Package: GOsummaries

Version: 2.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GOsummaries.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GOsummaries_2.22.0.tar.gz

StartedAt: 2020-04-15 02:49:09 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:50:11 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 61.8 seconds

RetCode: 0

Status:  OK

CheckDir: GOsummaries.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GOsummaries.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GOsummaries_2.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/GOsummaries.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOsummaries/DESCRIPTION’ ... OK
* this is package ‘GOsummaries’ version ‘2.22.0’
* 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 for sufficient/correct file permissions ... 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 compiled code ... NOTE
Note: information on .o files is not available
* 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
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/GOsummaries.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GOsummaries
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GOsummaries’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c findCoordinates.cpp -o findCoordinates.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GOsummaries.so findCoordinates.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-GOsummaries/00new/GOsummaries/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GOsummaries)

name	user	system	elapsed
add_expression.gosummaries	0	0	0
add_to_slot.gosummaries	0.380	0.008	0.401
customize	0.001	0.000	0.000
gosummaries.MArrayLM	0.000	0.001	0.001
gosummaries	0.590	0.008	0.681
gosummaries.kmeans	0.001	0.001	0.000
gosummaries.matrix	0.001	0.000	0.001
gosummaries.prcomp	1.805	0.017	1.893
panel_boxplot	0.000	0.001	0.000
plot.gosummaries	0	0	0
plotWordcloud	0.099	0.001	0.105