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BioC 3.2: CHECK report for GOSim on oaxaca

This page was generated on 2016-04-23 10:27:06 -0700 (Sat, 23 Apr 2016).

Package 452/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOSim 1.8.0
Holger Froehlich
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GOSim
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GOSim
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOSim_1.8.0.tar.gz
StartedAt: 2016-04-23 00:48:17 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:03:43 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 926.1 seconds
RetCode: 0
Status:  OK 
CheckDir: GOSim.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOSim_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GOSim.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [21s/22s] 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 ... [12m/13m] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getGeneSimPrototypes 626.628 49.998 709.035
getMinimumSubsumer    12.071  0.239  12.518
getTermSim            11.885  0.233  12.258
getDisjCommAnc        11.458  0.406  12.210
setEnrichmentFactors   9.174  0.163   9.359
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/GOSim.Rcheck/00check.log’
for details.


GOSim.Rcheck/00install.out:

* installing *source* package ‘GOSim’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "require(Rcpp); Rcpp:::CxxFlags()"` -fPIC  -Wall -mtune=core2 -g -O2  -c OAWrapper.cpp -o OAWrapper.o
Loading required package: Rcpp
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c hungarian2.c -o hungarian2.o
Loading required package: Rcpp
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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-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)

GOSim.Rcheck/GOSim-Ex.timings:

nameusersystemelapsed
GOenrichment0.0000.0000.001
calcICs0.0010.0000.001
evaluateClustering000
filterGO0.0010.0000.000
getAncestors0.0000.0000.001
getChildren0.0010.0000.001
getDisjCommAnc11.458 0.40612.210
getGOGraph0.0010.0000.001
getGOInfo0.0010.0000.000
getGeneFeatures0.0010.0000.000
getGeneFeaturesPrototypes0.0000.0000.001
getGeneSim000
getGeneSimPrototypes626.628 49.998709.035
getMinimumSubsumer12.071 0.23912.518
getOffsprings0.0010.0010.000
getParents0.0010.0000.001
getTermSim11.885 0.23312.258
selectPrototypes0.0010.0010.001
setEnrichmentFactors9.1740.1639.359
setEvidenceLevel000
setOntology000