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BioC 3.1: CHECK report for gaga on petty

This page was generated on 2015-10-09 09:33:28 -0700 (Fri, 09 Oct 2015).

Package 360/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaga 2.14.0
David Rossell
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/gaga
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gaga
Version: 2.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gaga_2.14.0.tar.gz
StartedAt: 2015-10-08 23:05:24 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:07:09 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 104.7 seconds
RetCode: 0
Status:  OK 
CheckDir: gaga.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gaga_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/gaga.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gaga/DESCRIPTION’ ... OK
* this is package ‘gaga’ version ‘2.14.0’
* 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 ‘gaga’ can be installed ... [13s/13s] 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
'library' or 'require' calls to packages already attached by Depends:
  ‘EBarrays’ ‘mgcv’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘coda’ ‘EBarrays’ ‘mgcv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘makeEBarraysSingleHyp’ ‘sigmaPriorEst’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
adjustfitNN: no visible global function definition for ‘gam’
checkfit.gagafit: no visible global function definition for ‘pData’
checkfit.gagafit: no visible global function definition for ‘exprs’
checkfit.gagafit: no visible global function definition for ‘fData’
classpred.gagafit: no visible global function definition for ‘pData’
classpred.gagafit: no visible global function definition for ‘exprs’
findgenes.gagafit: no visible global function definition for ‘pData’
findgenes.gagafit: no visible global function definition for ‘exprs’
fitGG: no visible global function definition for ‘pData’
fitGG: no visible global function definition for ‘exprs’
fitGG: no visible global function definition for ‘as.mcmc’
fitNN: no visible global function definition for ‘pData’
fitNN: no visible global function definition for ‘exprs’
fitNN: no visible global function definition for ‘eb.createFamilyLNNMV’
fitNN: no visible global function definition for ‘emfit’
fitNN: no visible global function definition for ‘postprob’
fitNNSingleHyp: no visible global function definition for ‘pData’
fitNNSingleHyp: no visible global function definition for ‘exprs’
forwsimDiffExpr.gagafit: no visible global function definition for
  ‘pData’
forwsimDiffExpr.gagafit: no visible global function definition for
  ‘exprs’
forwsimDiffExpr.nnfit: no visible global function definition for
  ‘pData’
forwsimDiffExpr.nnfit: no visible global function definition for
  ‘exprs’
forwsimDiffExpr.nnfit: no visible global function definition for
  ‘fData’
makeEBarraysHyp: no visible global function definition for ‘ebPatterns’
parest.gagafit: no visible global function definition for ‘pData’
parest.gagafit: no visible global function definition for ‘exprs’
parest.gagafit: no visible global function definition for ‘mcmc’
posmeansGG.gagafit: no visible global function definition for ‘pData’
posmeansGG.gagafit: no visible global function definition for ‘exprs’
powclasspred.gagafit: no visible global function definition for ‘pData’
powclasspred.gagafit: no visible global function definition for ‘exprs’
powfindgenes.gagafit: no visible global function definition for ‘pData’
powfindgenes.gagafit: no visible global function definition for ‘exprs’
powfindgenes.nnfit: no visible global function definition for ‘pData’
powfindgenes.nnfit: no visible global function definition for ‘exprs’
powfindgenes.nnfit : f: no visible global function definition for
  ‘exprs’
powsimprior.nnfit : f: no visible global function definition for
  ‘exprs’
ppGG: no visible global function definition for ‘pData’
ppGG: no visible global function definition for ‘exprs’
sigmaPriorEst: no visible global function definition for ‘exprs’
simGG: no visible global function definition for ‘sampleNames<-’
simGG: no visible global function definition for ‘varLabels<-’
simLNN: no visible global function definition for ‘exprs<-’
simLNN: no visible global function definition for ‘exprs’
simnewsamples.gagafit: no visible global function definition for
  ‘pData’
simnewsamples.gagafit: no visible global function definition for
  ‘exprs’
simnewsamples.gagafit: no visible global function definition for
  ‘sampleNames<-’
simnewsamples.gagafit: no visible global function definition for
  ‘varLabels<-’
simnewsamples.nnfit: no visible global function definition for ‘pData’
simnewsamples.nnfit: no visible global function definition for ‘exprs’
simnewsamples.nnfit: no visible global function definition for
  ‘sampleNames<-’
simnewsamples.nnfit: no visible global function definition for
  ‘varLabels<-’
updateNNfit: no visible global function definition for ‘postprob’
* 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 line endings in C/C++/Fortran sources/headers ... 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 ... [8s/8s] OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/gaga.Rcheck/00check.log’
for details.


gaga.Rcheck/00install.out:

* installing *source* package ‘gaga’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c cseqdesma.c -o cseqdesma.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c cstat.c -o cstat.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -L/usr/local/lib -o gaga.so cseqdesma.o cstat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/gaga.Rcheck/gaga/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gaga)

gaga.Rcheck/gaga-Ex.timings:

nameusersystemelapsed
buildPatterns0.0130.0000.014
classpred0.0020.0010.002
findgenes0.0010.0000.001
fitGG0.2330.0020.235
forwsimDiffExpr2.4380.0072.448
geneclus0.0030.0000.003
parest0.0020.0000.002
powfindgenes0.5340.0020.536
simGG0.0010.0000.001