Package: Biobase

Version: 2.11.10

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.11.10.tar.gz

StartedAt: 2011-03-17 15:43:11 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 15:44:31 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 80.1 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) (2011-03-06 r54683)
* 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 '2.11.10'
* 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 installed package size ... 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 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_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	0.037	0.000	0.037
addVig2Menu	0.001	0.001	0.001
anyMissing	0.001	0.000	0.001
biocReposList	0.001	0.000	0.000
cache	0.003	0.000	0.003
channel	0.213	0.000	0.214
channelNames	0.051	0.000	0.051
class.AnnotatedDataFrame	0.046	0.001	0.048
class.ExpressionSet	0.392	0.003	0.395
class.MIAxE	0.024	0.000	0.024
class.MultiSet	0.053	0.000	0.053
class.NChannelSet	0.317	0.002	0.319
class.Versioned	0.111	0.001	0.113
class.VersionedBiobase	0.054	0.001	0.054
class.Versions	0.021	0.001	0.022
class.VersionsNull	0.001	0.000	0.001
class.container	0.004	0.000	0.004
class.eSet	0.179	0.001	0.181
classVersion	0.012	0.000	0.012
combine	0.081	0.001	0.083
contents	0.001	0.001	0.001
copyEnv	0.000	0.000	0.001
copySubstitute	0.010	0.005	0.015
createPackage	0.008	0.002	0.010
data.aaMap	0.001	0.000	0.002
data.geneData	0.012	0.001	0.013
data.reporter	0.002	0.000	0.002
data.sample.ExpressionSet	0.025	0.001	0.026
data.sample.MultiSet	0.005	0.001	0.006
dumpPackTxt	0.003	0.001	0.035
esApply	2.581	0.002	2.583
getPkgVigs	0.035	0.004	0.039
isCurrent	0.098	0.001	0.099
isUnique	0.000	0.000	0.001
isVersioned	0.028	0.001	0.028
lcSuffix	0.001	0.000	0.002
listLen	0.000	0.001	0.001
makeDataPackage	0.123	0.004	0.126
matchpt	0.006	0.000	0.006
multiassign	0.001	0.001	0.001
note	0.001	0.000	0.000
openPDF	0.000	0.000	0.001
openVignette	0	0	0
package.version	0.001	0.000	0.001
read.AnnotatedDataFrame	0.015	0.001	0.016
read.MIAME	0.004	0.000	0.005
readExpressionSet	0.108	0.002	0.110
reverseSplit	0.001	0.000	0.000
rowMedians	0.062	0.003	0.065
rowQ	0.030	0.005	0.035
selectChannels	0.096	0.000	0.096
selectSome	0.001	0.000	0.000
strbreak	0.001	0.000	0.001
subListExtract	1.663	0.022	1.685
testBioCConnection	0.002	0.001	0.029
updateObject	0.247	0.006	0.254
updateOldESet	0	0	0
validMsg	0.000	0.001	0.000