BioC 3.5: CHECK report for GOSim on tokay2

Package: GOSim

Version: 1.14.0

Command: rm -rf GOSim.buildbin-libdir GOSim.Rcheck && mkdir GOSim.buildbin-libdir GOSim.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOSim.buildbin-libdir GOSim_1.14.0.tar.gz >GOSim.Rcheck\00install.out 2>&1 && cp GOSim.Rcheck\00install.out GOSim-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GOSim.buildbin-libdir --install="check:GOSim-install.out" --force-multiarch --no-vignettes --timings GOSim_1.14.0.tar.gz

StartedAt: 2017-10-18 00:19:29 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:32:08 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 758.5 seconds

RetCode: 0

Status:  OK

CheckDir: GOSim.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf GOSim.buildbin-libdir GOSim.Rcheck && mkdir GOSim.buildbin-libdir GOSim.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOSim.buildbin-libdir GOSim_1.14.0.tar.gz >GOSim.Rcheck\00install.out 2>&1 && cp GOSim.Rcheck\00install.out GOSim-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GOSim.buildbin-libdir --install="check:GOSim-install.out" --force-multiarch --no-vignettes --timings GOSim_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GOSim.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.14.0'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 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-3.5-bioc/meat/GOSim.buildbin-libdir/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)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getGeneSimPrototypes 190.64   0.25  190.89
getMinimumSubsumer    10.97   0.03   11.00
getTermSim            10.78   0.08   10.86
getDisjCommAnc        10.07   0.47   13.28
setEnrichmentFactors   7.97   0.02    8.00
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getGeneSimPrototypes 211.69   0.46  212.16
getDisjCommAnc        12.26   0.19   12.78
getMinimumSubsumer    12.28   0.02   12.30
getTermSim            12.29   0.00   12.29
setEnrichmentFactors   8.44   0.00    8.44
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/GOSim.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'GOSim' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  `C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/Rscript -e "require(Rcpp); Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=core2 -c OAWrapper.cpp -o OAWrapper.o
Loading required package: Rcpp
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c hungarian2.c -o hungarian2.o
Loading required package: Rcpp
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GOSim.dll tmp.def OAWrapper.o hungarian2.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
Loading required package: Rcpp
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/GOSim.buildbin-libdir/GOSim/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'GOSim' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  `C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/Rscript -e "require(Rcpp); Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=core2 -c OAWrapper.cpp -o OAWrapper.o
Loading required package: Rcpp
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c hungarian2.c -o hungarian2.o
Loading required package: Rcpp
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GOSim.dll tmp.def OAWrapper.o hungarian2.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
Loading required package: Rcpp
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/GOSim.buildbin-libdir/GOSim/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOSim' as GOSim_1.14.0.zip
* DONE (GOSim)

name	user	system	elapsed
GOenrichment	0	0	0
calcICs	0	0	0
evaluateClustering	0	0	0
filterGO	0	0	0
getAncestors	0	0	0
getChildren	0	0	0
getDisjCommAnc	10.07	0.47	13.28
getGOGraph	0	0	0
getGOInfo	0	0	0
getGeneFeatures	0.01	0.00	0.02
getGeneFeaturesPrototypes	0	0	0
getGeneSim	0	0	0
getGeneSimPrototypes	190.64	0.25	190.89
getMinimumSubsumer	10.97	0.03	11.00
getOffsprings	0	0	0
getParents	0	0	0
getTermSim	10.78	0.08	10.86
selectPrototypes	0	0	0
setEnrichmentFactors	7.97	0.02	8.00
setEvidenceLevel	0	0	0
setOntology	0	0	0

name	user	system	elapsed
GOenrichment	0	0	0
calcICs	0	0	0
evaluateClustering	0	0	0
filterGO	0	0	0
getAncestors	0	0	0
getChildren	0	0	0
getDisjCommAnc	12.26	0.19	12.78
getGOGraph	0	0	0
getGOInfo	0	0	0
getGeneFeatures	0	0	0
getGeneFeaturesPrototypes	0	0	0
getGeneSim	0	0	0
getGeneSimPrototypes	211.69	0.46	212.16
getMinimumSubsumer	12.28	0.02	12.30
getOffsprings	0	0	0
getParents	0	0	0
getTermSim	12.29	0.00	12.29
selectPrototypes	0	0	0
setEnrichmentFactors	8.44	0.00	8.44
setEvidenceLevel	0	0	0
setOntology	0	0	0