BioC 3.1: CHECK report for GOSim on zin2

Package: GOSim

Version: 1.6.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings GOSim_1.6.0.tar.gz

StartedAt: 2015-10-09 02:02:58 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:13:20 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 622.2 seconds

RetCode: 0

Status:  OK

CheckDir: GOSim.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings GOSim_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/GOSim.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.6.0’
* 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/24s] 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 ... [316s/440s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getGeneSimPrototypes 275.138  1.372 381.818
getTermSim             9.592  0.000  12.427
getDisjCommAnc         8.888  0.122  14.847
getMinimumSubsumer     8.513  0.007  12.315
setEnrichmentFactors   6.838  0.001  10.193
* 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-3.1-bioc/meat/GOSim.Rcheck/00check.log’
for details.

* installing *source* package ‘GOSim’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include"  `/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/lib -L/usr/local/lib -o GOSim.so OAWrapper.o hungarian2.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
Loading required package: Rcpp
installing to /home/biocbuild/bbs-3.1-bioc/meat/GOSim.Rcheck/GOSim/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (GOSim)

name	user	system	elapsed
GOenrichment	0.000	0.000	0.001
calcICs	0	0	0
evaluateClustering	0.001	0.000	0.000
filterGO	0.000	0.000	0.001
getAncestors	0	0	0
getChildren	0	0	0
getDisjCommAnc	8.888	0.122	14.847
getGOGraph	0.001	0.000	0.000
getGOInfo	0	0	0
getGeneFeatures	0	0	0
getGeneFeaturesPrototypes	0.001	0.000	0.000
getGeneSim	0.000	0.000	0.001
getGeneSimPrototypes	275.138	1.372	381.818
getMinimumSubsumer	8.513	0.007	12.315
getOffsprings	0.001	0.000	0.001
getParents	0.000	0.000	0.001
getTermSim	9.592	0.000	12.427
selectPrototypes	0.000	0.000	0.001
setEnrichmentFactors	6.838	0.001	10.193
setEvidenceLevel	0.000	0.000	0.001
setOntology	0	0	0