
Package required and available but unsuitable version: ‘splines’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
installed size is 50.2Mb
  sub-directories of 1Mb or more:
    libs  49.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 107 marked UTF-8 strings
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Package required but not available: ‘tweeDEseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
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Namespaces in Imports field not imported from:
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installed size is 51.3Mb
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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
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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installed size is 16.5Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
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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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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Missing or unexported objects:
  ‘async::http_get’ ‘async::http_stop_for_status’ ‘async::synchronise’
  ‘async::when_all’
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.
installed size is  8.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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installed size is 85.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 108.6Mb
  sub-directories of 1Mb or more:
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'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:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spDataLarge’
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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Note: found 76102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘missMethods’
  All declared Imports should be used.
installed size is  5.1Mb
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Namespaces in Imports field not imported from:
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installed size is 16.2Mb
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installed size is  8.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  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.
Note: found 6 marked UTF-8 strings
installed size is 12.5Mb
  sub-directories of 1Mb or more:
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    libs  11.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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installed size is 16.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 40.6Mb
  sub-directories of 1Mb or more:
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    libs     35.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
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    contrib   3.7Mb
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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
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   8.0Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.6Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> K_\text 
                   {max}
l.2230 ...to a user-specified \eqn{K_\text{max}}{}
                                                  )
! Undefined control sequence.
<argument> K_\text 
                   {max}
l.2256 ...er}{integer} scalar \eqn{K_\text{max}}{}
                                                  ,
! Undefined control sequence.
<argument> K^c+1=K_\text 
                         {max}
l.2282 ...is stopped if \eqn{K^c+1=K_\text{max}}{}
                                                  ,
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
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
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    libs   5.3Mb
Package suggested but not available for checking: ‘fastshp’
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    shiny_app   1.4Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
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’
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
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installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
'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’
Package unavailable to check Rd xrefs: ‘BRugs’
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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    htmlwidgets   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Package suggested but not available for checking: ‘slingshot’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(Rage)
  > 
  > test_check("Rage")
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 423 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-gen_time.R:34:3'): gen_time warns and fails gracefully ───────
  `gen_time(mat_u_na, mat_f, method = "age_diff")` did not throw the expected error.
  ── Failure ('test-gen_time.R:38:3'): gen_time warns and fails gracefully ───────
  `gen_time(mat_u_na, mat_f, method = "cohort")` did not throw the expected error.
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 423 ]
  Error: Test failures
  Execution halted
installed size is 35.5Mb
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Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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installed size is 10.1Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ragtop_convertibles_in_r.Rmd’ using rmarkdown
Quitting from lines 425-461 (ragtop_convertibles_in_r.Rmd) 
Error: processing vignette 'ragtop_convertibles_in_r.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘ragtop_convertibles_in_r.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 28.8Mb
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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
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
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    super-tiny-icons   1.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
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    htmlwidgets   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  ‘spatstat’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'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
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs     10.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'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:
    R      3.1Mb
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 62.7Mb
  sub-directories of 1Mb or more:
    libs  62.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs  11.3Mb
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
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   3.4Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespace in Imports field not imported from: ‘rex’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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    libs      3.9Mb
GNU make is a SystemRequirements.
Note: found 8 marked UTF-8 strings
installed size is 53.1Mb
  sub-directories of 1Mb or more:
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    libs  50.4Mb
GNU make is a SystemRequirements.
installed size is 54.0Mb
  sub-directories of 1Mb or more:
    libs  53.4Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rhdf5’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rblpapi.Rcheck/00install.out’ for details.
installed size is 40.6Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rborist.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
Note: found 26334 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 66.1Mb
  sub-directories of 1Mb or more:
    libs  65.4Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
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  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
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    doc   4.5Mb
    po    2.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Packages suggested but not available for checking:
  'ROntoTools', 'RCyjs', 'BrowserViz', 'oligo'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rcplex.Rcheck/00install.out’ for details.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      2.1Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RcppMeCab.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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installed size is  9.7Mb
  sub-directories of 1Mb or more:
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    libs      2.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
GNU make is a SystemRequirements.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
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    libs      4.9Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
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    jsonexamples   3.8Mb
    libs          12.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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installed size is  6.5Mb
  sub-directories of 1Mb or more:
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
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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
'LazyData' is specified without a 'data' directory
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
installed size is 20.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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    data   1.5Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
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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
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
installed size is 19.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
'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
'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: ‘Deriv’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   5.1Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      4.6Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \mathbb 
                        
l.780 ...\eqn{\mathbb{E}[Y \mid X = x] = \mu(x)}{}
                                                  . The mean function \eqn{\...
! Undefined control sequence.
<argument> g(\mathbb 
                     {E}[Y \mid X = x]) = \mu (x)
l.799 \mu(x)}{}
               , where \eqn{g}{} is a link function. Let
! Undefined control sequence.
<argument> Y \mid X \sim \text 
                               {SomeDistribution},
l.1093 ... \mid X \sim \text{SomeDistribution},}{}
                                                  
! Undefined control sequence.
<argument> \mathbb 
                   {E}[Y \mid X = x] = g^{-1}(\mu (x)).
l.1097 ...bb{E}[Y \mid X = x] = g^{-1}(\mu(x)).}{}
                                                  
! Undefined control sequence.
<argument> Y \mid X \sim \text 
                               {Normal}(\mu (X), \sigma ^2),
l.1115 ...\sim \text{Normal}(\mu(X), \sigma^2),}{}
                                                  
! Undefined control sequence.
<argument> Y \mid X \sim \text 
                               {Binomial}(N, g^{-1}(\mu (X))),
l.1133 ...m \text{Binomial}(N, g^{-1}(\mu(X))),}{}
                                                  
! Undefined control sequence.
<argument> Y \mid X \sim \text 
                               {Poisson}(g^{-1}(\mu (X))),
l.1143 ... \sim \text{Poisson}(g^{-1}(\mu(X))),}{}
                                                  
! Undefined control sequence.
<argument> Y \mid X \sim \text 
                               {SomeDistribution}(g^{-1}(\mu (X))),
l.1152 ...xt{SomeDistribution}(g^{-1}(\mu(X))),}{}
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.3Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  14.6Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs      3.4Mb
    swagger   1.4Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs     19.5Mb
    models    1.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Package suggested but not available for checking: ‘ccdata’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘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
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    libs  38.5Mb
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'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:
    libs   6.0Mb
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
installed size is 271.8Mb
  sub-directories of 1Mb or more:
    doc         3.3Mb
    libs      264.5Mb
    pictures    1.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
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
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs   22.8Mb
'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 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  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
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  15.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'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
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.4Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   9.0Mb
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 243 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/rJava.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    include   2.9Mb
    libs     17.5Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   16.4Mb
'LazyData' is specified without a 'data' directory
installed size is 96.8Mb
  sub-directories of 1Mb or more:
    libs  96.0Mb
GNU make is a SystemRequirements.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rlibkdv.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/rlibkriging.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'GenomicRanges', 'S4Vectors', 'IRanges', 'org.Hs.eg.db',
  'reactome.db', 'fgsea', 'AnnotationDbi'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
'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
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RMark.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is 134.2Mb
  sub-directories of 1Mb or more:
    libs  133.8Mb
GNU make is a SystemRequirements.
installed size is 84.1Mb
  sub-directories of 1Mb or more:
    libs  83.4Mb
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
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RmecabKo.Rcheck/00install.out’ for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ... (t+(r-1))\neq \mu (t+(s-1))\ \text 
                                                  {for some}\ t\in [0,1],\\ ...
l.380 \end{array}\right.}{}
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   5.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs       1.2Mb
    minizinc   3.3Mb
'LazyData' is specified without a 'data' directory
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    libs  41.0Mb
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs  29.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rmpi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is 53.3Mb
  sub-directories of 1Mb or more:
    libs  52.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
GNU make is a SystemRequirements.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Package suggested but not available for checking: ‘recount3’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘pbdMPI’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package unavailable to check Rd xrefs: ‘pbdMPI’
'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:
    libs   3.9Mb
installed size is 101.0Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     98.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R  11.4Mb
'LazyData' is specified without a 'data' directory
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.3Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
Package suggested but not available for checking: ‘illuminaHumanv3.db’
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 70.6Mb
  sub-directories of 1Mb or more:
    libs  69.9Mb
GNU make is a SystemRequirements.
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              5.0Mb
    simulationStudy   1.5Mb
Errors in running code in vignettes:
when running code in ‘rlmer.Rnw’
  ...

> fm <- lmer(diameter ~ (1 | plate) + (1 | sample), 
+     PenicillinC)

> rfm <- rlmer(diameter ~ (1 | plate) + (1 | sample), 
+     PenicillinC)

  When sourcing ‘rlmer.R’:
Error: invalid assignment for reference class field ‘b.s’, should be from class “numeric” or a subclass (was class “dgeMatrix”)
Execution halted
when running code in ‘simulationStudies.Rnw’
  ...

> source(system.file("simulationStudy/breakdown.R", 
+     package = "robustlmm"))
Error : invalid assignment for reference class field ‘b.s’, should be from class “numeric” or a subclass (was class “dgeMatrix”)
Error : invalid assignment for reference class field ‘b.s’, should be from class “numeric” or a subclass (was class “dgeMatrix”)

  When sourcing ‘simulationStudies.R’:
Error: Error calling function 'fitDatasets_rlmer_DAStau_lmerNoFit'. Running the function produced the following error:
Error : invalid assignment for reference class field ‘b.s’, should be from class “numeric” or a subclass (was class “dgeMatrix”)
Execution halted

  ‘rlmer.Rnw’ using ‘UTF-8’... failed
  ‘simulationStudies.Rnw’ using ‘UTF-8’... failed
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcplex’

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
Note: found 261 marked UTF-8 strings
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    extdata   2.7Mb
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
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
'LazyData' is specified without a 'data' directory
sh: cmake: command not found
sh: cmake: command not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: cmake: command not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/ROracle.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   5.6Mb
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
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
installed size is 55.1Mb
  sub-directories of 1Mb or more:
    libs  54.0Mb
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  47.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /opt/R/arm64/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
  #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RQuantLib.Rcheck/00install.out’ for details.
installed size is 103.3Mb
  sub-directories of 1Mb or more:
    libs  102.7Mb
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
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lubridate’ ‘reshape2’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  24.1Mb
Note: found 467 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: ‘gurobi’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespace in Imports field not imported from: ‘MatrixExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    2.4Mb
    help   1.4Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 191.3Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.8Mb
    libs  183.8Mb
GNU make is a SystemRequirements.
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
GNU make is a SystemRequirements.
installed size is 256.4Mb
  sub-directories of 1Mb or more:
    lib    26.5Mb
    libs  227.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
installed size is 108.5Mb
  sub-directories of 1Mb or more:
    libs  108.0Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs    2.0Mb
    swipl  20.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R           2.0Mb
    bootstrap   1.6Mb
    doc         1.3Mb
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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
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    rmarkdown   9.6Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs       2.4Mb
    projects   2.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 91.6Mb
  sub-directories of 1Mb or more:
    libs  90.2Mb
'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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.0Mb
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
Note: found 37 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  19.9Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 59.5Mb
  sub-directories of 1Mb or more:
    libs  59.1Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.6Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 47.0Mb
  sub-directories of 1Mb or more:
    libs  46.4Mb
Package which this enhances but not available for checking: ‘glmmADMB’
Package required but not available: ‘rWikiPathways’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 48.2Mb
  sub-directories of 1Mb or more:
    libs  47.0Mb
'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’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 63.3Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs     57.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    extdata   2.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
Note: found 4250 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Packages required but not available: 'biocViews', 'BiocPkgTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is 36.7Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs    8.1Mb
    yacas   1.3Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs    8.8Mb
    yacas   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is 38.3Mb
  sub-directories of 1Mb or more:
    libs  37.2Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Note: found 63 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
'LazyData' is specified without a 'data' directory
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  38.0Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   4.0Mb
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'org.Sc.sgd.db'
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
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  46.7Mb
'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
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    bin   4.4Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   3.2Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \dfrac 
                       
l.192 ...omputed by  \eqn{\dfrac{|I|-ec}{|I|-1}}{}
                                                  .
! Undefined control sequence.
<argument> 1 - \dfrac 
                      {\hat {\ell }_{k,n}(1_I,0_{I^c})}{|I|}
l.280 ...ac{\hat{\ell}_{k,n}(1_I,0_{I^c})}{|I|}}{}
                                                  .
! Undefined control sequence.
<argument> S_I(\ell )=\dfrac 
                             {D_I(\ell )}{D(\ell )}
l.1278 ...{S_I(\ell)=\dfrac{D_I(\ell)}{D(\ell)}}{}
                                                  .
! Undefined control sequence.
<argument> S_I(\ell )=\dfrac 
                             {D_I(\ell )}{D(\ell )}
l.1364 ...{S_I(\ell)=\dfrac{D_I(\ell)}{D(\ell)}}{}
                                                  .
! Undefined control sequence.
<argument> \hat {S}_{I,k,n}=\dfrac 
                                   {\hat {D}_{I,k,n}}{\hat {D}_{k,n}}
l.1374 ...dfrac{\hat{D}_{I,k,n}}{\hat{D}_{k,n}}}{}
                                                  
