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CHECK results for GOSim on riesling1

This page was generated on 2021-06-12 12:05:05 -0400 (Sat, 12 Jun 2021).

Package 769/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOSim 1.31.0  (landing page)
Holger Froehlich
Snapshot Date: 2021-06-11 14:50:09 -0400 (Fri, 11 Jun 2021)
URL: https://git.bioconductor.org/packages/GOSim
Branch: master
Last Commit: 88e442e
Last Changed Date: 2021-05-19 12:00:43 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
To the developers/maintainers of the GOSim package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GOSim.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

Summary

Package: GOSim
Version: 1.31.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOSim.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GOSim_1.31.0.tar.gz
StartedAt: 2021-06-12 00:27:12 -0400 (Sat, 12 Jun 2021)
EndedAt: 2021-06-12 00:38:34 -0400 (Sat, 12 Jun 2021)
EllapsedTime: 682.7 seconds
RetCode: 0
Status:   OK   
CheckDir: GOSim.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOSim.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GOSim_1.31.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/GOSim.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GOSim/DESCRIPTION' ... OK
* this is package 'GOSim' version '1.31.0'
* 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 'GOSim' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
GOGraph: no visible global function definition for 'new'
GOenrichment: no visible global function definition for 'new'
calc.diffusion.kernel: no visible global function definition for 'as'
evaluateClustering: no visible global function definition for 'median'
evaluateClustering: no visible global function definition for 'mad'
evaluateClustering: no visible global function definition for 'as.dist'
norm: no visible global function definition for 'dist'
pca: no visible global function definition for 'prcomp'
selectPrototypes : <anonymous>: no visible global function definition
  for 'cutree'
selectPrototypes : <anonymous>: no visible global function definition
  for 'hclust'
selectPrototypes : <anonymous>: no visible global function definition
  for 'dist'
selectPrototypes: no visible binding for global variable 'BIC'
setEvidenceLevel: no visible global function definition for 'is'
Undefined global functions or variables:
  BIC as as.dist cutree dist hclust is mad median new prcomp
Consider adding
  importFrom("methods", "as", "is", "new")
  importFrom("stats", "BIC", "as.dist", "cutree", "dist", "hclust",
             "mad", "median", "prcomp")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.14-bioc/R/library/GOSim/libs/i386/GOSim.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'D:/biocbuild/bbs-3.14-bioc/R/library/GOSim/libs/x64/GOSim.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
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
getGeneSimPrototypes 182.77   0.70  189.94
getMinimumSubsumer     7.51   0.06    8.58
getTermSim             7.33   0.05    8.36
setEnrichmentFactors   6.39   0.05    7.14
getDisjCommAnc         5.25   0.22    5.47
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
getGeneSimPrototypes 179.72   0.26  188.28
getDisjCommAnc         8.94   0.50   10.69
getTermSim             6.42   0.02    6.44
setEnrichmentFactors   6.09   0.03    6.13
getMinimumSubsumer     5.80   0.02    5.81
* 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/GOSim.Rcheck/00check.log'
for details.



Installation output

GOSim.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GOSim_1.31.0.tar.gz && rm -rf GOSim.buildbin-libdir && mkdir GOSim.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GOSim.buildbin-libdir GOSim_1.31.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GOSim_1.31.0.zip && rm GOSim_1.31.0.tar.gz GOSim_1.31.0.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
100  198k  100  198k    0     0  1052k      0 --:--:-- --:--:-- --:--:-- 1052k

install for i386

* installing *source* package 'GOSim' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e "require(Rcpp); Rcpp:::CxxFlags()"`   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c OAWrapper.cpp -o OAWrapper.o
Loading required package: Rcpp
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hungarian2.c -o hungarian2.o
Loading required package: Rcpp
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o GOSim.dll tmp.def OAWrapper.o hungarian2.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
Loading required package: Rcpp
installing to D:/biocbuild/bbs-3.14-bioc/meat/GOSim.buildbin-libdir/00LOCK-GOSim/00new/GOSim/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GOSim'
    finding HTML links ... done
    GOenrichment                            html  
    IC                                      html  
    calc.diffusion.kernel                   html  
    calcICs                                 html  
    evaluateClustering                      html  
    filterGO                                html  
    getAncestors                            html  
    getChildren                             html  
    getDisjCommAnc                          html  
    getGOGraph                              html  
    getGOInfo                               html  
    getGeneFeatures                         html  
    getGeneFeaturesPrototypes               html  
    getGeneSim                              html  
    getGeneSimPrototypes                    html  
    getMinimumSubsumer                      html  
    getOffsprings                           html  
    getParents                              html  
    getTermSim                              html  
    internal                                html  
    selectPrototypes                        html  
    setEnrichmentFactors                    html  
    setEvidenceLevel                        html  
    setOntology                             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 'GOSim' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e "require(Rcpp); Rcpp:::CxxFlags()"`   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c OAWrapper.cpp -o OAWrapper.o
Loading required package: Rcpp
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hungarian2.c -o hungarian2.o
Loading required package: Rcpp
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o GOSim.dll tmp.def OAWrapper.o hungarian2.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
Loading required package: Rcpp
installing to D:/biocbuild/bbs-3.14-bioc/meat/GOSim.buildbin-libdir/GOSim/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOSim' as GOSim_1.31.0.zip
* DONE (GOSim)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'GOSim' successfully unpacked and MD5 sums checked

Tests output


Example timings

GOSim.Rcheck/examples_i386/GOSim-Ex.timings

nameusersystemelapsed
GOenrichment000
calcICs000
evaluateClustering000
filterGO000
getAncestors000
getChildren000
getDisjCommAnc5.250.225.47
getGOGraph000
getGOInfo000
getGeneFeatures000
getGeneFeaturesPrototypes000
getGeneSim000
getGeneSimPrototypes182.77 0.70189.94
getMinimumSubsumer7.510.068.58
getOffsprings000
getParents000
getTermSim7.330.058.36
selectPrototypes000
setEnrichmentFactors6.390.057.14
setEvidenceLevel000
setOntology000

GOSim.Rcheck/examples_x64/GOSim-Ex.timings

nameusersystemelapsed
GOenrichment000
calcICs000
evaluateClustering000
filterGO000
getAncestors000
getChildren000
getDisjCommAnc 8.94 0.5010.69
getGOGraph000
getGOInfo000
getGeneFeatures000
getGeneFeaturesPrototypes000
getGeneSim000
getGeneSimPrototypes179.72 0.26188.28
getMinimumSubsumer5.800.025.81
getOffsprings000
getParents000
getTermSim6.420.026.44
selectPrototypes000
setEnrichmentFactors6.090.036.13
setEvidenceLevel000
setOntology000