GOSim 1.8.0
Holger Froehlich
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GOSim | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | TIMEOUT | skipped | skipped |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | TIMEOUT | skipped | skipped |
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### Running command:
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### /home/biocbuild/bbs-3.0-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-3.0-bioc/meat/GOSim.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.8.0’
* 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 ... [25s/26s] 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 loading without being on the library search path ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GOenrichment: no visible binding for global variable ‘GOTERM’
calc.diffusion.kernel: no visible binding for global variable ‘GOTERM’
calcICs: no visible binding for global variable ‘GOTERM’
getAncestors: no visible binding for global variable ‘GOBPANCESTOR’
getAncestors: no visible binding for global variable ‘GOMFANCESTOR’
getAncestors: no visible binding for global variable ‘GOCCANCESTOR’
getChildren: no visible binding for global variable ‘GOBPCHILDREN’
getChildren: no visible binding for global variable ‘GOMFCHILDREN’
getChildren: no visible binding for global variable ‘GOCCCHILDREN’
getGOGraph: no visible binding for global variable ‘GOBPPARENTS’
getGOGraph: no visible binding for global variable ‘GOMFPARENTS’
getGOGraph: no visible binding for global variable ‘GOCCPARENTS’
getGOInfo: no visible binding for global variable ‘GOTERM’
getOffsprings: no visible binding for global variable ‘GOBPOFFSPRING’
getOffsprings: no visible binding for global variable ‘GOMFOFFSPRING’
getOffsprings: no visible binding for global variable ‘GOCCOFFSPRING’
getParents: no visible binding for global variable ‘GOBPPARENTS’
getParents: no visible binding for global variable ‘GOMFPARENTS’
getParents: no visible binding for global variable ‘GOCCPARENTS’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [55s/56s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getDisjCommAnc 12.973 0.152 14.063
getMinimumSubsumer 11.781 0.040 12.040
getTermSim 11.632 0.040 11.783
setEnrichmentFactors 8.401 0.028 8.650
* 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
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/GOSim.Rcheck/00check.log’
for details.
* installing *source* package ‘GOSim’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" `/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/lib -L/usr/local/lib -o GOSim.so OAWrapper.o hungarian2.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
Loading required package: Rcpp
installing to /home/biocbuild/bbs-3.0-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)