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1607 ...hat{\Upsilon}_{I,k,n}}{\hat{D}_{k,n}}}{}
                                                   the empirical counterpart...
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1607 ...n{\dfrac{\Upsilon_I(\ell)}{D_I(\ell)}}{}
                                                  .
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1609 ... by \eqn{\dfrac{(2|I|+2)!}{2(|I|!)^2}}{}
                                                  .
'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.
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
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.6Mb
'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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Packages suggested but not available for checking:
  'DropletUtils', 'Nebulosa'
Package unavailable to check Rd xrefs: ‘Nebulosa’
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   3.1Mb
Package suggested but not available for checking: ‘ontoProc’
Namespaces in Imports field not imported from:
  ‘future’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DuoClustering2018’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mathjaxr’
  All declared Imports should be used.
Package required and available but unsuitable version: ‘UCell’

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
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘scran’

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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'AUCell', 'decoupleR', 'infercnv', 'Nebulosa'
Unknown package ‘infercnv’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘oligoClasses’
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘crayon’ ‘knitr’ ‘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
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 2 marked UTF-8 strings
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
installed size is 57.5Mb
  sub-directories of 1Mb or more:
    libs  55.7Mb
Package unavailable to check Rd xrefs: ‘INLA’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   8.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  14.5Mb
GNU make is a SystemRequirements.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   7.7Mb
Packages required but not available: 'ggmsa', 'msa'

Package suggested but not available for checking: ‘org.Rn.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rsbml’
Package suggested but not available for checking: ‘ArrayExpress’
Package unavailable to check Rd xrefs: ‘ArrayExpress’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘flowMerge’
Package unavailable to check Rd xrefs: ‘flowMerge’
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
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.
'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
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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   2.4Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs    21.4Mb
    models   1.6Mb
Note: found 836 marked UTF-8 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.3Mb
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘widgetTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   1.2Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [21s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-zzz_seriate_extra.R:38:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-seriate.R:262:3'): test if seriate.dist returns expected results ──
  Seriation method R2E does not return the correct order!
   is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 326 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is 17.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘monocle’
installed size is 10.2Mb
  sub-directories of 1Mb or more:
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    libs   7.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
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installed size is  5.8Mb
  sub-directories of 1Mb or more:
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installed size is 261.4Mb
  sub-directories of 1Mb or more:
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    libs    255.0Mb
    sqlite    1.5Mb
'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
installed size is 11.1Mb
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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
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
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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’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘websocket’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
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'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
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    www   8.6Mb
'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
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> X \in \mathbb 
                         {R}{n\times p}
l.3264 ...data \eqn{X \in \mathbb{R}{n\times p}}{}
                                                   such that its rows are
! Undefined control sequence.
<argument> ...Delta _{p-1} =\lbrace z \in \mathbb 
                                                  {R}^p~|~z_j > 0, \sum _{i=...
l.3267 }{}
           test whether the data is uniformly distributed.
'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
Note: found 1231 marked UTF-8 strings
Note: found 28 marked UTF-8 strings
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    help      1.7Mb
Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.9Mb
Packages unavailable to check Rd xrefs: ‘motifmatchr’, ‘TFBSTools’, ‘chromVAR’
Package suggested but not available for checking: ‘rhdf5’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
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
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Namespaces in Imports field not imported from:
  ‘pedtools’ ‘readr’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
GNU make is a SystemRequirements.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  12.6Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
Note: found 1 marked UTF-8 string
Packages suggested but not available for checking: 'clipper', 'topologyGSA'
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
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.6Mb
'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.
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
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    libs  19.9Mb
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   6.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
Packages unavailable to check Rd xrefs: ‘Rgraphviz’, ‘graph’
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lubridate’ ‘rmarkdown’ ‘yaml’
  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
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
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    libs   5.0Mb
GNU make is a SystemRequirements.
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Note: found 23 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
installed size is  5.1Mb
  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
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespaces in Imports field not imported from:
  ‘checkmate’ ‘glmnet’ ‘mice’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: ‘gurobi’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SMITIDstruct’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'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
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.3Mb
    libs  10.6Mb
'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: ‘nlme’
  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
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
Package which this enhances but not available for checking: ‘Rmpi’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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    libs      2.9Mb
Package required but not available: ‘GWASTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘flextable’ ‘htmlTable’ ‘stringr’
  All declared Imports should be used.
Note: found 938 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
'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.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
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    libs   9.6Mb
'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:
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  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
Package suggested but not available for checking: ‘DropletUtils’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.0Mb
Packages suggested but not available for checking:
  'r2cytoscape', 'hgu95av2.db'
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'hgu95av2.db''

Quitting from lines 512-527 [unnamed-chunk-25] (SourceSet.Rmd)
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.list': object 'org.Hs.egSYMBOL' not found
--- failed re-building ‘SourceSet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 17.8Mb
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    libs  13.0Mb
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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    libs      3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.6Mb
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 37.4Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs  32.9Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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    java   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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'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
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 30.6Mb
  sub-directories of 1Mb or more:
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'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
Packages required but not available: 'SpatialExperiment', 'zinbwave'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
installed size is 54.6Mb
  sub-directories of 1Mb or more:
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
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Note: found 283 marked UTF-8 strings
installed size is 14.7Mb
  sub-directories of 1Mb or more:
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    libs  13.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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Depends: includes the non-default packages:
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  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
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installed size is 13.6Mb
  sub-directories of 1Mb or more:
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    libs  10.1Mb
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘spDataLarge’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
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    shapes   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    help   1.5Mb
Note: found 34 marked UTF-8 strings
installed size is  8.7Mb
  sub-directories of 1Mb or more:
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    etc   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
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Undocumented S4 methods:
  generic '[' and siglist 'SpectraInTime,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTime,missing,ANY,ANY'
  generic '[' and siglist 'SpectraInTime,missing,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,ANY,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,missing,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  7.4Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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installed size is 24.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘sf’ ‘spData’
  All declared Imports should be used.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
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installed size is  6.6Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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    libs   3.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using rmarkdown
--- finished re-building ‘basics.Rmd’

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

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs     11.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
Note: found 7587 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sampling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘rgeoda’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Note: found 199 marked UTF-8 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
installed size is 51.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  49.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘RSQLite’ ‘dbplyr’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    help   1.1Mb
    libs  10.0Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.4Mb
Namespaces in Imports field not imported from:
  ‘arm’ ‘brms’ ‘lme4’ ‘plotly’ ‘shinyMatrix’
  All declared Imports should be used.
'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
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  25.5Mb
'LazyData' is specified without a 'data' directory
installed size is 104.3Mb
  sub-directories of 1Mb or more:
    libs  103.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scanstatistics’
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘mice’ ‘sandwich’ ‘zoo’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘stacomir.Rmd’ using rmarkdown

Quitting from lines 302-324 [rmmstd] (stacomir.Rmd)
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
duplicated values in No.pas
--- failed re-building ‘stacomir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.1Mb
Namespaces in Imports field not imported from:
  ‘reshape2’ ‘stats’
  All declared Imports should be used.
installed size is 52.8Mb
  sub-directories of 1Mb or more:
    libs  52.4Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    include  12.1Mb
    lib       2.4Mb
GNU make is a SystemRequirements.
installed size is 85.8Mb
  sub-directories of 1Mb or more:
    libs  85.0Mb
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
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘starsdata’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    1.7Mb
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
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
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.4Mb
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      4.0Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
'LazyData' is specified without a 'data' directory
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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.2Mb
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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.3Mb
Package suggested but not available for checking: ‘INLA’
installed size is 65.4Mb
  sub-directories of 1Mb or more:
    libs  64.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.8Mb
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> \mathbf {u},\mathbf {u}\in \mathbb 
                                              {R}^3
l.2149 ...{\mathbf{u},\mathbf{u}\in\mathbb{R}^3}{}
                                                   is defined
! Undefined control sequence.
<recently read> \mathbb 
                        
l.2158 ...uples of vectors in \eqn{\mathbb{R}^3}{}
                                                  , given by
! Undefined control sequence.
<recently read> \mathbb 
                        
l.2178 ...esenting vectors in \eqn{\mathbb{R}^3}{}
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Note: found 1 marked UTF-8 string
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \mathbb 
                        
l.349 The minimization is on \eqn{\mathbb R_+^H}{}
                                                  .
! Undefined control sequence.
<recently read> \mathbb 
                        
l.537 minimization is on \eqn{\mathbb R_+^H}{}
                                              .
! Undefined control sequence.
<recently read> \mathbb 
                        
l.637 ... minimization is on \eqn{\mathbb R_+^H}{}
                                                  .
! Misplaced alignment tab character &.
<argument>  I(x) = \begin {cases} 0, &
                                       x \text { is } FALSE \\ 1, & x \text ...
l.929 }{}
         
! Undefined control sequence.
<argument>  I(x) = \begin {cases} 0, & x \text 
                                               { is } FALSE \\ 1, & x \text ...
l.929 }{}
         
! Misplaced alignment tab character &.
<argument> ...s} 0, & x \text { is } FALSE \\ 1, &
                                                   x \text { is } TRUE, \end...
l.929 }{}
         
! Undefined control sequence.
<argument> ... \text { is } FALSE \\ 1, & x \text 
                                                  { is } TRUE, \end {cases} 
l.929 }{}
         
! Undefined control sequence.
<recently read> \mathbb 
                        
l.975 The minimization is on \eqn{\mathbb R_+^H}{}
                                                  .
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
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.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  10.2Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   1.8Mb
'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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.3Mb
'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
Note: found 78 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.3Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
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.
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocParallel’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'INLA', 'sf'
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.2Mb
    libs   1.6Mb
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    libs  44.9Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.3Mb
    doc    3.9Mb
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
'LazyData' is specified without a 'data' directory
installed size is 42.9Mb
  sub-directories of 1Mb or more:
    libs  42.4Mb
GNU make is a SystemRequirements.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
installed size is 48.5Mb
  sub-directories of 1Mb or more:
    libs  48.0Mb
'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: ‘swephRdata’
Namespaces in Imports field not imported from:
  ‘mapdata’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘mnorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘StackImpute’ ‘arm’ ‘boot’ ‘broom’ ‘knitr’ ‘mvtnorm’
  ‘randomForest’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   3.4Mb
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
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    fonts   1.7Mb
    libs   17.6Mb
'LazyData' is specified without a 'data' directory
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R         2.3Mb
    extdata   3.1Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 551 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
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
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
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   4.7Mb
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 301 marked UTF-8 strings
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
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
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'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.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument>  \text 
                  {logit} \big ( E(Y) \big ) = \tau + \alpha + \delta (r - 1), 
l.172 ...g ) = \tau + \alpha + \delta (r - 1), }{}
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 37.6Mb
  sub-directories of 1Mb or more:
    libs  36.3Mb
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    apps   2.3Mb
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘R2wd’
'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
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       3.7Mb
    libs      2.0Mb
    telemac   1.0Mb
Package suggested but not available for checking: ‘INLA’
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
installed size is 292.9Mb
  sub-directories of 1Mb or more:
    R       3.1Mb
    libs  288.5Mb
installed size is 30.9Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       7.6Mb
    tessdata  22.2Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘mnlogit’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.0Mb
    libs   4.2Mb
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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  19.2Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.8Mb
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
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> x_{i} - \text 
                         {min}(\mathbf {x})
l.527 ...(\mathbf{x}) - \text{min}(\mathbf{x})}}{}
                                                  
! Undefined control sequence.
<argument> \text 
                 {max}(\mathbf {x}) - \text {min}(\mathbf {x})
l.527 ...(\mathbf{x}) - \text{min}(\mathbf{x})}}{}
                                                  
! Undefined control sequence.
<argument> \text {max}(\mathbf {x}) - \text 
                                            {min}(\mathbf {x})
l.527 ...(\mathbf{x}) - \text{min}(\mathbf{x})}}{}
                                                  
! Undefined control sequence.
<argument> x_{i} - \text 
                         {median}(\mathbf {x})
l.852 ...\mathbf{x})/{1.35}}\right)\right]^{-1}}{}
                                                  
