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 18:22:58 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:24:46 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 107.3 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: UTF-8
* 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	0.015	0.000	0.015
ScalarObject-class	0.056	0.001	0.056
addVig2Menu	0.001	0.000	0.001
anyMissing	0.002	0.001	0.002
biocReposList	0.001	0.000	0.001
cache	0.004	0.001	0.006
channel	0.310	0.002	0.312
channelNames	0.074	0.000	0.074
class.AnnotatedDataFrame	0.068	0.001	0.069
class.ExpressionSet	0.563	0.008	0.573
class.MIAxE	0.038	0.001	0.039
class.MultiSet	0.079	0.001	0.081
class.NChannelSet	0.461	0.005	0.470
class.Versioned	0.159	0.002	0.161
class.VersionedBiobase	0.078	0.001	0.079
class.Versions	0.030	0.001	0.030
class.VersionsNull	0.002	0.000	0.002
class.container	0.006	0.001	0.006
class.eSet	0.263	0.002	0.265
classVersion	0.017	0.001	0.018
combine	0.119	0.002	0.143
contents	0.001	0.000	0.002
copyEnv	0.001	0.001	0.001
copySubstitute	0.015	0.006	0.023
createPackage	0.011	0.003	0.015
data.aaMap	0.004	0.001	0.004
data.geneData	0.050	0.003	0.054
data.reporter	0.003	0.000	0.004
data.sample.ExpressionSet	0.039	0.001	0.041
data.sample.MultiSet	0.007	0.000	0.008
dumpPackTxt	0.002	0.000	0.035
esApply	3.978	0.019	4.032
getPkgVigs	0.054	0.007	0.062
isCurrent	0.104	0.001	0.106
isUnique	0.001	0.000	0.001
isVersioned	0.044	0.000	0.045
lcSuffix	0.003	0.001	0.003
listLen	0.001	0.000	0.001
makeDataPackage	0.167	0.010	0.177
matchpt	0.009	0.001	0.010
multiassign	0.001	0.000	0.002
note	0.000	0.000	0.001
openPDF	0.001	0.000	0.001
openVignette	0.000	0.000	0.001
package.version	0.001	0.000	0.002
read.AnnotatedDataFrame	0.024	0.003	0.027
read.MIAME	0.006	0.000	0.007
readExpressionSet	0.137	0.005	0.143
reverseSplit	0.001	0.000	0.001
rowMedians	0.087	0.006	0.093
rowQ	0.048	0.008	0.056
selectChannels	0.136	0.001	0.137
selectSome	0.001	0.000	0.000
strbreak	0.001	0.000	0.001
subListExtract	2.284	0.063	2.371
testBioCConnection	0.002	0.001	0.009
updateObject	0.338	0.003	0.341
updateOldESet	0	0	0
validMsg	0.000	0.000	0.001