BioC 3.1: CHECK report for Biobase on petty

Package: Biobase

Version: 2.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.28.0.tar.gz

StartedAt: 2015-10-08 21:40:10 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 21:42:37 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 146.5 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Biobase.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 ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.28.0’
* 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 ‘Biobase’ can be installed ... [9s/10s] 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 ... 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 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 ... [9s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [33s/33s]
  Running ‘test-rowMedians.R’ [27s/27s]
 [60s/60s] 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: OK

* installing *source* package ‘Biobase’ ...
** 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 Rinit.c -o Rinit.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 anyMissing.c -o anyMissing.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 envir.c -o envir.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 matchpt.c -o matchpt.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 rowMedians.c -o rowMedians.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 sublist_extract.c -o sublist_extract.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 Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/Biobase.Rcheck/Biobase/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 (Biobase)

name	user	system	elapsed
Aggregate	0.014	0.000	0.015
ScalarObject-class	0.025	0.000	0.025
addVig2Menu	0.001	0.001	0.002
anyMissing	0.003	0.000	0.003
cache	0.006	0.001	0.007
channel	0.228	0.001	0.232
channelNames	0.117	0.000	0.118
class.AnnotatedDataFrame	0.058	0.001	0.059
class.ExpressionSet	0.471	0.011	0.482
class.MIAxE	0.035	0.001	0.036
class.MultiSet	0.076	0.000	0.076
class.NChannelSet	0.430	0.010	0.441
class.Versioned	0.121	0.001	0.123
class.VersionedBiobase	0.054	0.001	0.056
class.Versions	0.026	0.001	0.027
class.VersionsNull	0.003	0.000	0.003
class.container	0.007	0.000	0.006
class.eSet	0.181	0.002	0.183
classVersion	0.010	0.001	0.009
contents	0.002	0.001	0.003
copyEnv	0.002	0.000	0.002
copySubstitute	0.019	0.006	0.027
createPackage	0.011	0.003	0.014
data.aaMap	0.004	0.001	0.004
data.geneData	0.056	0.004	0.059
data.reporter	0.003	0.001	0.004
data.sample.ExpressionSet	0.022	0.005	0.027
data.sample.MultiSet	0.009	0.005	0.014
dumpPackTxt	0.003	0.001	0.014
esApply	2.640	0.013	2.657
getPkgVigs	0.017	0.003	0.041
isCurrent	0.069	0.001	0.071
isUnique	0.001	0.001	0.001
isVersioned	0.027	0.000	0.028
lcSuffix	0.006	0.000	0.006
listLen	0.002	0.001	0.002
makeDataPackage	0.122	0.007	0.131
matchpt	0.011	0.000	0.011
multiassign	0.003	0.001	0.003
note	0.001	0.000	0.001
openPDF	0.001	0.001	0.001
openVignette	0.001	0.000	0.001
package.version	0.002	0.001	0.002
read.AnnotatedDataFrame	0.024	0.001	0.025
read.MIAME	0.004	0.000	0.005
readExpressionSet	0.210	0.002	0.213
reverseSplit	0.002	0.000	0.002
rowMedians	0.070	0.003	0.072
rowQ	0.029	0.008	0.037
selectChannels	0.103	0.000	0.103
selectSome	0.001	0.000	0.001
strbreak	0.003	0.000	0.003
subListExtract	1.785	0.032	1.821
testBioCConnection	0.004	0.002	0.256
updateOldESet	0.001	0.000	0.000
validMsg	0.002	0.001	0.002