BioC 3.2: CHECK report for Biobase on perceval

Package: Biobase

Version: 2.29.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.29.1.tar.gz

StartedAt: 2015-08-23 22:31:08 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:33:03 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 114.9 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_2.29.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-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 ‘2.29.1’
* 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 ... [7s/8s] 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 ... [6s/6s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [25s/25s]
  Running ‘test-rowMedians.R’ [25s/25s]
 [50s/50s] 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-3.2-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	0.009	0.000	0.009
ScalarObject-class	0.016	0.000	0.017
addVig2Menu	0.001	0.001	0.001
anyMissing	0.002	0.000	0.002
cache	0.005	0.002	0.006
channel	0.174	0.001	0.175
channelNames	0.099	0.001	0.099
class.AnnotatedDataFrame	0.037	0.001	0.038
class.ExpressionSet	0.304	0.016	0.320
class.MIAxE	0.023	0.001	0.024
class.MultiSet	0.039	0.000	0.038
class.NChannelSet	0.293	0.010	0.303
class.Versioned	0.076	0.002	0.078
class.VersionedBiobase	0.027	0.001	0.029
class.Versions	0.015	0.001	0.016
class.VersionsNull	0.002	0.000	0.002
class.container	0.003	0.001	0.004
class.eSet	0.096	0.001	0.098
classVersion	0.006	0.000	0.006
contents	0.001	0.001	0.001
copyEnv	0.001	0.000	0.001
copySubstitute	0.012	0.005	0.018
createPackage	0.007	0.003	0.009
data.aaMap	0.003	0.000	0.003
data.geneData	0.035	0.003	0.038
data.reporter	0.003	0.001	0.003
data.sample.ExpressionSet	0.014	0.008	0.022
data.sample.MultiSet	0.006	0.007	0.013
dumpPackTxt	0.002	0.000	0.027
esApply	1.547	0.013	1.561
getPkgVigs	0.010	0.002	0.038
isCurrent	0.039	0.001	0.040
isUnique	0.001	0.001	0.001
isVersioned	0.018	0.000	0.019
lcSuffix	0.004	0.001	0.004
listLen	0.001	0.000	0.001
makeDataPackage	0.076	0.011	0.086
matchpt	0.005	0.000	0.006
multiassign	0.001	0.000	0.002
note	0.001	0.000	0.001
openPDF	0.000	0.000	0.001
openVignette	0.000	0.001	0.001
package.version	0.001	0.000	0.001
read.AnnotatedDataFrame	0.013	0.001	0.014
read.MIAME	0.003	0.001	0.003
readExpressionSet	0.147	0.002	0.149
reverseSplit	0.001	0.001	0.002
rowMedians	0.039	0.001	0.041
rowQ	0.017	0.012	0.030
selectChannels	0.055	0.000	0.055
selectSome	0.000	0.000	0.001
strbreak	0.001	0.000	0.002
subListExtract	1.081	0.029	1.111
testBioCConnection	0.003	0.002	0.396
updateOldESet	0.001	0.000	0.000
validMsg	0.001	0.000	0.001