! Undefined control sequence.
<argument> \text 
                 {IQR}(\mathbf {x})/{1.35}
l.852 ...\mathbf{x})/{1.35}}\right)\right]^{-1}}{}
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    data   3.0Mb
Note: found 197527 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘readr’ ‘tidyverse’ ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 51.5Mb
  sub-directories of 1Mb or more:
    libs  51.1Mb
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Warning: declared S3 method 'filter.edsurvey.data.frame' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rblpapi’
Package unavailable to check Rd xrefs: ‘Rblpapi’
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SingleR’
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  43.8Mb
Note: found 34206 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   4.5Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 63.4Mb
  sub-directories of 1Mb or more:
    libs    13.9Mb
    tiledb  47.2Mb
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: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   D
l.967 visjs documentation}}
                           .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   D
l.967 visjs documentation}}
                           .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   D
l.967 visjs documentation}}
                           .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   g
l.1023 visjs documentation}}
                            .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   g
l.1023 visjs documentation}}
                            .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   g
l.1023 visjs documentation}}
                            .
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘org.Rn.eg.db’
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 54.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  51.0Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   4.9Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    examples  12.0Mb
    include    3.6Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Packages required but not available: 'EnhancedVolcano', 'Mfuzz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 160 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘corpus.JSS.papers’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
installed size is 227.6Mb
  sub-directories of 1Mb or more:
    R          6.2Mb
    help       1.6Mb
    include    3.4Mb
    libs     215.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Note: found 100 marked Latin-1 strings
  Note: found 548 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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘jpeg’ ‘pastecs’ ‘plyr’ ‘raster’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxidata’
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
installed size is 49.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  46.4Mb
Note: found 827 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR'
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Packages required but not available: 'csaw', 'HiCDOC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘TreeDistData’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   2.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.2Mb
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    doc       1.3Mb
    extdata  14.8Mb
installed size is 121.2Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    libs  116.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  37.5Mb
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: ‘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
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   9.3Mb
'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
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: declared S3 method 'transform.bal_oversampling' not found
Warning: declared S3 method 'transform.bal_subsampling' not found
Warning: declared S3 method 'transform.cla_fs' not found
Warning: declared S3 method 'transform.ts_aug_awareness' not found
Warning: declared S3 method 'transform.ts_aug_awaresmooth' not found
Warning: declared S3 method 'transform.ts_aug_flip' not found
Warning: declared S3 method 'transform.ts_aug_jitter' not found
Warning: declared S3 method 'transform.ts_aug_none' not found
Warning: declared S3 method 'transform.ts_aug_shrink' not found
Warning: declared S3 method 'transform.ts_aug_stretch' not found
Warning: declared S3 method 'transform.ts_aug_wormhole' not found
Warning: declared S3 method 'transform.ts_fil_ema' not found
Warning: declared S3 method 'transform.ts_fil_ma' not found
Warning: declared S3 method 'transform.ts_fil_none' not found
Warning: declared S3 method 'transform.ts_fil_smooth' not found
Warning: declared S3 method 'transform.ts_norm_none' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘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.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'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
'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
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    ubinc   2.0Mb
installed size is 98.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.0Mb
    libs  94.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
Note: found 2 marked UTF-8 strings
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       23.0Mb
'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:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
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
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    help   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
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.4Mb
    libs  41.3Mb
GNU make is a SystemRequirements.
Note: found 3347 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘USA.state.boundaries.data’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   6.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
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.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  30.6Mb
Packages required and available but unsuitable versions:
  'methods', 'splines', 'stats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  22.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is 271.2Mb
  sub-directories of 1Mb or more:
    extdata    2.8Mb
    libs     267.1Mb
'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
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   7.5Mb
'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:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
'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
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    help   3.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 468 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.0Mb
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
installed size is 55.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  53.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       5.4Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     30.2Mb
GNU make is a SystemRequirements.
installed size is 61.1Mb
  sub-directories of 1Mb or more:
    libs  60.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.4Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
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
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘changing_default_parameters.Rmd’ using rmarkdown
--- finished re-building ‘changing_default_parameters.Rmd’

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

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

Quitting from lines 68-71 [unnamed-chunk-2] (process_bouts.Rmd)
Error: processing vignette 'process_bouts.Rmd' failed with diagnostics:
'origin' must be supplied
--- failed re-building ‘process_bouts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 90.1Mb
  sub-directories of 1Mb or more:
    libs  88.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   5.5Mb
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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'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:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Note: found 3133 marked UTF-8 strings
Note: found 4413 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Package suggested but not available for checking: ‘prepr’
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
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
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  29.2Mb
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
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.5Mb
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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘plotly’ ‘shinythemes’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Note: found 933 marked UTF-8 strings
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
'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:
    data   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
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.
Package suggested but not available for checking: ‘ROTS’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   1.4Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    bin   4.2Mb
    lib   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 60.1Mb
  sub-directories of 1Mb or more:
    libs  59.2Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    java  27.2Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  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: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
'LazyData' is specified without a 'data' directory
Note: found 268 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: ‘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
installed size is 43.0Mb
  sub-directories of 1Mb or more:
    libs  42.7Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    libs  41.8Mb
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
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   4.6Mb
Package suggested but not available for checking: ‘RNRCS’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
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
'LazyData' is specified without a 'data' directory
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘zdat’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 86.4Mb
  sub-directories of 1Mb or more:
    libs  85.4Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 134469 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
'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.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Packages required but not available:
  'BSgenome.Hsapiens.UCSC.hg19', 'BSgenome.Hsapiens.UCSC.hg38',
  'BSgenome.Mmusculus.UCSC.mm9', 'BSgenome.Mmusculus.UCSC.mm10'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'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
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   3.0Mb
    libs   2.6Mb
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
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
Package suggested but not available for checking: ‘HiTC’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rjags’
'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.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
Package which this enhances but not available for checking: ‘asreml’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
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
Running ‘testthat.R’ [30s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    'test-09_train_longformer_model.R:1:1',
    'test-10_text_embedding_model_bert.R:2:1',
    'test-11_text_embedding_model_roberta.R:2:1',
    'test-12_text_embedding_model_longformer.R:2:1',
    'test-13_text_embedding_model_transformer.R:2:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-15_install_and_config.R:7:3'): check_python_modules ──────────
  Expected `set_config_os_environ_logger(level = "ERROR")` to run without any errors.
  i Actually got a <Rcpp::exception> with text:
    PyType_GetFlags - dlsym(0x7f822cc728e0, PyType_GetFlags): symbol not found
  
  [ FAIL 1 | WARN 18 | SKIP 12 | PASS 48 ]
  Error: Test failures
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
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
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       3.5Mb
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 apparent S3 methods exported but not registered:
  print.amAlleleFreq print.amDataset summary.amCluster
  summary.amPairwise summary.amUnique
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  23.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    25.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mcclust’
  All declared Imports should be used.
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
'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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Note: found 76 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘bannerCommenter’ ‘config’ ‘feather’ ‘here’ ‘knitr’ ‘log4r’ ‘ps’
  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.1Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 97.9Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    libs  93.0Mb
Note: found 1409 marked UTF-8 strings
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   8.2Mb
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
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘asteRiskData’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.4Mb
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘lubridate’ ‘openair’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘lubridate’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Note: found 552 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘readxl’ ‘reshape2’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
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
Namespaces in Imports field not imported from:
  ‘MixAll’ ‘dplyr’ ‘lqmm’ ‘matrixcalc’ ‘rmutil’ ‘rootSolve’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Package suggested but not available for checking: ‘lixoftConnectors’
Note: found 64209 marked UTF-8 strings
Note: found 133353 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 76.9Mb
  sub-directories of 1Mb or more:
    libs  75.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 260 marked UTF-8 strings
installed size is 74.0Mb
  sub-directories of 1Mb or more:
    libs  72.2Mb
GNU make is a SystemRequirements.
installed size is 63.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  61.2Mb
GNU make is a SystemRequirements.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument>  \text 
                  {E}[s_i|\omega ,y_{ij}]=\exp ({f(y_{ij},\omega )}) 
l.301   }{}
           
! Undefined control sequence.
<argument> ...athcal {N}(\boldsymbol {\mu }^\text 
                                                  {T}\boldsymbol {K},\sigma ...
l.603   }{}
           
! Undefined control sequence.
<argument> P(\text 
                   {\textbf {error}})=2\Phi (-\left |\boldsymbol {\mu }_{\bo...
l.609 ...dot\boldsymbol{\tau}_{\boldsymbol{D}})}{}
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fs’ ‘testthat’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.2/banditpam.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘fdpbandsdata’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
Note: found 148 marked UTF-8 strings
Package suggested but not available for checking: ‘ArrayExpress’
'LazyData' is specified without a 'data' directory
Note: found 13825 marked UTF-8 strings
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.4Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
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
Namespaces in Imports field not imported from:
  ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Namespace in Imports field not imported from: ‘vtable’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
installed size is 62.8Mb
  sub-directories of 1Mb or more:
    libs  60.7Mb
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 42.8Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 83.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  82.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   5.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  13.2Mb
Package suggested but not available for checking: ‘INLA’
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is 69.7Mb
  sub-directories of 1Mb or more:
    libs  68.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘StanHeaders’ ‘astsa’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 83.6Mb
  sub-directories of 1Mb or more:
    libs  82.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppParallel’ ‘mlbench’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 56.6Mb
  sub-directories of 1Mb or more:
    libs  55.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Package suggested but not available for checking: ‘PottsUtils’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
GNU make is a SystemRequirements.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  14.2Mb
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  20.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.9Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘MCMCpack’ ‘R2WinBUGS’ ‘R2jags’ ‘carData’ ‘rjags’
  All declared Imports should be used.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Note: found 1924 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘matrixcalc’ ‘stats’
  All declared Imports should be used.
installed size is 69.7Mb
  sub-directories of 1Mb or more:
    libs  69.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  15.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
Package suggested but not available for checking: ‘BayesTree’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
GNU make is a SystemRequirements.
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  34.1Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.5Mb
installed size is 37.6Mb
  sub-directories of 1Mb or more:
    libs  36.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Packages suggested but not available for checking: 'BRugs', 'rjags'
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
Package suggested but not available for checking: ‘webshot2’
'LazyData' is specified without a 'data' directory
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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
'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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 87.5Mb
  sub-directories of 1Mb or more:
    libs  85.9Mb
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.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs  43.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
'LazyData' is specified without a 'data' directory
installed size is 42.7Mb
  sub-directories of 1Mb or more:
    libs  42.4Mb
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
'LazyData' is specified without a 'data' directory
installed size is 38.6Mb
  sub-directories of 1Mb or more:
    libs  38.1Mb
GNU make is a SystemRequirements.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \text 
                      
l.267 \eqn{\text{logit}^{-1}(p) \sim N(2,5)}{}
                                               which produces a mean reporti...
installed size is 51.4Mb
  sub-directories of 1Mb or more:
    libs  50.8Mb
GNU make is a SystemRequirements.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
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.
installed size is 60.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  56.8Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    help   1.1Mb
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   6.2Mb
Note: found 582 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is 151.5Mb
  sub-directories of 1Mb or more:
    include  151.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
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.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   8.3Mb
Package suggested but not available for checking: ‘ffbase’
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.9Mb
    libs      2.4Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      8.9Mb
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.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  18.2Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 660 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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is 75.3Mb
  sub-directories of 1Mb or more:
    libs  74.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘msa’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'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  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      2.8Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Note: found 46 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:
  ‘stats’ ‘utils’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 39.6Mb
  sub-directories of 1Mb or more:
    libs  38.7Mb
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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Package suggested but not available for checking: ‘cmdstanr’
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Namespace in Imports field not imported from: ‘RcppArmadillo’
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'LazyData' is specified without a 'data' directory
installed size is 33.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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Namespace in Imports field not imported from: ‘shiny’
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
installed size is 122.9Mb
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GNU make is a SystemRequirements.
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
installed size is 51.4Mb
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘INLA’
installed size is 76.5Mb
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GNU make is a SystemRequirements.
installed size is  7.0Mb
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Namespace in Imports field not imported from: ‘dplyr’
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
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Package suggested but not available for checking: ‘sangerseqR’
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installed size is 394.5Mb
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GNU make is a SystemRequirements.
installed size is 78.3Mb
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installed size is  6.3Mb
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Namespace in Imports field not imported from: ‘usethis’
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Namespace in Imports field not imported from: ‘R6’
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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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
installed size is  6.0Mb
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Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.9Mb
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘kableExtra’
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Packages suggested but not available for checking:
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'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
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Package suggested but not available for checking: ‘cmdstanr’
installed size is  7.9Mb
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Package suggested but not available for checking: ‘glmmADMB’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 11.4Mb
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 32.1Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 103.9Mb
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installed size is  8.5Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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installed size is  6.1Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
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installed size is 21.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘doMPI’
installed size is 19.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 54.9Mb
  sub-directories of 1Mb or more:
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installed size is 43.4Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 179 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
installed size is 61.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Note: found 58 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
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'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:
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Note: found 287 marked UTF-8 strings
'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
'LazyData' is specified without a 'data' directory
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability will be removed in an upcoming reticulate release.

