Package: Biobase

Version: 2.11.9

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.11.9.tar.gz

StartedAt: 2011-02-24 15:08:31 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 15:11:29 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 177.8 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/Biobase.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Biobase/DESCRIPTION' ... OK
* this is package 'Biobase' version '2.11.9'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Biobase' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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 ... NOTE
cache: no visible binding for global variable 'cache_old'
* 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-rowMedians.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'Biobase' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c Rinit.c -o Rinit.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c anyMissing.c -o anyMissing.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c envir.c -o envir.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c matchpt.c -o matchpt.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c rowMedians.c -o rowMedians.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c sublist_extract.c -o sublist_extract.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-2.8-bioc/meat/Biobase.Rcheck/Biobase/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Biobase)

name	user	system	elapsed
Aggregate	0.011	0.001	0.011
ScalarObject-class	0.044	0.000	0.044
addVig2Menu	0.000	0.001	0.000
anyMissing	0.001	0.000	0.001
biocReposList	0.000	0.000	0.001
cache	0.003	0.000	0.004
channel	0.242	0.001	0.244
channelNames	0.058	0.000	0.057
class.AnnotatedDataFrame	0.052	0.000	0.053
class.ExpressionSet	0.437	0.004	0.440
class.MIAxE	0.028	0.001	0.029
class.MultiSet	0.064	0.000	0.064
class.NChannelSet	0.357	0.002	0.359
class.Versioned	0.122	0.001	0.123
class.VersionedBiobase	0.060	0.001	0.060
class.Versions	0.023	0.001	0.024
class.VersionsNull	0.001	0.000	0.001
class.container	0.005	0.000	0.005
class.eSet	0.200	0.002	0.202
classVersion	0.014	0.000	0.013
combine	0.089	0.002	0.090
contents	0.001	0.000	0.001
copyEnv	0.000	0.001	0.001
copySubstitute	0.010	0.004	0.014
createPackage	0.008	0.002	0.010
data.aaMap	0.003	0.001	0.003
data.geneData	0.041	0.002	0.042
data.reporter	0.002	0.000	0.003
data.sample.ExpressionSet	0.027	0.001	0.028
data.sample.MultiSet	0.005	0.001	0.006
dumpPackTxt	0.003	0.001	0.067
esApply	2.899	0.004	2.903
getPkgVigs	0.038	0.004	0.042
isCurrent	0.082	0.002	0.084
isUnique	0.000	0.001	0.000
isVersioned	0.034	0.001	0.035
lcSuffix	0.002	0.000	0.002
listLen	0.000	0.000	0.001
makeDataPackage	0.126	0.003	0.130
matchpt	0.007	0.001	0.007
multiassign	0.001	0.000	0.001
note	0	0	0
openPDF	0.000	0.001	0.000
openVignette	0.000	0.000	0.001
package.version	0.001	0.000	0.001
read.AnnotatedDataFrame	0.017	0.001	0.019
read.MIAME	0.005	0.000	0.005
readExpressionSet	0.126	0.003	0.130
reverseSplit	0.001	0.000	0.001
rowMedians	0.073	0.004	0.077
rowQ	0.035	0.005	0.040
selectChannels	0.140	0.000	0.141
selectSome	0.000	0.000	0.001
strbreak	0	0	0
subListExtract	1.782	0.045	1.827
testBioCConnection	0.002	0.001	0.075
updateObject	0.266	0.011	0.278
updateOldESet	0	0	0
validMsg	0	0	0