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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GOsummaries.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings GOsummaries_2.34.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/GOsummaries.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GOsummaries/DESCRIPTION' ... OK
* this is package 'GOsummaries' version '2.34.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GOsummaries' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
adjust_wordcloud_appearance: no visible global function definition for
  'colorRampPalette'
annotate.gosummaries: no visible global function definition for
  'packageVersion'
gen_wordcloud_legend: no visible global function definition for
  'colorRampPalette'
open_file_con : <anonymous>: no visible global function definition for
  'pdf'
open_file_con : <anonymous>: no visible global function definition for
  'png'
open_file_con : <anonymous>: no visible global function definition for
  'jpeg'
open_file_con : <anonymous>: no visible global function definition for
  'tiff'
open_file_con : <anonymous>: no visible global function definition for
  'bmp'
panel_boxplot : qq: no visible global function definition for
  'boxplot.stats'
panel_boxplot: no visible binding for global variable 'x'
panel_boxplot: no visible binding for global variable 'y'
panel_boxplot: no visible binding for global variable 'Class'
panel_dummy: no visible binding for global variable 'y'
panel_dummy: no visible binding for global variable 'x'
plotWordcloud: no visible global function definition for
  'colorRampPalette'
plotWordcloud: no visible global function definition for 'runif'
plot_motor: no visible global function definition for 'dev.off'
print.gosummaries: no visible global function definition for 'head'
pspearman: no visible global function definition for 'pt'
spearman_mds: no visible global function definition for 'cor'
Undefined global functions or variables:
  Class bmp boxplot.stats colorRampPalette cor dev.off head jpeg
  packageVersion pdf png pt runif tiff x y
Consider adding
  importFrom("grDevices", "bmp", "boxplot.stats", "colorRampPalette",
             "dev.off", "jpeg", "pdf", "png", "tiff")
  importFrom("stats", "cor", "pt", "runif")
  importFrom("utils", "head", "packageVersion")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/GOsummaries/libs/x64/GOsummaries.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (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. 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.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/GOsummaries.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL GOsummaries
###
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'GOsummaries' ...
** using staged installation
** libs
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c findCoordinates.cpp -o findCoordinates.o
g++ -std=gnu++14 -shared -s -static-libgcc -o GOsummaries.dll tmp.def findCoordinates.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-GOsummaries/00new/GOsummaries/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GOsummaries)