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is  5.9Mb
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installed size is 10.8Mb
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Note: found 1 marked UTF-8 string
installed size is  8.7Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
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installed size is 38.5Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
installed size is 12.2Mb
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GNU make is a SystemRequirements.
installed size is  5.8Mb
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...}} \lbrace \xi _{i,j} w_{i,j} \text 
                                                  {exp}(\eta ' A_{i,j}) A_{i...
l.272 ...A_{i,j}) A_{i,j} - A_{i,j} \rbrace = 0}{}
                                                  ,
! Undefined control sequence.
<argument> w_{i,j} \text 
                         {exp}(\hat \eta ' A_{i,j})
l.279 ...w_{i,j} \text{exp}(\hat \eta' A_{i,j})}{}
                                                  , and
! Undefined control sequence.
<argument> ...}} \lbrace \xi _{i,j} w_{i,j} \text 
                                                  {exp}(\hat \eta ' A_{i,j})...
l.281 ...p}(\hat \eta' A_{i,j}) A_{i,j} \rbrace}{}
                                                  
! Undefined control sequence.
<argument> ...}} \lbrace \xi _{i,j} V_{i,j} \text 
                                                  {exp}( \gamma ' B_{i,j}) B...
l.1093 ...i,j} - \xi_{i,j} B_{i,j} \rbrace = 0,}{}
                                                  
! Undefined control sequence.
<recently read> \text 
                      
l.1100 ...\eqn{\text{exp}(\hat \gamma' B_{i,j})}{}
                                                  ,
! Undefined control sequence.
<argument> ...^{n^{(j)}} \xi _{i,j} V_{i,j} \text 
                                                  {exp}(\hat \gamma ' B_{i,j...
l.1101 ...xt{exp}(\hat \gamma' B_{i,j}) B_{i,j}}{}
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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installed size is 38.0Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  7.3Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
installed size is 43.6Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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installed size is  6.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 133.7Mb
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GNU make is a SystemRequirements.
Running examples in ‘cbsodataR-Ex.R’ failed
The error most likely occurred in:

> ### Name: cbs_get_catalogs
> ### Title: Retrieves the possible catalog values that can be used for
> ###   retrieving data
> ### Aliases: cbs_get_catalogs
> 
> ### ** Examples
> 
> catalogs <- cbs_get_catalogs()
Warning in readBin(3L, raw(0), 32768L) :
  URL 'https://opendata.cbs.nl/ODataCatalog/Tables?$format=json': Timeout of 60 seconds was reached
Warning: Failing: http://opendata.cbs.nl/ODataCatalog/Tables?$format=json
Retrying...
Warning in readBin(3L, raw(0), 32768L) :
  URL 'https://opendata.cbs.nl/ODataCatalog/Tables?$format=json': Timeout of 60 seconds was reached
Error in readBin(3L, raw(0), 32768L) : cannot read from connection
Calls: cbs_get_catalogs ... parse_and_simplify -> parseJSON -> parse_con -> readBin
Execution halted
installed size is 17.8Mb
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Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 22.4Mb
  sub-directories of 1Mb or more:
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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    libs   3.4Mb
'LazyData' is specified without a 'data' directory
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.1Mb
    libs   9.9Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 104 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘batchtools’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘htmltools’
  ‘jsonlite’ ‘magrittr’ ‘methods’ ‘plotly’ ‘reshape’ ‘rlang’ ‘shiny’
  ‘shinyWidgets’ ‘shinyjqui’ ‘shinyjs’ ‘shinymaterial’ ‘sortable’ ‘ssh’
  ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bench’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'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
'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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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    help   2.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
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    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Package required but not available: ‘TxDb.Mmusculus.UCSC.mm10.knownGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 28982 marked UTF-8 strings
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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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
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.5Mb
    libs   1.2Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
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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
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...{C}=c\mathbf {U}\cdot \operatorname 
                                                  {diag}(\mathbf {s}) + \mat...
l.149 \mathbf{1}\,\mathbf{o}^T}{}
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Package required but not available: ‘IsoGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Namespaces in Imports field not imported from:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
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
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FNN’ ‘R.utils’ ‘SearchTrees’ ‘colorspace’ ‘colourpicker’
  ‘data.table’ ‘fields’ ‘mapproj’ ‘maps’ ‘maptools’ ‘ncdf4’ ‘raster’
  ‘rworldxtra’ ‘shinyFiles’ ‘shinyWidgets’ ‘shinyjs’ ‘shinythemes’ ‘sp’
  ‘tcltk’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.7Mb
Package suggested but not available for checking: ‘disttree’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Package suggested but not available for checking: ‘userfriendlyscience’
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: control reaches end of non-void function [-Wreturn-type]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.2/cold.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
'LazyData' is specified without a 'data' directory
Note: found 4186 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 742 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  15.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘CAM’
Running examples in ‘CompareMultipleModels-Ex.R’ failed
The error most likely occurred in:

> ### Name: best_model_finder
> ### Title: Finding the Best Model Using Eight Metrics Values
> ### Aliases: best_model_finder
> 
> ### ** Examples
> 
> set.seed(123) # for reproducibility
> Y <- rnorm(100, 100, 10)
> model_1 <-CEEMDANML::carigaan(Y, ratio = 0.8, n_lag = 4)
Error in optim(init[mask], armafn, method = optim.method, hessian = TRUE,  : 
  non-finite finite-difference value [1]
Calls: <Anonymous> -> arima -> optim
Execution halted
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  28.9Mb
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Note: found 92 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘lwgeom’ ‘s2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
installed size is 59.9Mb
  sub-directories of 1Mb or more:
    libs  58.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   2.6Mb
    libs   3.2Mb
Packages required and available but unsuitable versions:
  'stats', 'grDevices'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘cec2005benchmark’
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs          2.8Mb
    sample_data   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> \log _2 \dfrac 
                          {f_1 + \frac 12}{n_1 + \frac 12} - \log _2 \dfrac ...
l.1526           }{}
                    
! Undefined control sequence.
<argument> ...2}{n_1 + \frac 12} - \log _2 \dfrac 
                                                  {f_2 + \frac 12}{n_2 + \fr...
l.1526           }{}
                    
! Undefined control sequence.
<argument>  \dfrac 
                   {10^6 \cdot \frac {f_1}{n_1} + \lambda }{10^6 \cdot \frac...
l.1554           }{}
                    
! Undefined control sequence.
<argument> z := \dfrac 
                       {k - np}{\sqrt {n p (1-p)}} 
l.2597 ... := \dfrac{k - np}{\sqrt{n p (1-p)}} }{}
'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:
    extdata   3.8Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProData’
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Note: found 59 marked UTF-8 strings
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.6Mb
Package suggested but not available for checking: ‘rjags’
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Package unavailable to check Rd xrefs: ‘rjags’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘colourpicker’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   2.6Mb
Note: found 1934235 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Aux_info_data.Rmd’ using rmarkdown
--- finished re-building ‘Aux_info_data.Rmd’

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

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

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

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

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

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

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

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

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

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

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

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

Quitting from lines 68-97 [using offset] (time_series_offset.Rmd)
Error: processing vignette 'time_series_offset.Rmd' failed with diagnostics:
Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `as.Date.numeric()`:
! 'origin' must be supplied
--- failed re-building ‘time_series_offset.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
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
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Package suggested but not available for checking: ‘BEST’
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.2Mb
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer3’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 500 marked UTF-8 strings
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
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
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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘akde.Rmd’ using rmarkdown
--- finished re-building ‘akde.Rmd’

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


Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
'LazyData' is specified without a 'data' directory
Note: found 1350 marked UTF-8 strings
installed size is 138.9Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    data    1.5Mb
    libs  135.0Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘IRanges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘pbdMPI’
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 459 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    help   1.0Mb
    libs   4.8Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    docs          1.0Mb
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘plyr’ ‘simpleboot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 109157 marked UTF-8 strings
Note: found 2020 marked UTF-8 strings
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 212 marked Latin-1 strings
  Note: found 12719 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   4.2Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'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:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 8 marked Latin-1 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs    1.2Mb
    tests   1.5Mb
Package suggested but not available for checking: ‘msa’
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 360 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
Package required and available but unsuitable version: ‘methods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dblog’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.7Mb
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.
Note: found 122 marked UTF-8 strings
Package suggested but not available for checking: ‘BRugs’
Package suggested but not available for checking: ‘INLA’
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    libs  51.6Mb
Note: found 38 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.3Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘qpdf’
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \operatorname 
                              
l.514 \eqn{\operatorname{supp} D = \{0,1\}}{}
                                             , \eqn{E[U\vert D, X] = 0}{}, and
! Undefined control sequence.
<recently read> \operatorname 
                              
l.914 ...p} D = \operatorname{supp} Z = \{0,1\}}{}
                                                  ,
! Undefined control sequence.
<argument> \operatorname {supp} D = \operatorname 
                                                  {supp} Z = \{0,1\}
l.914 ...p} D = \operatorname{supp} Z = \{0,1\}}{}
                                                  ,
'LazyData' is specified without a 'data' directory
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  24.7Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...ilon _t(i) \right )= \left ( \dfrac 
                                                  {1}{\sqrt {p}}\sqrt {\sum ...
l.551     }{}
             
! Undefined control sequence.
<argument> ...}\sqrt {\sum _{j=1}^p \left (\dfrac 
                                                  {\left [\hat {\mathbf {x}}...
l.551     }{}
             
! Undefined control sequence.
<argument> ...sigma }_j^{(x)}}\right )^2}, \dfrac 
                                                  {1}{\sqrt {R}}\sqrt {\sum ...
l.551     }{}
             
! Undefined control sequence.
<argument> ...}\sqrt {\sum _{r=1}^R \left (\dfrac 
                                                  {\hat {{t}}_i^{(r)}} {\hat...
l.551     }{}
             
! Undefined control sequence.
<argument>  \hat {\mathbf {x}}_i = \dfrac 
                                          {1}{R}(\mathbf {x}_i-\hat {\boldsy...
l.561     }{}
             
! Undefined control sequence.
<argument> \hat {\sigma }_r^2=\dfrac 
                                     {1}{n}\sum _{j=1}^n\left ((\mathbf {x}_...
l.566     \mathbf{u}_r\right)^2}{}
                                   is thus the estimated empirical variance of
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  35.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 5764 marked UTF-8 strings
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
    libs   3.2Mb
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'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.3Mb
'LazyData' is specified without a 'data' directory
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.7Mb
GNU make is a SystemRequirements.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
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
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.9Mb
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  13.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Note: found 8014 marked UTF-8 strings
Package suggested but not available for checking: ‘rlibkriging’
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
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  34.0Mb
installed size is 57.8Mb
  sub-directories of 1Mb or more:
    libs  56.9Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 31 - 28 == 3
  ── Failure ('test-realized_duration.R:158:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 31 - 28 == 3
  ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 31 - 28 == 3
  
  [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
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
Namespace in Imports field not imported from: ‘truncnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggmulti’ ‘loon’ ‘loon.data’ ‘loon.ggplot’ ‘loon.shiny’ ‘loon.tourr’
  ‘stats’ ‘zenplots’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Package suggested but not available for checking: ‘BOLTSSIRR’
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.2Mb
Note: found 9796 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs  11.9Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
Note: found 100 marked UTF-8 strings
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘doMPI’
Package suggested but not available for checking: ‘DiPs’
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.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘parallel’ ‘rgdal’ ‘sp’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
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
Running ‘simpleTests.R’ [0s/0s]
  Running ‘skeleton_git2r.R’ [3s/3s]
Running the tests in ‘tests/skeleton_git2r.R’ failed.
Last 13 lines of output:
  * saving partial Rd database
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * building ‘foo_1.0.tar.gz’
  
  dratting
  Added and committed foo_1.0.tar.gz plus PACKAGES files. Still need to push.
  
  Error in testRepoActions(repodir) : 
    Wrong package files found after pruning for version = NA
  Calls: runTest -> testRepoActions
  In addition: Warning message:
  In (function (dir = ".", fields = NULL, type = c("source", "mac.binary",  :
    PACKAGES files do not include MD5 sums in the win.binary case, so strict checking is impossible. Calling down to write_PACKAGES directly.
  Execution halted
'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:
    libs   6.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’
  All declared Imports should be used.
installed size is 78.8Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  77.2Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> f:\mathbb 
                     {R}^K -> \mathbb {R}^L, (x_{n1},x_{n2},...,x_{nK}) -> f...
l.2519 ..._{nK}) -> f(x_{n1},x_{n2},...,x_{nK})}{}
                                                   be differentiable up to o...
! Undefined control sequence.
<argument> f:\mathbb {R}^K -> \mathbb 
                                      {R}^L, (x_{n1},x_{n2},...,x_{nK}) -> f...
l.2519 ..._{nK}) -> f(x_{n1},x_{n2},...,x_{nK})}{}
                                                   be differentiable up to o...
Note: found 149 marked UTF-8 strings
Package suggested but not available for checking: ‘dsBaseClient’
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.6Mb
Note: found 1 marked Latin-1 string
'LazyData' is specified without a 'data' directory
'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:
    htmlwidgets   4.7Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.4Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.0Mb
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 311.1Mb
  sub-directories of 1Mb or more:
    libs  310.5Mb
Running ‘testthat.R’ [24s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error in `as.POSIXct.numeric(1.234567 + (1:100) * 1e-06, tz = "UTC")`: 'origin' must be supplied
  Backtrace:
      ▆
   1. ├─base::data.frame(a = as.POSIXct(1.234567 + (1:100) * 1e-06, tz = "UTC")) at test_timestamp.R:5:2
   2. ├─base::as.POSIXct(1.234567 + (1:100) * 1e-06, tz = "UTC")
   3. └─base::as.POSIXct.numeric(1.234567 + (1:100) * 1e-06, tz = "UTC")
  
  [ FAIL 1 | WARN 0 | SKIP 20 | PASS 571 ]
  Error: Test failures
  In addition: Warning messages:
  1: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. 
  2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. 
  Execution halted
  Warning message:
  Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2854 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    R      3.3Mb
    data   8.3Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
Namespaces in Imports field not imported from:
  ‘NatureSounds’ ‘av’ ‘magrittr’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'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:
    data   2.5Mb
    doc    1.5Mb
    libs   3.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Note: found 9 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   7.8Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘eaf/libs/eaf.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘eaf/io.o’, ‘mo-tools/hv.o’
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘eaf/io.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs        8.5Mb
    shiny_app   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  11.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘diffcoexp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qcr’
  All declared Imports should be used.
'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
Error: package or namespace load failed for ‘echarty’:
 .onLoad failed in loadNamespace() for 'echarty', details:
  call: loadNamespace(x)
  error: there is no package called ‘shiny’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  10.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
installed size is 91.6Mb
  sub-directories of 1Mb or more:
    libs  90.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘econet.tex’ using tex
Error: processing vignette 'econet.tex' failed with diagnostics:
Running 'texi2dvi' on 'econet.tex' failed.
LaTeX errors:
! LaTeX Error: File `orcidlink.sty' not found.

