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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: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.10.0.tar.gz
StartedAt: 2011-03-31 04:37:31 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 04:38:48 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 77.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Biobase.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/Biobase.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/biocbuild/bbs-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-bioc/meat/Biobase.Rcheck/Biobase/libs
** 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
Aggregate0.0120.0000.010
ScalarObject-class0.0560.0000.056
addVig2Menu0.0000.0000.001
anyMissing0.0040.0000.001
biocReposList000
cache0.0040.0000.002
channel0.2280.0000.229
channelNames0.0480.0000.048
class.AnnotatedDataFrame0.0440.0000.046
class.ExpressionSet0.3760.0040.381
class.MultiSet0.0560.0000.057
class.NChannelSet0.3040.0000.303
class.Versioned0.1600.0040.163
class.VersionedBiobase0.0480.0040.051
class.Versions0.0160.0040.020
class.VersionsNull0.0000.0000.001
class.container0.0040.0040.005
class.eSet0.1680.0000.173
classVersion0.0120.0000.009
combine0.080.000.08
contents0.0000.0000.001
copyEnv0.0040.0000.001
copySubstitute0.0080.0000.010
createPackage0.0000.0080.008
data.aaMap0.0040.0000.002
data.geneData0.0240.0040.028
data.reporter0.0000.0000.001
data.sample.ExpressionSet0.0160.0000.017
data.sample.MultiSet0.0040.0000.004
dumpPackTxt0.0000.0000.012
esApply2.6840.0082.693
getPkgVigs0.0360.0000.039
isCurrent0.0760.0000.075
isUnique0.0000.0000.001
isVersioned0.0280.0040.032
lcSuffix0.0040.0000.001
listLen0.0000.0000.001
makeDataPackage0.0760.0000.077
matchpt0.0040.0000.005
multiassign0.0000.0000.001
note0.0040.0000.001
openPDF000
openVignette000
package.version0.0000.0000.001
read.AnnotatedDataFrame0.020.000.02
read.MIAME0.0040.0000.004
readExpressionSet0.1520.0000.154
reverseSplit0.0000.0000.001
rowMedians0.0560.0040.060
rowQ0.0240.0000.023
selectChannels0.0880.0000.086
selectSome0.0000.0000.001
strbreak0.0000.0000.001
subListExtract1.7920.0161.805
testBioCConnection0.0000.0000.006
updateObject0.2200.0000.222
updateOldESet000
validMsg000