BioC 2.13: CHECK report for GOSim on zin1

Package: GOSim

Version: 1.4.2

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings GOSim_1.4.2.tar.gz

StartedAt: 2014-04-05 01:39:18 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:43:15 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 236.3 seconds

RetCode: 0

Status:  OK

CheckDir: GOSim.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/GOSim.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOSim/DESCRIPTION’ ... OK
* this is package ‘GOSim’ version ‘1.4.2’
* 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 ... [22s/22s] 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
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘GO.db’ ‘annotate’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
‘:::’ call which should be ‘::’: ‘Matrix:::t’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘GOSim.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [69s/69s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getDisjCommAnc       16.645  0.100  16.784
getTermSim           15.861  0.044  15.931
getMinimumSubsumer   15.105  0.032  15.170
setEnrichmentFactors 11.597  0.028  11.642
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/GOSim.Rcheck/00check.log’
for details.

* installing *source* package ‘GOSim’ ...
** libs
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"  `/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c hungarian2.c -o hungarian2.o
Loading required package: Rcpp
g++ -shared -L/usr/local/lib -o GOSim.so OAWrapper.o hungarian2.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
Loading required package: Rcpp
installing to /home/biocbuild/bbs-2.13-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	0.000	0.004	0.005
calcICs	0.000	0.004	0.003
evaluateClustering	0.000	0.000	0.001
filterGO	0.000	0.000	0.002
getAncestors	0.004	0.000	0.004
getChildren	0.000	0.000	0.001
getDisjCommAnc	16.645	0.100	16.784
getGOGraph	0.000	0.000	0.002
getGOInfo	0.008	0.004	0.013
getGeneFeatures	0.000	0.000	0.001
getGeneFeaturesPrototypes	0.000	0.000	0.002
getGeneSim	0.000	0.004	0.006
getGeneSimPrototypes	0.000	0.000	0.001
getMinimumSubsumer	15.105	0.032	15.170
getOffsprings	0.012	0.000	0.013
getParents	0.004	0.000	0.000
getTermSim	15.861	0.044	15.931
selectPrototypes	0.000	0.000	0.001
setEnrichmentFactors	11.597	0.028	11.642
setEvidenceLevel	0.000	0.000	0.001
setOntology	0.000	0.000	0.001