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 22 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:
  ‘dplyr’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘opGMMassessment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
Package suggested but not available for checking: ‘eggCountsExtra’
installed size is 80.3Mb
  sub-directories of 1Mb or more:
    libs  79.6Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_eHDPrep.Rmd’ using rmarkdown
! Missing endcsname inserted.
<to be read again> 
                   unhbox 
l.302 ...ics[width=1\linewidth]{./images/Figure_1}

Error: processing vignette 'Introduction_to_eHDPrep.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/high-sierra-x86_64/results/4.2/eHDPrep.Rcheck/vign_test/eHDPrep/vignettes/Introduction_to_eHDPrep.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Introduction_to_eHDPrep.log for more info.
--- failed re-building ‘Introduction_to_eHDPrep.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘bisg.Rmd’ using rmarkdown

Quitting from lines 164-175 [unnamed-chunk-16] (bisg.Rmd)
Error: processing vignette 'bisg.Rmd' failed with diagnostics:
no applicable method for 'tbl_vars' applied to an object of class "NULL"
--- failed re-building ‘bisg.Rmd’

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

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

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

Quitting from lines 235-263 [performance_analysis] (performance_analysis.Rmd)
Error: processing vignette 'performance_analysis.Rmd' failed with diagnostics:
No columns selected for aggregation.
--- failed re-building ‘performance_analysis.Rmd’

SUMMARY: processing the following files failed:
  ‘bisg.Rmd’ ‘performance_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 130.2Mb
  sub-directories of 1Mb or more:
    libs  130.0Mb
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  46.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
'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
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 58.1Mb
  sub-directories of 1Mb or more:
    libs  56.8Mb
GNU make is a SystemRequirements.
Running ‘testthat.R’ [62s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    1. ├─testthat::skip_if(is.null(tensorflow::tf_version())) at test-feature_hash.R:252:2
    2. │ └─base::isTRUE(condition)
    3. └─tensorflow::tf_version()
    4.   └─tensorflow::tf_config()
    5.     └─reticulate::py_config()
    6.       └─reticulate:::ensure_python_initialized()
    7.         └─reticulate:::initialize_python()
    8.           └─base::tryCatch(...)
    9.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   10.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11.                 └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 34 | SKIP 83 | PASS 231 ]
  Error: Test failures
  Execution halted
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
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  15.5Mb
Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

> ### Name: CInp2TS
> ### Title: Function to convert Constant Input to Time Series
> ### Aliases: CInp2TS
> ### Keywords: CInp2TS
> 
> ### ** Examples
> 
> library(EmiStatR)
> library(zoo)

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> data("qs_factor")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> 
> cinp.daily.file <- qs_factor
> cinp.weekly     <- list(mon=1, tue=.83, wed=.83, thu=.83, fri=1, sat=1.25, sun=1.25)  
> # factors average to 1
> cinp.seasonal   <- list(jan=.79, feb=.79, mar=1.15, apr=1.15, may=1.15, jun=1.15,
+                         jul=1.15, aug=1.15, sep=1.15, oct=1.15, nov=.79, dec=.79) 
> # factors average to 1
> ts1 <- CInp2TS(cinp, prec, cinp.daily.file, cinp.weekly, cinp.seasonal)
Error in `[.xts`(cinp.ts.deltap, 1:nrow(P1), ) : subscript out of bounds
Calls: CInp2TS -> [ -> [.xts
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
Note: found 16919 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 23639 marked Latin-1 strings
Namespace in Imports field not imported from: ‘BBmisc’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   2.7Mb
Package suggested but not available for checking: ‘epidict’
installed size is 107.5Mb
  sub-directories of 1Mb or more:
    help    1.5Mb
    libs  105.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘knitr’ ‘plyr’ ‘rgdal’ ‘tidyverse’ ‘tokenizers’ ‘xml2’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.7Mb
    libs   3.1Mb
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
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
'LazyData' is specified without a 'data' directory
Packages required and available but unsuitable versions: 'stats', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.2/eummd.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Running ‘testthat.R’ [40s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_helper_blocksize.R:34:3'): blockSize reports block size in row-col order ──
  Error: [writeRaster] invalid driver
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test_helper_blocksize.R:34:2
   2. │ └─base::withCallingHandlers(...)
   3. ├─terra::writeRaster(...) at test_helper_blocksize.R:35:4
   4. └─terra::writeRaster(...)
   5.   └─terra (local) .local(x, filename, ...)
   6.     └─terra:::messages(x, "writeRaster")
   7.       └─terra:::error(f, x@ptr$getError())
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 463 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘ExactData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 342 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    exiftool  14.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
installed size is 80.4Mb
  sub-directories of 1Mb or more:
    libs  78.2Mb
GNU make is a SystemRequirements.
'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:
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘exuberdata’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 5 marked Latin-1 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘data.table’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.0Mb
    help   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:
    libs   8.5Mb
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: ‘RWeka’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   1.2Mb
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

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

Probably some imports need to be declared in the NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     2.9Mb
installed size is 47.8Mb
  sub-directories of 1Mb or more:
    libs  47.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 31.7Mb
  sub-directories of 1Mb or more:
    libs  31.4Mb
Package suggested but not available for checking: ‘coxKM’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.8Mb
Package suggested but not available for checking: ‘NNLM’
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   4.9Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.5Mb
    help   2.1Mb
    libs   8.5Mb
Unexported objects imported by ':::' calls:
  ‘fdapace:::GCVLwls1D1’ ‘fdapace:::GetSmoothedMeanCurve’
  ‘fdapace:::HandleNumericsAndNAN’ ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘FastGP’ ‘MASS’ ‘fdapace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.2Mb
Note: found 76 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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.
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespace in Imports field not imported from: ‘panelView’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'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
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    extdata   2.8Mb
    libs      1.2Mb
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MicrobeDS’
installed size is 37.8Mb
  sub-directories of 1Mb or more:
    libs  36.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    2.2Mb
    help   1.1Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R         4.5Mb
    doc       2.1Mb
    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
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  8.2Mb
  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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 7 marked UTF-8 strings
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    lib   11.1Mb
    libs  19.7Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Running ‘testthat.R’ [30s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(fitHeavyTail)
  > 
  > test_check("fitHeavyTail")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 71 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-fit_mvst.R:47:3'): default mode works ────────────────────────
  ...[] not equal to ...[].
  Component "num_iterations": Mean relative difference: 0.002739726
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 71 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Misplaced alignment tab character &.
<argument> ...} \pi + \frac {(1-\pi )}{\zeta (s)}&
                                                  ,k=0, \\ \frac {(1-\pi )k^...
l.512 }{}
         
! Misplaced alignment tab character &.
<argument> ...\ \frac {(1-\pi )k^{-s}}{\zeta (s)}&
                                                  ,k=1,2,\ldots \end {cases} 
l.512 }{}
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘reliaR’
'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
Found the following apparent S3 methods exported but not registered:
  plot.fpp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.6Mb
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   3.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 256.2Mb
  sub-directories of 1Mb or more:
    libs  255.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Malformed Description field: should contain one or more complete sentences.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.2/FLSSS.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 446 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘Rcpp’ ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without 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 31 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘LaplacesDemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   5.5Mb
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
Package suggested but not available for checking: ‘epiR’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Note: found 50 marked UTF-8 strings
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 81.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.7Mb
    libs  74.2Mb
installed size is 50.4Mb
  sub-directories of 1Mb or more:
    libs  49.9Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'rrlda', 'RWeka'
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 39 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 120 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘WGCNA’
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   4.2Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘cBioPortalData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
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
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   5.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Package which this enhances but not available for checking: ‘doMPI’
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Environment aligned undefined.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Misplaced alignment tab character &.
<argument>  \begin {aligned} L &
                                 = m - z_\alpha s \cr U & = m + z_\alpha s \...
l.1068 }{}
          
! Misplaced \cr.
<argument> ... {aligned} L & = m - z_\alpha s \cr 
                                                  U & = m + z_\alpha s \end ...
l.1068 }{}
          
! Misplaced alignment tab character &.
<argument> ...ligned} L & = m - z_\alpha s \cr U &
                                                   = m + z_\alpha s \end {al...
l.1068 }{}
          
! LaTeX Error: \begin{list} on input line 1059 ended by \end{aligned}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Environment aligned undefined.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Misplaced alignment tab character &.
<argument>  \begin {aligned} m &
                                 = \frac {U + L}{2} \cr s & = \frac {U - L}{...
l.1075 }{}
          
! Misplaced \cr.
<argument> ...aligned} m & = \frac {U + L}{2} \cr 
                                                  s & = \frac {U - L}{2 z_\a...
l.1075 }{}
          
! Misplaced alignment tab character &.
<argument> ...gned} m & = \frac {U + L}{2} \cr s &
                                                   = \frac {U - L}{2 z_\alph...
l.1075 }{}
          
! LaTeX Error: \begin{list} on input line 1059 ended by \end{aligned}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    doc   44.3Mb
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   9.7Mb
installed size is 68.6Mb
  sub-directories of 1Mb or more:
    libs  68.1Mb
GNU make is a SystemRequirements.
installed size is 60.3Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     56.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  16.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
Package suggested but not available for checking: ‘gputools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 295.8Mb
  sub-directories of 1Mb or more:
    L8NY18    2.2Mb
    libs    292.5Mb
installed size is 262.7Mb
  sub-directories of 1Mb or more:
    extdata    1.0Mb
    libs     261.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    perl   3.9Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Namespace in Imports field not imported from: ‘badger’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.4Mb
    libs      1.5Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘genderdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘R.utils’ ‘markdown’
  All declared Imports should be used.
Package suggested but not available for checking: ‘muscle’
Package suggested but not available for checking: ‘rrvgo’
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   8.9Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
  ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   4.0Mb
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
Package suggested but not available for checking: ‘INLA’
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
Note: found 58 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   3.0Mb
    libs      4.4Mb
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
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   4.2Mb
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R         9.6Mb
    extdata   2.5Mb
    help      2.4Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 66.1Mb
  sub-directories of 1Mb or more:
    libs  64.5Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
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
Packages required and available but unsuitable versions:
  'biomaRt', 'grDevices', 'graphics', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pipeR’ ‘rlang’
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...s ,C_k)^\top = \mathbf {0}\,\,\text 
                                                  {and}\,\,\mathcal H_0: \ma...
l.238 ...H} (B_1,\ldots,B_k)^\top = \mathbf{0},}{}
                                                  
! Undefined control sequence.
<argument> ...\mathbf {C} = \mathbf {0}\,\, \text 
                                                  {or}\,\,\mathcal H_{0,\ell...
l.249 ...{B} = \mathbf{0}, \,\,\ell=1,\ldots,q,}{}
                                                  
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.251 ...s \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.252 \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                             , respectively, are calculated.
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.265 ...r \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.266 for \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                                 , the test statistics and c...
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘googlesheets4’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggmsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘scagnostics’
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Package required but not available: ‘ggbio’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 2356 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  18.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  8.5Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Packages required but not available: 'memes', 'universalmotif'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  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
Packages required but not available: 'lefser', 'Maaslin2', 'metagenomeSeq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lixoftConnectors’
installed size is  8.8Mb
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'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
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installed size is  9.4Mb
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Note: found 6242 marked UTF-8 strings
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 138 marked UTF-8 strings
installed size is  9.2Mb
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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.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
installed size is 17.9Mb
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installed size is  5.2Mb
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GNU make is a SystemRequirements.
installed size is  6.1Mb
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installed size is  8.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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:
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  All declared Imports should be used.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is  7.1Mb
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installed size is 10.3Mb
  sub-directories of 1Mb or more:
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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 149.5Mb
  sub-directories of 1Mb or more:
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installed size is 18.7Mb
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Namespace in Imports field not imported from: ‘ordinal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 50.2Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
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installed size is 53.7Mb
  sub-directories of 1Mb or more:
    libs  52.6Mb
GNU make is a SystemRequirements.
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    libs  40.9Mb
installed size is 39.7Mb
  sub-directories of 1Mb or more:
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Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 67.4Mb
  sub-directories of 1Mb or more:
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installed size is 37.2Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \mathbb 
                        
l.97 ...ong to a compact set of \eqn{\mathbb{R}}{}
                                                  .
! Undefined control sequence.
<recently read> \mathbb 
                        
l.161 ... to a compact set of \eqn{\mathbb{R}^2}{}
                                                  .
Namespace in Imports field not imported from: ‘rnaturalearthdata’
  All declared Imports should be used.
Note: found 1191 marked UTF-8 strings
installed size is 12.0Mb
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'LazyData' is specified without a 'data' directory
Running examples in ‘gluvarpro-Ex.R’ failed
The error most likely occurred in:

