BioC 3.2: CHECK report for Biobase on perceval

Package: Biobase

Version: 2.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.30.0.tar.gz

StartedAt: 2015-11-10 02:31:41 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 02:33:25 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 103.9 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_2.30.0.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 (2015-10-08 r69496)
* 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 ‘2.30.0’
* 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 ... [6s/6s] 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’ [24s/24s]
  Running ‘test-rowMedians.R’ [22s/22s]
 [46s/47s] 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	0.008	0.001	0.009
ScalarObject-class	0.014	0.000	0.015
addVig2Menu	0.001	0.001	0.001
anyMissing	0.002	0.000	0.002
cache	0.004	0.001	0.005
channel	0.143	0.001	0.144
channelNames	0.07	0.00	0.07
class.AnnotatedDataFrame	0.038	0.000	0.038
class.ExpressionSet	0.289	0.008	0.297
class.MIAxE	0.024	0.001	0.025
class.MultiSet	0.045	0.000	0.045
class.NChannelSet	0.272	0.007	0.278
class.Versioned	0.072	0.001	0.073
class.VersionedBiobase	0.032	0.000	0.033
class.Versions	0.018	0.000	0.018
class.VersionsNull	0.002	0.001	0.001
class.container	0.004	0.000	0.004
class.eSet	0.112	0.001	0.113
classVersion	0.006	0.000	0.006
contents	0.001	0.001	0.002
copyEnv	0.002	0.000	0.001
copySubstitute	0.014	0.005	0.020
createPackage	0.007	0.002	0.010
data.aaMap	0.003	0.001	0.004
data.geneData	0.034	0.003	0.037
data.reporter	0.002	0.000	0.003
data.sample.ExpressionSet	0.016	0.004	0.020
data.sample.MultiSet	0.006	0.002	0.008
dumpPackTxt	0.001	0.000	0.007
esApply	1.605	0.006	1.611
getPkgVigs	0.011	0.002	0.031
isCurrent	0.043	0.001	0.044
isUnique	0.000	0.001	0.001
isVersioned	0.016	0.000	0.016
lcSuffix	0.004	0.001	0.004
listLen	0.001	0.000	0.001
makeDataPackage	0.081	0.007	0.087
matchpt	0.006	0.000	0.006
multiassign	0.002	0.000	0.001
note	0.001	0.000	0.001
openPDF	0.001	0.000	0.001
openVignette	0.000	0.000	0.001
package.version	0.002	0.000	0.001
read.AnnotatedDataFrame	0.015	0.000	0.015
read.MIAME	0.003	0.000	0.003
readExpressionSet	0.137	0.002	0.139
reverseSplit	0.002	0.000	0.001
rowMedians	0.046	0.002	0.048
rowQ	0.021	0.007	0.028
selectChannels	0.061	0.001	0.061
selectSome	0	0	0
strbreak	0.001	0.000	0.001
subListExtract	1.057	0.022	1.079
testBioCConnection	0.003	0.002	0.217
updateOldESet	0	0	0
validMsg	0.000	0.000	0.001