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Package 49/419HostnameOS / ArchBUILDCHECKBUILD BIN
Biobase 2.10.0
Biocore Team c/o BioC user list
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/Biobase
Last Changed Rev: 50293 / Revision: 54281
Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: Biobase
Version: 2.10.0
Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.10.0.tar.gz
StartedAt: 2011-03-31 04:45:47 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 04:47:44 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 116.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Biobase.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/Biobase.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* 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 ‘2.10.0’
* 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) 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

Biobase.Rcheck/00install.out:

* installing *source* package ‘Biobase’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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-2.7-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)

Biobase.Rcheck/Biobase-Ex.timings:

nameusersystemelapsed
Aggregate0.0150.0010.015
ScalarObject-class0.030.000.03
addVig2Menu0.0010.0000.001
anyMissing0.0270.0000.027
biocReposList0.0010.0010.001
cache0.0040.0010.005
channel0.3050.0020.308
channelNames0.0730.0000.074
class.AnnotatedDataFrame0.0690.0010.071
class.ExpressionSet0.5620.0070.577
class.MultiSet0.0780.0000.079
class.NChannelSet0.4300.0020.435
class.Versioned0.2120.0040.218
class.VersionedBiobase0.0800.0010.081
class.Versions0.0300.0010.030
class.VersionsNull0.0010.0010.002
class.container0.0060.0000.006
class.eSet0.2640.0020.268
classVersion0.0170.0000.019
combine0.1220.0020.125
contents0.0010.0010.002
copyEnv0.0010.0000.002
copySubstitute0.0160.0070.033
createPackage0.0120.0040.019
data.aaMap0.0040.0000.004
data.geneData0.0500.0020.053
data.reporter0.0030.0010.003
data.sample.ExpressionSet0.0390.0020.042
data.sample.MultiSet0.0080.0010.008
dumpPackTxt0.0020.0010.010
esApply3.7300.0193.784
getPkgVigs0.0540.0070.061
isCurrent0.1030.0010.104
isUnique0.0010.0010.000
isVersioned0.0430.0000.044
lcSuffix0.0030.0000.004
listLen0.0010.0000.001
makeDataPackage0.1570.0070.165
matchpt0.0090.0000.010
multiassign0.0010.0000.001
note0.0010.0000.000
openPDF000
openVignette0.0010.0000.001
package.version0.0010.0000.002
read.AnnotatedDataFrame0.0250.0020.027
read.MIAME0.0060.0000.007
readExpressionSet0.1760.0060.192
reverseSplit0.0010.0000.002
rowMedians0.0840.0080.091
rowQ0.0470.0080.054
selectChannels0.1320.0000.138
selectSome000
strbreak0.0000.0000.001
subListExtract2.3920.0582.467
testBioCConnection0.0020.0000.010
updateObject0.3390.0050.347
updateOldESet0.0010.0000.001
validMsg0.0000.0000.001