> ### Name: preprocessgvp
> ### Title: preprocessing raw data from continuous glucose monitoring
> ### Aliases: preprocessgvp
> 
> ### ** Examples
> 
> data("datagvp4")
> preprocessgvp(datagvp4)
Error in preprocessgvp(datagvp4) : 
  Variable date and time must have yyyy/mm/dd and hh:mm:ss format.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
GNU make is a SystemRequirements.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 1352 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘future’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
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installed size is 31.6Mb
  sub-directories of 1Mb or more:
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installed size is 140.2Mb
  sub-directories of 1Mb or more:
    libs  139.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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    doc    3.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   5.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  ‘dplyr’ ‘ggplot2’ ‘ggpubr’ ‘gridGraphics’ ‘gtools’ ‘kableExtra’
  ‘knitr’ ‘magrittr’ ‘pastecs’ ‘reshape2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘summarytools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
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installed size is  7.8Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
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installed size is 18.7Mb
  sub-directories of 1Mb or more:
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Note: found 989 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 51.8Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
installed size is 31.2Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘pdftools’
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Running ‘testpage.R’ [1s/1s]
Running the tests in ‘tests/testpage.R’ failed.
Last 13 lines of output:
  > # Now import testpage.ps and draw it in various ways
  > #######################################
  > 
  > require(grImport)
  Loading required package: grImport
  Loading required package: XML
  > 
  > PostScriptTrace("testpage.ps", "testpage.xml")
  sh: gs: command not found
  Error in PostScriptTrace("testpage.ps", "testpage.xml") : 
    sorry, 'gs' cannot be found
  In addition: Warning message:
  In system(paste(shQuote(gsexe), "-help > /dev/null")) :
    error in running command
  Execution halted
Errors in running code in vignettes:
when running code in ‘import.Rnw’
  ...
Loading required package: XML

> PostScriptTrace("chess_game_01.fromInkscape.eps")
sh: gs: command not found
Warning in system(paste(shQuote(gsexe), "-help > /dev/null")) :
  error in running command

  When sourcing 'import.R':
Error: sorry, 'gs' cannot be found
Execution halted
when running code in ‘importText.Rnw’
  ...
Loading required package: XML

> PostScriptTrace("hello.ps", "hello.xml")
sh: gs: command not found
Warning in system(paste(shQuote(gsexe), "-help > /dev/null")) :
  error in running command

  When sourcing 'importText.R':
Error: sorry, 'gs' cannot be found
Execution halted

  ‘import.Rnw’... failed
  ‘importText.Rnw’... failed
Error(s) in re-building vignettes:
--- re-building ‘import.Rnw’ using Sweave
Loading required package: XML
sh: gs: command not found
Warning in system(paste(shQuote(gsexe), "-help > /dev/null")) :
  error in running command

Error: processing vignette 'import.Rnw' failed with diagnostics:
 chunk 5 (label = chesspiece) 
Error in PostScriptTrace("chess_game_01.fromInkscape.eps") : 
  sorry, 'gs' cannot be found

--- failed re-building 'import.Rnw'

--- re-building 'importText.Rnw' using Sweave
sh: gs: command not found
Warning in system(paste(shQuote(gsexe), "-help > /dev/null")) :
  error in running command

Error: processing vignette 'importText.Rnw' failed with diagnostics:
 chunk 4 (label = simpleimport) 
Error in PostScriptTrace("hello.ps", "hello.xml") : 
  sorry, 'gs' cannot be found

--- failed re-building 'importText.Rnw'

SUMMARY: processing the following files failed:
  'import.Rnw' 'importText.Rnw'

Error: Vignette re-building failed.
Execution halted
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
installed size is  9.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘rjags’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument>  \min _{\boldsymbol \beta \in \mathbb 
                                                 {R}^p} L(\boldsymbol \beta ...
l.648 }{}
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.4Mb
Package required but not available: ‘CelliD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.3Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 269 marked UTF-8 strings
Note: found 42384 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
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    libs   4.7Mb
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.
'LazyData' is specified without a 'data' directory
installed size is 250.2Mb
  sub-directories of 1Mb or more:
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    java  247.1Mb
'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:
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    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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installed size is 128.9Mb
  sub-directories of 1Mb or more:
    doc     1.2Mb
    libs  127.1Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Note: found 3 marked UTF-8 strings
Note: found 104392 marked UTF-8 strings
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  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 21.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Heatplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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'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   6.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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    help      1.6Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
installed size is 23.4Mb
  sub-directories of 1Mb or more:
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    libs  19.3Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      2.5Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘fmrs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.8Mb
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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
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.1Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
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    libs        7.6Mb
Package required and available but unsuitable version: ‘fitHeavyTail’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
installed size is 46.2Mb
  sub-directories of 1Mb or more:
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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
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.9Mb
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
installed size is 48.9Mb
  sub-directories of 1Mb or more:
    libs  48.4Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
Note: found 9638 marked UTF-8 strings
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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installed size is  7.8Mb
  sub-directories of 1Mb or more:
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installed size is 11.4Mb
  sub-directories of 1Mb or more:
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html_describe_con: multiple local function definitions for ‘g’ with
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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
installed size is 64.7Mb
  sub-directories of 1Mb or more:
    libs  63.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Package required but not available: ‘bamsignals’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
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
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 59.2Mb
  sub-directories of 1Mb or more:
    libs  58.6Mb
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
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘HTSFilter’
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    2.1Mb
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    libs  38.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
'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:
    libs   7.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.1Mb
'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.
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    libs  42.7Mb
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
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    exdata   6.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Package suggested but not available for checking: ‘webshot2’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 38558 marked UTF-8 strings
Note: found 1058038 marked UTF-8 strings
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Note: found 1 marked UTF-8 string
Note: found 359 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: ‘SparkR’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'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
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.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Namespaces in Imports field not imported from:
  ‘digest’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  32.2Mb
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.
Note: found 1 marked UTF-8 string
Note: found 40 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘IFCdata’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   5.3Mb
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   1.5Mb
    libs  14.8Mb
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  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         4.5Mb
Package suggested but not available for checking: ‘tesseract’
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.2Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     23.1Mb
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    libs   13.8Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rcccd’

See section ‘The DESCRIPTION file’ 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
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.1Mb
  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
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package required but not available: ‘RankProd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'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
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘splines2’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
'LazyData' is specified without a 'data' directory
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
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  32.0Mb
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
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.6Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘surveyspec’
Note: found 102 marked UTF-8 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gmodels’ ‘lmtest’ ‘testthat’ ‘tidyverse’ ‘zoo’
  All declared Imports should be used.
Note: found 46 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Package suggested but not available for checking: ‘Rmpi’
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘glmnet’
  All declared Imports should be used.
'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   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
Note: found 104 marked UTF-8 strings
'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.
'LazyData' is specified without a 'data' directory
installed size is 57.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.3Mb
    libs  52.0Mb
GNU make is a SystemRequirements.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  13.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘stars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
Note: found 58 marked UTF-8 strings
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'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
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          15.8Mb
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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    docs   3.5Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 1984 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘mcmcplots’ ‘tidyverse’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Namespace in Imports field not imported from: ‘GA’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.4Mb
installed size is 47.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  44.4Mb
GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.7Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘knitr’ ‘markdown’
  All declared Imports should be used.
Note: found 85 marked UTF-8 strings
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  25.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    i18n   4.0Mb
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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.9Mb
Packages which this enhances but not available for checking:
  'remMap', 'MultivariateRandomForest'
'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.
Note: found 176 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> v^{\text 
                    {th}}
l.1131 ...hbf{W}^v}{} in the \eqn{v^{\text{th}}}{}
                                                   modality
'LazyData' is specified without a 'data' directory
installed size is 29.5Mb
  sub-directories of 1Mb or more:
    libs  28.1Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    examples      2.8Mb
    htmlwidgets   1.1Mb
    www           2.7Mb
'LazyData' is specified without a 'data' directory
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
Namespace in Imports field not imported from: ‘gifski’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
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
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Running examples in ‘keyperm-Ex.R’ failed
The error most likely occurred in:

> ### Name: keyperm-package
> ### Title: keyperm: Keyword Analysis Using Permutation Tests
> ### Aliases: keyperm-package _PACKAGE
> ### Keywords: internal
> 
> ### ** Examples
> 
> library(tm)
Loading required package: NLP
> library(keyperm)
> 
> # load subcorpora "acq" and "crude" from Reuters
> 
> data(acq)
> data(crude)
> 
> # convert to term-document-matrices and combine into single tdm
> 
> acq_tdm <- TermDocumentMatrix(acq, control = list(removePunctuation = TRUE))
> crude_tdm <- TermDocumentMatrix(crude, control = list(removePunctuation = TRUE))
> tdm <- c(acq_tdm, crude_tdm)
> 
> # generate a logical that indicates whether document comes from "acq" or "crude"
> 
> ndoc_A <- dim(acq_tdm)[2]
> ndoc_B <- dim(crude_tdm)[2]
> corpus <- rep(c(TRUE, FALSE), c(ndoc_A, ndoc_B))
> 
> # generate an indexed frequency list, the data structure used by keyperm
> 
> reuters_ifl <- create_ifl(tdm, corpus = corpus)
Error in UseMethod("TermDocumentMatrix", x) : 
  no applicable method for 'TermDocumentMatrix' applied to an object of class "NULL"
Calls: create_ifl -> <Anonymous>
Execution halted
'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
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘Rsamtools’ ‘rtracklayer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fitdistrplus’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
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
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
Unknown package ‘REdaS’ in Rd xrefs
Note: found 9 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.0Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 12.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  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
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘mixAK’
Package unavailable to check Rd xrefs: ‘mixAK’
'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
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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’ ‘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.
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:
  ‘devtools’ ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
Note: found 75 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
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
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
'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
installed size is 58.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  54.2Mb
GNU make is a SystemRequirements.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
installed size is  6.0Mb
  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
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.9Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
GNU make is a SystemRequirements.
'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
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs  10.4Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 67.6Mb
  sub-directories of 1Mb or more:
    libs  66.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  44.4Mb
'LazyData' is specified without a 'data' directory
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    doc       1.0Mb
    extdata   1.2Mb
    libs      8.8Mb
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
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.6Mb
installed size is 42.8Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘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
'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
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: ‘RWeka’
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs      22.4Mb
    testdata   1.3Mb
installed size is 57.1Mb
  sub-directories of 1Mb or more:
    libs  56.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘base’ ‘qpdf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lestat’
  All declared Imports should be used.
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘lolog-ergm.Rmd’ using rmarkdown

Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
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 994 marked Latin-1 strings
Package suggested but not available for checking: ‘RDRToolbox’
'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
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GeneticsPed’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
Note: found 55 marked UTF-8 strings
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
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
'LazyData' is specified without a 'data' directory
installed size is 50.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  48.3Mb
'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
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Icens’ ‘interval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpostgis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs   1.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R   4.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 71.0Mb
  sub-directories of 1Mb or more:
    libs  70.8Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘orthogene’
Package unavailable to check Rd xrefs: ‘orthogene’
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.
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quitte’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 133.6Mb
  sub-directories of 1Mb or more:
    doc     6.2Mb
    libs  126.8Mb
'LazyData' is specified without a 'data' directory
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
Package suggested but not available for checking: ‘dittoSeq’
Package suggested but not available for checking: ‘ssize’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocCheck’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   4.9Mb
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
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Namespaces in Imports field not imported from:
  ‘cli’ ‘nomnoml’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
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
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
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
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Note: found 55 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
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
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs         11.8Mb
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   4.3Mb
Namespace in Imports field not imported from: ‘pbmcapply’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.0Mb
Note: found 1 marked UTF-8 string
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
GNU make is a SystemRequirements.
Note: found 5210 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:
  ‘bookdown’ ‘kableExtra’ ‘knitr’
  All declared Imports should be used.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs      11.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘marssTMB’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.NCBI.GRCh38', 'wiggleplotr'
Package suggested but not available for checking: ‘flashier’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 42.5Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   9.1Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   9.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘Matrix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
GNU make is a SystemRequirements.
qr.X: no visible binding for global variable ‘R’
Undefined global functions or variables:
  R
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 18 marked UTF-8 strings
Note: found 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
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...{i-1}}{x_{p_{i}}-x_{p_{i-1}}} \text 
                                                  { for } x_{p_{i-1}} \le x ...
l.2828  i = 1,\dots,4}{}
                        
! Undefined control sequence.
<argument> f(x) = 0, \text 
                           { otherwise}
l.2829 \deqn{f(x) = 0, \text{ otherwise}}{}
                                           
! Undefined control sequence.
<argument> F(x) = 0 \text 
                          { for } x < x_{p_{0}}
l.2832 ...n{F(x) = 0 \text{ for } x < x_{p_{0}}}{}
                                                  
! Undefined control sequence.
<argument> ...-1}}}*(x-x_{p_{i-1}})+p_{i-1} \text 
                                                  { for } x_{p_{i-1}} \le x ...
l.2833 ...-1}} \le x < x_{p_{i}}, i = 1,\dots,4}{}
                                                  
