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BioC 2.13: CHECK report for GOSim on perceval

This page was generated on 2014-04-05 09:53:14 -0700 (Sat, 05 Apr 2014).

Package 319/750HostnameOS / ArchBUILDCHECKBUILD BIN
GOSim 1.4.2
Holger Froehlich
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/GOSim
Last Changed Rev: 86171 / Revision: 88450
Last Changed Date: 2014-02-06 11:34:29 -0800 (Thu, 06 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: GOSim
Version: 1.4.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GOSim_1.4.2.tar.gz
StartedAt: 2014-04-05 01:45:52 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:53:02 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 430.5 seconds
RetCode: 0
Status:  OK 
CheckDir: GOSim.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/GOSim.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [39s/39s] 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:
  ‘annotate’ ‘GO.db’ ‘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 sizes of PDF files under ‘inst/doc’ ... 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 ... [115s/116s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getDisjCommAnc       29.493  0.946  30.919
getMinimumSubsumer   25.158  1.033  26.507
getTermSim           23.636  0.988  24.880
setEnrichmentFactors 16.383  0.665  17.245
* 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
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/GOSim.Rcheck/00check.log’
for details.

GOSim.Rcheck/00install.out:

* installing *source* package ‘GOSim’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "require(Rcpp); Rcpp:::CxxFlags()"` -fPIC  -mtune=core2 -g -O2 -Wall  -c OAWrapper.cpp -o OAWrapper.o
Loading required package: Rcpp
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c hungarian2.c -o hungarian2.o
Loading required package: Rcpp
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o GOSim.so OAWrapper.o hungarian2.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Loading required package: Rcpp
installing to /Users/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)

GOSim.Rcheck/GOSim-Ex.timings:

nameusersystemelapsed
GOenrichment0.4700.0050.480
calcICs0.0060.0010.007
evaluateClustering0.0090.0020.027
filterGO0.0080.0010.010
getAncestors0.0090.0010.011
getChildren0.0090.0020.011
getDisjCommAnc29.493 0.94630.919
getGOGraph0.0020.0040.007
getGOInfo0.0210.0050.027
getGeneFeatures0.0020.0030.006
getGeneFeaturesPrototypes0.0020.0020.004
getGeneSim0.0020.0030.006
getGeneSimPrototypes0.0020.0040.006
getMinimumSubsumer25.158 1.03326.507
getOffsprings0.0020.0030.005
getParents0.0020.0040.005
getTermSim23.636 0.98824.880
selectPrototypes0.0170.0100.027
setEnrichmentFactors16.383 0.66517.245
setEvidenceLevel0.0020.0030.005
setOntology0.0010.0040.005