Package: Biobase

Version: 2.17.6

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.17.6.tar.gz

StartedAt: 2012-06-20 22:09:57 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 22:12:34 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 156.7 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/Biobase.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '2.17.6'
* 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 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R'
  Running 'test-rowMedians.R'
 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/Biobase.Rcheck/00check.log'
for details.

* installing *source* package 'Biobase' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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-2.11-bioc/meat/Biobase.Rcheck/Biobase/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'BiobaseDevelopment.Rnw' 
   'Bioconductor.Rnw' 
   'ExpressionSetIntroduction.Rnw' 
   'HowTo.Rnw' 
   'Qviews.Rnw' 
   'esApply.Rnw' 
** testing if installed package can be loaded

* DONE (Biobase)

name	user	system	elapsed
Aggregate	0.012	0.000	0.013
ScalarObject-class	0.024	0.000	0.024
addVig2Menu	0.001	0.000	0.000
anyMissing	0.002	0.000	0.002
cache	0.004	0.002	0.007
channel	0.226	0.001	0.228
channelNames	0.06	0.00	0.06
class.AnnotatedDataFrame	0.061	0.001	0.062
class.ExpressionSet	0.482	0.011	0.494
class.MIAxE	0.086	0.001	0.088
class.MultiSet	0.068	0.003	0.071
class.NChannelSet	0.344	0.001	0.345
class.Versioned	0.122	0.001	0.123
class.VersionedBiobase	0.058	0.001	0.058
class.Versions	0.021	0.000	0.023
class.VersionsNull	0.002	0.000	0.001
class.container	0.005	0.000	0.005
class.eSet	0.205	0.001	0.207
classVersion	0.016	0.000	0.021
contents	0.001	0.001	0.003
copyEnv	0.000	0.001	0.001
copySubstitute	0.013	0.008	0.034
createPackage	0.010	0.005	0.017
data.aaMap	0.003	0.001	0.005
data.geneData	0.048	0.005	0.059
data.reporter	0.002	0.001	0.003
data.sample.ExpressionSet	0.024	0.002	0.028
data.sample.MultiSet	0.009	0.001	0.010
dumpPackTxt	0.002	0.001	0.023
esApply	2.899	0.017	2.945
getPkgVigs	0.051	0.010	0.085
isCurrent	0.085	0.000	0.086
isUnique	0.000	0.000	0.001
isVersioned	0.035	0.001	0.036
lcSuffix	0.002	0.001	0.003
listLen	0.001	0.000	0.002
makeDataPackage	0.131	0.009	0.140
matchpt	0.007	0.001	0.007
multiassign	0.001	0.000	0.001
note	0	0	0
openPDF	0	0	0
openVignette	0.000	0.000	0.001
package.version	0.002	0.001	0.001
read.AnnotatedDataFrame	0.022	0.002	0.024
read.MIAME	0.005	0.001	0.005
readExpressionSet	0.180	0.007	0.187
reverseSplit	0.001	0.000	0.001
rowMedians	0.078	0.007	0.085
rowQ	0.032	0.010	0.041
selectChannels	0.118	0.001	0.119
selectSome	0	0	0
strbreak	0.001	0.000	0.002
subListExtract	3.758	0.096	3.909
testBioCConnection	0.003	0.001	0.013
updateOldESet	0	0	0
validMsg	0.000	0.000	0.001