BioC 3.2: CHECK report for GOSim on zin1

Package: GOSim

Version: 1.8.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GOSim_1.8.0.tar.gz

StartedAt: 2016-04-23 01:27:03 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:34:48 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 464.4 seconds

RetCode: 0

Status:  OK

CheckDir: GOSim.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GOSim_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GOSim.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOSim/DESCRIPTION’ ... OK
* this is package ‘GOSim’ version ‘1.8.0’
* 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 ‘GOSim’ can be installed ... [16s/16s] 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
* 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 ... OK
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [349s/349s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getGeneSimPrototypes 309.098  1.316 310.305
getTermSim             9.206  0.032   9.235
getDisjCommAnc         8.844  0.100   8.937
getMinimumSubsumer     8.590  0.016   8.606
setEnrichmentFactors   6.926  0.044   6.975
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/GOSim.Rcheck/00check.log’
for details.

* installing *source* package ‘GOSim’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include"  `/home/biocbuild/bbs-3.2-bioc/R/bin/Rscript -e "require(Rcpp); Rcpp:::CxxFlags()"` -fpic  -g -O2  -Wall -c OAWrapper.cpp -o OAWrapper.o
Loading required package: Rcpp
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c hungarian2.c -o hungarian2.o
Loading required package: Rcpp
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o GOSim.so OAWrapper.o hungarian2.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
Loading required package: Rcpp
installing to /home/biocbuild/bbs-3.2-bioc/meat/GOSim.Rcheck/GOSim/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GOSim)

name	user	system	elapsed
GOenrichment	0.001	0.000	0.000
calcICs	0	0	0
evaluateClustering	0.000	0.000	0.001
filterGO	0.001	0.000	0.000
getAncestors	0	0	0
getChildren	0.000	0.000	0.001
getDisjCommAnc	8.844	0.100	8.937
getGOGraph	0	0	0
getGOInfo	0.001	0.000	0.000
getGeneFeatures	0.000	0.000	0.001
getGeneFeaturesPrototypes	0	0	0
getGeneSim	0	0	0
getGeneSimPrototypes	309.098	1.316	310.305
getMinimumSubsumer	8.590	0.016	8.606
getOffsprings	0	0	0
getParents	0	0	0
getTermSim	9.206	0.032	9.235
selectPrototypes	0.000	0.000	0.001
setEnrichmentFactors	6.926	0.044	6.975
setEvidenceLevel	0.001	0.000	0.001
setOntology	0.000	0.000	0.001