! Undefined control sequence.
<argument> F(x) = 1 \text 
                          { for } x_{p_{4}}\le x
l.2835 ...{F(x) = 1 \text{ for } x_{p_{4}}\le x}{}
'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
'LazyData' is specified without a 'data' directory
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  10.7Mb
Namespace in Imports field not imported from: ‘boot.heterogeneity’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 46 marked UTF-8 strings
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    libs  29.9Mb
'LazyData' is specified without a 'data' directory
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
'LazyData' is specified without a 'data' directory
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'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: ‘psych’
  All declared Imports should be used.
'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:
    libs  10.7Mb
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
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 59.8Mb
  sub-directories of 1Mb or more:
    libs  58.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    libs  40.8Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
ADPopSel: no visible global function definition for ‘%dorng%’
ADRand: no visible global function definition for ‘%dorng%’
ADSSMod: no visible global function definition for ‘%dorng%’
ADTreatSel: no visible global function definition for ‘%dorng%’
ClustRand: no visible global function definition for ‘%dorng%’
EventPred: no visible global function definition for ‘%dorng%’
FutRuleNCores: no visible global function definition for ‘%dorng%’
MultAdj1NCores: no visible global function definition for ‘%dorng%’
MultAdj2NCores: no visible global function definition for ‘%dorng%’
MultAdj3NCores: no visible global function definition for ‘%dorng%’
Undefined global functions or variables:
  %dorng%
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
'LazyData' is specified without a 'data' directory
installed size is 134.5Mb
  sub-directories of 1Mb or more:
    libs  133.2Mb
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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.1Mb
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
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
    libs      3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.4Mb
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
installed size is 89.9Mb
  sub-directories of 1Mb or more:
    libs  89.2Mb
GNU make is a SystemRequirements.
Note: found 37 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:
  ‘e1071’ ‘gbm’ ‘ggplot2’ ‘graphics’ ‘randomForest’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'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.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
Package required but not available: ‘metagenomeSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
'LazyData' is specified without a 'data' directory
Running ‘mpost.R’ [1s/1s]
Running the tests in ‘tests/mpost.R’ failed.
Last 13 lines of output:
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  > 
  > library(grImport)
  Loading required package: XML
  > PostScriptTrace("fig.1")
  sh: gs: command not found
  Error in PostScriptTrace("fig.1") : sorry, 'gs' cannot be found
  In addition: Warning message:
  In system(paste(shQuote(gsexe), "-help > /dev/null")) :
    error in running command
  Execution halted
'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.
installed size is 58.4Mb
  sub-directories of 1Mb or more:
    libs  58.0Mb
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.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Note: found 1 marked UTF-8 string
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.6Mb
    libs  20.1Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Misplaced alignment tab character &.
<argument> \left (\begin {matrix} \cos (\rho ) &
                                                 \sin (\rho ) \\ - \sigma \s...
l.457 ... \sigma\cos(\rho) \end{matrix} \right)}{}
                                                  
! Misplaced alignment tab character &.
<argument> ...n (\rho ) \\ - \sigma \sin (\rho ) &
                                                   \sigma \cos (\rho ) \end ...
l.457 ... \sigma\cos(\rho) \end{matrix} \right)}{}
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘fs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘boot’ ‘energy’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘webshot2’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \mathbb 
                        
l.268 ..., a random vector of \eqn{\mathbb{R}^p}{}
                                                   (\eqn{p > 1}{}) distribut...
! Undefined control sequence.
<recently read> \mathbb 
                        
l.270 ..., a random vector of \eqn{\mathbb{R}^p}{}
                                                   distributed according to ...
'LazyData' is specified without a 'data' directory
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  19.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'DAPAR', 'ProteoMM'
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Note: found 9345 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    lib    9.2Mb
    libs   4.4Mb
Found the following apparent S3 methods exported but not registered:
  plot.icss print.icss print.micss
See section ‘Registering S3 methods’ 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: ‘midfielddata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'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
'LazyData' is specified without a 'data' directory
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
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
installed size is 101.8Mb
  sub-directories of 1Mb or more:
    libs  101.2Mb
Namespaces in Imports field not imported from:
  ‘pracma’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package required but not available: ‘GlobalAncova’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Package unavailable to check Rd xrefs: ‘mixAK’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   1.2Mb
    libs      1.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Package suggested but not available for checking: ‘karyoploteR’
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Packages which this enhances but not available for checking:
  'pbdMPI', 'AnalyzeFMRI'
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Namespaces in Imports field not imported from:
  ‘ashr’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ConfusionTableR’ ‘OddsPlotty’ ‘caret’ ‘dplyr’ ‘ggplot2’ ‘parsnip’
  ‘ranger’ ‘recipes’ ‘rsample’ ‘varhandle’ ‘workflows’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 237.5Mb
  sub-directories of 1Mb or more:
    include    9.6Mb
    libs     227.5Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘randomForest’
  All declared Imports should be used.
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
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:
  ‘datasets’ ‘doParallel’ ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  15.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 68.4Mb
  sub-directories of 1Mb or more:
    doc    5.9Mb
    libs  61.9Mb
'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 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
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
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...}, \frac {v}{2}, \frac {1}{2})\text 
                                                  {, if }x \geq 0\\ \frac {1...
l.1646 }{}
          
! Undefined control sequence.
<argument> ...}, \frac {v}{2}, \frac {1}{2})\text 
                                                  {, if }x < 0 \end {cases}, 
l.1646 }{}
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'doMPI', 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'MoBPSmaps'
Packages required but not available: 'RaggedExperiment', 'ggbio'

Packages suggested but not available for checking:
  'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'BSgenome.Hsapiens.UCSC.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lazyeval’
  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:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 18 marked Latin-1 strings
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
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.7Mb
    libs   4.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 13 marked UTF-8 strings
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.1Mb
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
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs     3.0Mb
    raster   2.2Mb
Package suggested but not available for checking: ‘readbulk’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.6Mb
Package unavailable to check Rd xrefs: ‘readbulk’
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Package suggested but not available for checking: ‘glmulti’
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rjags’
installed size is 65.3Mb
  sub-directories of 1Mb or more:
    libs  64.9Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘rjags’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> \gamma (s,t) = \sigma \text 
                                       {exp}\left (\frac {-(s-t)^2}{l}\right ),
l.342 ...t{exp}\left(\frac{-(s-t)^2}{l}\right),}{}
                                                  
! Undefined control sequence.
<argument> \gamma (s,t) = \sigma \text 
                                       {exp}\left (\frac {-|s-t|}{l}\right )
l.344 ...text{exp}\left(\frac{-|s-t|}{l}\right)}{}
                                                  
! Undefined control sequence.
<argument> \gamma (s,t) = \sigma ^2 \text 
                                          {exp}\left (\frac {-(s-t)^2}{2 l^2...
l.346 ...xp}\left(\frac{-(s-t)^2}{2 l^2}\right)}{}
                                                  .
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'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
Note: found 75 marked UTF-8 strings
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    data   4.5Mb
    libs   3.6Mb
installed size is 48.4Mb
  sub-directories of 1Mb or more:
    libs  48.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.9Mb
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  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
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  17.1Mb
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
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Namespaces in Imports field not imported from:
  ‘markdown’ ‘methods’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> j\text 
                  {th}
l.86 ...d \eqn{R_{j}^{2}}{} the \eqn{j\text{th}}{}
                                                   coefficient of determinat...
! Undefined control sequence.
<argument> j\text 
                  {th}
l.86 ...of determination of the \eqn{j\text{th}}{}
                                                   auxiliary regression.
'LazyData' is specified without 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:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
Note: found 2632 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘polycor’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘multgee_vignette.Rmd’ using rmarkdown
! LaTeX Error: File `orcidlink.sty' not found.

! Emergency stop.
<read *> 

Error: processing vignette 'multgee_vignette.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/high-sierra-x86_64/results/4.2/multgee.Rcheck/vign_test/multgee/vignettes/multgee_vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See multgee_vignette.log for more info.
--- failed re-building ‘multgee_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.3Mb
Running examples in ‘multiblock-Ex.R’ failed
The error most likely occurred in:

> ### Name: basic
> ### Title: Single- and Two-Block Methods
> ### Aliases: basic
> 
> ### ** Examples
> 
> data(potato)
> X <- potato$Chemical
> y <- potato$Sensory[,1,drop=FALSE]
> 
> pca.pot  <- pca(X, ncomp = 2)
> pcr.pot  <- pcr(y ~ X, ncomp = 2)
> pls.pot  <- plsr(y ~ X, ncomp = 2)
> cca.pot  <- cca(potato[1:2])
> ifa.pot  <- ifa(potato[1:2])
Error in RGCCA::rgcca(blocks = X, connection = matrix(c(0, 1, 1, 0), 2,  : 
  unused arguments (blocks = X, connection = matrix(c(0, 1, 1, 0), 2, 2))
Calls: ifa
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vignette_A_data.Rmd’ using rmarkdown
--- finished re-building ‘vignette_A_data.Rmd’

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

Quitting from lines 66-79 [unnamed-chunk-3] (vignette_B_basic.Rmd)
Error: processing vignette 'vignette_B_basic.Rmd' failed with diagnostics:
unused arguments (blocks = X, connection = matrix(c(0, 1, 1, 0), 2, 2))
--- failed re-building ‘vignette_B_basic.Rmd’

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

Quitting from lines 82-97 [unnamed-chunk-3] (vignette_C_unsupervised.Rmd)
Error: processing vignette 'vignette_C_unsupervised.Rmd' failed with diagnostics:
unused arguments (blocks = X, connection = C)
--- failed re-building ‘vignette_C_unsupervised.Rmd’

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

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

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

SUMMARY: processing the following files failed:
  ‘vignette_B_basic.Rmd’ ‘vignette_C_unsupervised.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GFDmcv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Package suggested but not available for checking: ‘cmdstanr’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is 81.6Mb
  sub-directories of 1Mb or more:
    libs  81.4Mb
installed size is 123.1Mb
  sub-directories of 1Mb or more:
    doc     4.0Mb
    libs  117.7Mb
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
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
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─testthat::expect_null(...) at test-unstash.R:2:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─mustashe::stash(...)
   5.   └─mustashe:::check_stash_dir()
   6.     └─base::tryCatch(...)
   7.       └─base tryCatchList(expr, classes, parentenv, handlers)
   8.         └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.           └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 60 ]
  Error: Test failures
  Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
    libs   6.7Mb
'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: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
Note: found 50 marked UTF-8 strings
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
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’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    23.2Mb
    models   1.1Mb
Note: found 47936 marked UTF-8 strings
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
'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.
'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
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    6.5Mb
    libs   4.9Mb
GNU make is a SystemRequirements.
Note: found 140 marked UTF-8 strings
Package suggested but not available for checking: ‘DEXSeq’
Package unavailable to check Rd xrefs: ‘DEXSeq’
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘rrpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘sSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'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:
    data   1.5Mb
    libs   4.3Mb
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
installed size is  6.3Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  19.2Mb
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   5.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.6Mb
Packages required and available but unsuitable versions: 'stats', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 171.1Mb
  sub-directories of 1Mb or more:
    libs  170.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
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.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [7s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-ptd_create_ggplot.R:79:3): it returns a ggplot object ─────────
  p$labels (`actual`) not equal to list(...) (`expected`).
  
  `actual$title`:   "SPC Chart of Y, starting 01/01/2020"
  `expected$title`: "SPC Chart of Y, starting 02/01/2020"
  ── Failure (test-ptd_create_ggplot.R:299:3): it sets the main title correctly ──
  p1$labels$title (`actual`) not equal to "SPC Chart of Y, starting 02/01/2020" (`expected`).
  
  `actual`:   "SPC Chart of Y, starting 01/01/2020"
  `expected`: "SPC Chart of Y, starting 02/01/2020"
  
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 430 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.8Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 41.4Mb
  sub-directories of 1Mb or more:
    CppCode        3.6Mb
    R              7.4Mb
    classic-bugs   1.5Mb
    include       10.3Mb
    libs          17.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
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
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘nlraa’
  All declared Imports should be used.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Package suggested but not available for checking: ‘doMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
'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
'LazyData' is specified without 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’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.5Mb
    mods   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘pedtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> x_i = a_i \, \mod 
                             \, m_i, \quad 1 \le i \le n 
l.562 ...i \, \mod \, m_i, \quad 1 \le i \le n }{}
                                                  
! Undefined control sequence.
<argument> a_i = a_j \, \mod 
                             \, \gcd (m_i, m_j)
l.566 \deqn{a_i = a_j \, \mod \, \gcd(m_i, m_j)}{}
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs  14.5Mb
'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
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    doc       5.7Mb
    extdata   1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.0Mb
    libs   3.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.0Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 86.2Mb
  sub-directories of 1Mb or more:
    libs  85.2Mb
'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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> [0,\text 
                    {min}(p_1,p_2))
l.77 a number in \eqn{[0,\text{min}(p_1,p_2))}{}
                                                , indicating the cross-secti...
'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:
    data   4.6Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Note: found 842 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘crayon’ ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 50.1Mb
  sub-directories of 1Mb or more:
    libs  48.2Mb
GNU make is a SystemRequirements.
installed size is 42.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  40.3Mb
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
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
'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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.7Mb
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
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
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.2/OpenCL.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    exampledata   1.5Mb
    libs          3.5Mb
GNU make is a SystemRequirements.
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs   14.8Mb
    share  10.2Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   7.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
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
installed size is 201.5Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    data      1.4Mb
    libs    190.4Mb
    models    4.7Mb
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  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Note: found 167 marked UTF-8 strings
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   5.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      4.7Mb
installed size is 38.6Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs     34.9Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.9Mb
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.
Package suggested but not available for checking: ‘gurobi’
'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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'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.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'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
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   6.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rcplex’
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
GNU make is a SystemRequirements.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘flexsurv’ ‘nlme’ ‘tibble’ ‘tidyverse’ ‘tm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Package required but not available: ‘genbankr’

