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Package 61/553HostnameOS / ArchBUILDCHECKBUILD BIN
Biobase 2.16.0
Bioconductor Package Maintainer
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/Biobase
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: Biobase
Version: 2.16.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.16.0.tar.gz
StartedAt: 2012-09-23 23:25:11 -0700 (Sun, 23 Sep 2012)
EndedAt: 2012-09-23 23:26:53 -0700 (Sun, 23 Sep 2012)
EllapsedTime: 102.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Biobase.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/Biobase.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '2.16.0'
* 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
.esApply: warning in multiassign(names(pData(X)), pData(X), env = e1):
  partial argument match of 'env' to 'envir'
Aggregate: warning in exists(nm, env = aggenv(agg), inherits = FALSE):
  partial argument match of 'env' to 'envir'
Aggregate: warning in assign(nm, env = aggenv(agg), initfun(agg)(nm,
  x)): partial argument match of 'env' to 'envir'
Aggregate: warning in get(nm, env = aggenv(agg)): partial argument
  match of 'env' to 'envir'
Aggregate: warning in assign(nm, aggfun(agg)(nm, v1), env =
  aggenv(agg)): partial argument match of 'env' to 'envir'
Aggregate: warning in assign(nm, env = aggenv(agg), initfun(agg)(nm,
  x[[i]])): partial argument match of 'env' to 'envir'
Aggregate: warning in assign(nm, env = aggenv(agg), aggfun(agg)(nm, v1,
  x[[i]])): partial argument match of 'env' to 'envir'
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-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-2.10-bioc/meat/Biobase.Rcheck/00check.log'
for details.

Biobase.Rcheck/00install.out:

* 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-2.10-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)

Biobase.Rcheck/Biobase-Ex.timings:

nameusersystemelapsed
Aggregate0.0150.0000.015
ScalarObject-class0.0280.0000.028
addVig2Menu0.0000.0000.001
anyMissing0.0020.0000.002
biocReposList0.0840.0120.100
cache0.0040.0010.005
channel0.1880.0010.189
channelNames0.0490.0010.049
class.AnnotatedDataFrame0.0540.0010.055
class.ExpressionSet0.5500.0080.558
class.MIAxE0.0410.0010.041
class.MultiSet0.0800.0010.080
class.NChannelSet0.4000.0020.401
class.Versioned0.1010.0010.103
class.VersionedBiobase0.0480.0010.048
class.Versions0.0180.0010.017
class.VersionsNull0.0010.0000.001
class.container0.0050.0000.005
class.eSet0.1620.0010.163
classVersion0.010.000.01
contents0.0010.0000.002
copyEnv000
copySubstitute0.0100.0090.033
createPackage0.0070.0050.013
data.aaMap0.0020.0000.004
data.geneData0.0330.0030.036
data.reporter0.0020.0000.002
data.sample.ExpressionSet0.0180.0020.021
data.sample.MultiSet0.0060.0010.007
dumpPackTxt0.0010.0010.023
esApply2.1250.0122.138
getPkgVigs0.0350.0110.046
isCurrent0.0670.0010.069
isUnique0.0000.0000.001
isVersioned0.0300.0010.032
lcSuffix0.0010.0000.001
listLen0.0010.0000.001
makeDataPackage0.1080.0070.116
matchpt0.0080.0000.008
multiassign0.0010.0000.002
note0.0010.0000.001
openPDF000
openVignette0.0000.0000.001
package.version0.0010.0000.001
read.AnnotatedDataFrame0.0170.0020.021
read.MIAME0.0090.0010.009
readExpressionSet0.1040.0070.110
reverseSplit0.0010.0000.000
rowMedians0.0640.0050.069
rowQ0.0240.0070.031
selectChannels0.1010.0000.101
selectSome000
strbreak0.0010.0000.001
subListExtract2.9200.0712.992
testBioCConnection0.0020.0010.013
updateOldESet000
validMsg000