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CHECK report for GOsummaries on tokay2

This page was generated on 2019-10-16 12:31:05 -0400 (Wed, 16 Oct 2019).

Package 702/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOsummaries 2.20.0
Raivo Kolde
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GOsummaries
Branch: RELEASE_3_9
Last Commit: 9da9f0c
Last Changed Date: 2019-05-02 11:53:49 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOsummaries
Version: 2.20.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOsummaries.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GOsummaries_2.20.0.tar.gz
StartedAt: 2019-10-16 04:10:09 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:11:32 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 82.6 seconds
RetCode: 0
Status:  OK  
CheckDir: GOsummaries.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOsummaries.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GOsummaries_2.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GOsummaries.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GOsummaries/DESCRIPTION' ... OK
* this is package 'GOsummaries' version '2.20.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 : : no visible global function definition for
  'pdf'
open_file_con : : no visible global function definition for
  'png'
open_file_con : : no visible global function definition for
  'jpeg'
open_file_con : : no visible global function definition for
  'tiff'
open_file_con : : 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/GOsummaries/libs/i386/GOsummaries.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/GOsummaries/libs/x64/GOsummaries.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GOsummaries.Rcheck/00check.log'
for details.



Installation output

GOsummaries.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GOsummaries_2.20.0.tar.gz && rm -rf GOsummaries.buildbin-libdir && mkdir GOsummaries.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GOsummaries.buildbin-libdir GOsummaries_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GOsummaries_2.20.0.zip && rm GOsummaries_2.20.0.tar.gz GOsummaries_2.20.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 1973k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1973k  100 1973k    0     0  12.0M      0 --:--:-- --:--:-- --:--:-- 12.5M

install for i386

* installing *source* package 'GOsummaries' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findCoordinates.cpp -o findCoordinates.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GOsummaries.dll tmp.def findCoordinates.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/GOsummaries.buildbin-libdir/00LOCK-GOsummaries/00new/GOsummaries/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GOsummaries'
    finding HTML links ... done
    GOsummaries-package                     html  
    add_expression.gosummaries              html  
    add_to_slot.gosummaries                 html  
    customize                               html  
    gosummaries.MArrayLM                    html  
    finding level-2 HTML links ... done

    gosummaries                             html  
    gosummaries.kmeans                      html  
    gosummaries.matrix                      html  
    gosummaries.prcomp                      html  
    metabolomic_example                     html  
    metagenomic_example                     html  
    panel_boxplot                           html  
    plot.gosummaries                        html  
    plotWordcloud                           html  
    tissue_example                          html  
** 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

install for x64

* installing *source* package 'GOsummaries' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findCoordinates.cpp -o findCoordinates.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GOsummaries.dll tmp.def findCoordinates.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/GOsummaries.buildbin-libdir/GOsummaries/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOsummaries' as GOsummaries_2.20.0.zip
* DONE (GOsummaries)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GOsummaries' successfully unpacked and MD5 sums checked

Tests output


Example timings

GOsummaries.Rcheck/examples_i386/GOsummaries-Ex.timings

nameusersystemelapsed
add_expression.gosummaries000
add_to_slot.gosummaries0.240.000.24
customize000
gosummaries.MArrayLM000
gosummaries0.360.010.38
gosummaries.kmeans000
gosummaries.matrix000
gosummaries.prcomp0.990.000.98
panel_boxplot000
plot.gosummaries000
plotWordcloud0.060.000.07

GOsummaries.Rcheck/examples_x64/GOsummaries-Ex.timings

nameusersystemelapsed
add_expression.gosummaries000
add_to_slot.gosummaries0.360.000.36
customize000
gosummaries.MArrayLM000
gosummaries0.580.000.61
gosummaries.kmeans000
gosummaries.matrix000
gosummaries.prcomp1.240.001.24
panel_boxplot000
plot.gosummaries000
plotWordcloud0.070.000.07