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
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'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
Namespaces in Imports field not imported from:
  ‘DT’ ‘dbplyr’ ‘downloadthis’ ‘ggExtra’ ‘htmlwidgets’ ‘methods’
  ‘rmarkdown’ ‘scales’
  All declared Imports should be used.
Note: found 34 marked UTF-8 strings
Package required but not available: ‘heatmapFlex’

See section ‘The DESCRIPTION file’ 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
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘gstat’ ‘pryr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 16 marked UTF-8 strings
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
'LazyData' is specified without a 'data' directory
installed size is 50.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs  46.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
‘constparty.Rnw’... [5s/5s] OK
  ‘ctree.Rnw’ using ‘UTF-8’... [5s/5s] NOTE
differences from ‘ctree.Rout.save’
1409,1412d1408
< Deviance Residuals: 
<     Min       1Q   Median       3Q      Max  
< -45.801  -11.208   -1.049   10.903   53.615  
< 
  ‘mob.Rnw’... [7s/7s] OK
  ‘partykit.Rnw’... [2s/2s] OK
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.2/pastclim.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘logger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      6.0Mb
    help   1.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    help   3.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    help   3.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   3.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.2/pbdMPI.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

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  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.3Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 106.8Mb
  sub-directories of 1Mb or more:
    doc     2.9Mb
    libs  103.2Mb
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.
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    libs  35.7Mb
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘partsm’
Package suggested but not available for checking: ‘PythonInR’
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs    7.6Mb
    share  12.8Mb
'LazyData' is specified without a 'data' directory
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
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  14.7Mb
Note: found 6 marked UTF-8 strings
installed size is 108.6Mb
  sub-directories of 1Mb or more:
    libs  107.6Mb
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Package suggested but not available for checking: ‘ptmixed’
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   7.6Mb
installed size is 57.4Mb
  sub-directories of 1Mb or more:
    libs  56.2Mb
Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
'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
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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    application   4.9Mb
Namespaces in Imports field not imported from:
  ‘rJava’ ‘shinyWidgets’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    libs  36.0Mb
GNU make is a SystemRequirements.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
Note: found 114 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
installed size is 43.9Mb
  sub-directories of 1Mb or more:
    libs  43.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
installed size is 44.7Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggmsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
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
Note: found 2048 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ggsubplot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   3.4Mb
    doc   1.2Mb
'LazyData' is specified without a 'data' directory
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
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.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc          1.0Mb
    libs         3.2Mb
    tmp_images   1.2Mb
'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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    tests   3.1Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   9.9Mb
'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
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.0Mb
'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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
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.
Namespaces in Imports field not imported from:
  ‘base’ ‘grDevices’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 62 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘argonDash’ ‘argonR’ ‘colourpicker’ ‘ggplot2’ ‘grid’ ‘hexSticker’
  ‘png’ ‘shinyWidgets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: ‘pollimetrydata’
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
    libs   1.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      3.0Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data      2.7Mb
    extdata   3.5Mb
installed size is 42.5Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-predict.R:12:3): map.predict function works ───────────────────
  p[56, 1] (`actual`) not equal to "versicolor" (`expected`).
  
  `actual`:   "virginica" 
  `expected`: "versicolor"
  ── Failure (test-predict.R:13:3): map.predict function works ───────────────────
  p[145, 1] (`actual`) not equal to "virginica" (`expected`).
  
  `actual`:   "versicolor"
  `expected`: "virginica" 
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘psych’ ‘zoo’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Package suggested but not available for checking: ‘readtext’
'LazyData' is specified without a 'data' directory
installed size is 42.6Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> \hat d:=\underset 
                             {|d|<0.5}{\mathrm {argmin}}\bigg \{\sum _{h=s}^...
l.90 ...d)}h^{2d-1}\bigg|^r\bigg\}, \quad r > 0}{}
                                                  .
! Undefined control sequence.
<argument> K_1 = \iint 
                       _{I^2}\frac {1}{l_0(u)l_n(v)}\lim _{\theta \to a}\fra...
l.271 ...{\theta}(u,v)}{\partial\theta}\,dudv, }{}
                                                  
! Undefined control sequence.
<argument> \{F_n\}_{n\in \mathbb 
                                 {N}}
l.273 \eqn{\{F_n\}_{n\in\mathbb{N}}}{}
                                       is a sequence of absolutely continuou...
! Undefined control sequence.
<argument> K_1 = \iint 
                       _{I^2}\frac {1}{l_0(u)l_n(v)}\lim _{\theta \rightarro...
l.471 ...{\theta}(u,v)}{\partial\theta}\,dudv, }{}
                                                  
! Undefined control sequence.
<argument> \{F_n\}_{n\in \mathbb 
                                 {N}}
l.474 \eqn{\{F_n\}_{n\in\mathbb{N}}}{}
                                       is a sequence of absolutely continuou...
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc  10.4Mb
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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
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
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    libs   8.9Mb
Namespace in Imports field not imported from: ‘here’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata  11.6Mb
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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...1}^{C+1} \hat {\sigma }^2_c}, \text 
                                                  { } \hat {\mu } + q^{calib...
l.965 ...m_{c=1}^{C+1} \hat{\sigma}^2_c} \Big].}{}
                                                  
! Undefined control sequence.
<argument> ...1}^{C+1} \hat {\sigma }^2_c}, \text 
                                                  { } \hat {\mu } + q^{calib...
l.1140 ..._{c=1}^{C+1} \hat{\sigma}^2_c} \Big].}{}
                                                  
! Undefined control sequence.
<argument> ...1}^{C+1} \hat {\sigma }^2_c}, \text 
                                                  { } \hat {\mu } + q^{calib...
l.1291 ..._{c=1}^{C+1} \hat{\sigma}^2_c} \Big].}{}
'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
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
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 42966 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    extdata   9.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinyApp   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 165 marked UTF-8 strings
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'rcbc'
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   4.9Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    4.7Mb
    libs   8.6Mb
'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
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
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
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      2.6Mb
'LazyData' is specified without a 'data' directory
installed size is 64.8Mb
  sub-directories of 1Mb or more:
    libs  64.7Mb
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’
installed size is 106.2Mb
  sub-directories of 1Mb or more:
    libs  105.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cin’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.9Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.2Mb
Note: found 12717 marked UTF-8 strings
Packages suggested but not available for checking: 'rdtLite', 'rdt'
Package suggested but not available for checking: ‘rdt’
Packages suggested but not available for checking: 'rdt', 'rdtLite'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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    libs   3.0Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Note: found 26 marked Latin-1 strings
Package required and available but unsuitable version: ‘splines’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is 49.0Mb
  sub-directories of 1Mb or more:
    libs  48.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
Namespaces in Imports field not imported from:
  ‘lifecycle’ ‘patchwork’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 107 marked UTF-8 strings
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Package required but not available: ‘tweeDEseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘muscle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 28898 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.5Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘sjPlot’
  All declared Imports should be used.
installed size is 48.4Mb
  sub-directories of 1Mb or more:
    libs  47.9Mb
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
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
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
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
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Missing or unexported objects:
  ‘async::http_get’ ‘async::http_stop_for_status’ ‘async::synchronise’
  ‘async::when_all’
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.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    libs         2.7Mb
    staticdocs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 85.8Mb
  sub-directories of 1Mb or more:
    libs  85.2Mb
'LazyData' is specified without a 'data' directory
installed size is 98.6Mb
  sub-directories of 1Mb or more:
    libs  97.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spDataLarge’
Running ‘platform-info.R’ [1s/1s]
  Running ‘testthat.R’ [10s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    'test-qgis-run-algorithm.R:7:3', 'test-qgis-run-algorithm.R:40:3',
    'test-qgis-run-algorithm.R:55:3', 'test-qgis-run-algorithm.R:73:3',
    'test-qgis-run-algorithm.R:91:3', 'test-qgis-run-algorithm.R:105:3',
    'test-qgis-run-algorithm.R:146:3', 'test-qgis-run-algorithm.R:193:3',
    'test-qgis-run-algorithm.R:225:3', 'test-qgisprocess-deprecated.R:17:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-compat-stars.R:43:3'): stars argument coercers work ──────────
  `as_qgis_argument(obj1, qgis_argument_spec(qgis_type = "layer"))` did not produce any messages.
  ── Failure ('test-compat-stars.R:47:3'): stars argument coercers work ──────────
  `res` is not an S3 object
  
  [ FAIL 2 | WARN 0 | SKIP 54 | PASS 165 ]
  Error: Test failures
  Execution halted
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
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Note: found 76102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘missMethods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘readxl’ ‘reshape2’ ‘sjmisc’ ‘stringr’ ‘xlsx’
  All declared Imports should be used.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  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.
Note: found 6 marked UTF-8 strings
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  11.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
'LazyData' is specified without a 'data' directory
installed size is 38.4Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs     33.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       3.0Mb
    libs      1.3Mb
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
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   8.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.7Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> K_\text 
                   {max}
l.2230 ...to a user-specified \eqn{K_\text{max}}{}
                                                  )
! Undefined control sequence.
<argument> K_\text 
                   {max}
l.2256 ...er}{integer} scalar \eqn{K_\text{max}}{}
                                                  ,
! Undefined control sequence.
<argument> K^c+1=K_\text 
                         {max}
l.2282 ...is stopped if \eqn{K^c+1=K_\text{max}}{}
                                                  ,
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
Namespaces in Imports field not imported from:
  ‘psych’ ‘psychTools’
  All declared Imports should be used.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    lib    6.3Mb
    libs   6.4Mb
Package suggested but not available for checking: ‘fastshp’
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 12928 marked UTF-8 strings
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    shiny_app   1.4Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
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’
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   5.0Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
Package suggested but not available for checking: ‘BRugs’
Package unavailable to check Rd xrefs: ‘BRugs’
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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 suggested but not available for checking: ‘slingshot’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.7Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(Rage)
  > 
  > test_check("Rage")
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 423 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-gen_time.R:34:3'): gen_time warns and fails gracefully ───────
  `gen_time(mat_u_na, mat_f, method = "age_diff")` did not throw the expected error.
  ── Failure ('test-gen_time.R:38:3'): gen_time warns and fails gracefully ───────
  `gen_time(mat_u_na, mat_f, method = "cohort")` did not throw the expected error.
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 423 ]
  Error: Test failures
  Execution halted
installed size is 32.2Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘CGHbase’
  All declared Imports should be used.
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
'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 11.4Mb
  sub-directories of 1Mb or more:
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    super-tiny-icons   1.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      9.8Mb
'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
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 60.5Mb
  sub-directories of 1Mb or more:
    libs  59.7Mb
GNU make is a SystemRequirements.
'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
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs  10.1Mb
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
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   3.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Namespace in Imports field not imported from: ‘rex’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      4.0Mb
GNU make is a SystemRequirements.
Note: found 8 marked UTF-8 strings
installed size is 57.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  55.0Mb
GNU make is a SystemRequirements.
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    libs  52.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   5.0Mb
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    libs  40.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.2/Rborist.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
Note: found 26334 marked UTF-8 strings
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
installed size is 62.1Mb
  sub-directories of 1Mb or more:
    libs  61.4Mb
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
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    cont  24.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   4.5Mb
    po    2.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Packages suggested but not available for checking: 'RCyjs', 'BrowserViz'
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.2/Rcplex.Rcheck/00install.out’ for details.
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      2.1Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.2/RcppMeCab.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
GNU make is a SystemRequirements.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      4.8Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    include        2.0Mb
    jsonexamples   3.8Mb
    libs          13.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    include   1.1Mb
    libs      5.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.2Mb
'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
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.5Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 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
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  14.7Mb
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'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
'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.
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.9Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      5.1Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \mathbb 
                        
l.780 ...\eqn{\mathbb{E}[Y \mid X = x] = \mu(x)}{}
                                                  . The mean function \eqn{\...
! Undefined control sequence.
<argument> g(\mathbb 
                     {E}[Y \mid X = x]) = \mu (x)
l.799 \mu(x)}{}
               , where \eqn{g}{} is a link function. Let
! Undefined control sequence.
<argument> Y \mid X \sim \text 
                               {SomeDistribution},
l.1093 ... \mid X \sim \text{SomeDistribution},}{}
                                                  
! Undefined control sequence.
<argument> \mathbb 
                   {E}[Y \mid X = x] = g^{-1}(\mu (x)).
l.1097 ...bb{E}[Y \mid X = x] = g^{-1}(\mu(x)).}{}
                                                  
! Undefined control sequence.
<argument> Y \mid X \sim \text 
                               {Normal}(\mu (X), \sigma ^2),
l.1115 ...\sim \text{Normal}(\mu(X), \sigma^2),}{}
                                                  
! Undefined control sequence.
<argument> Y \mid X \sim \text 
                               {Binomial}(N, g^{-1}(\mu (X))),
l.1133 ...m \text{Binomial}(N, g^{-1}(\mu(X))),}{}
                                                  
! Undefined control sequence.
<argument> Y \mid X \sim \text 
                               {Poisson}(g^{-1}(\mu (X))),
l.1143 ... \sim \text{Poisson}(g^{-1}(\mu(X))),}{}
                                                  
! Undefined control sequence.
<argument> Y \mid X \sim \text 
                               {SomeDistribution}(g^{-1}(\mu (X))),
l.1152 ...xt{SomeDistribution}(g^{-1}(\mu(X))),}{}
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory