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Package 58/462HostnameOS / ArchBUILDCHECKBUILD BIN
Biobase 2.13.2
Biocore Team c/o BioC user list
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase
Last Changed Rev: 55198 / Revision: 55359
Last Changed Date: 2011-05-01 23:56:27 -0700 (Sun, 01 May 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: Biobase
Version: 2.13.2
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings Biobase_2.13.2.tar.gz
StartedAt: 2011-05-09 12:44:06 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 12:45:37 -0700 (Mon, 09 May 2011)
EllapsedTime: 90.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Biobase.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/Biobase.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Biobase/DESCRIPTION' ... OK
* this is package 'Biobase' version '2.13.2'
* 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 installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 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 examples ... WARNING
Found the following significant warnings:

  Warning: '.readRDS' is deprecated.
  Warning: '.readRDS' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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

WARNING: There was 1 warning, see
  'E:/biocbld/bbs-2.9-bioc/meat/Biobase.Rcheck/00check.log'
for details

Biobase.Rcheck/00install.out:

* installing *source* package 'Biobase' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c Rinit.c -o Rinit.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c anyMissing.c -o anyMissing.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c envir.c -o envir.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c matchpt.c -o matchpt.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c rowMedians.c -o rowMedians.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c sublist_extract.c -o sublist_extract.o
gcc -shared -s -static-libgcc -o Biobase.dll tmp.def Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/Biobase.Rcheck/Biobase/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   '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
Aggregate000
ScalarObject-class0.050.000.05
addVig2Menu000
anyMissing0.010.000.01
biocReposList000
cache000
channel0.220.000.22
channelNames0.050.000.05
class.AnnotatedDataFrame0.040.000.05
class.ExpressionSet0.390.010.40
class.MIAxE0.040.000.03
class.MultiSet0.060.000.07
class.NChannelSet0.370.000.37
class.Versioned0.110.000.11
class.VersionedBiobase0.070.000.06
class.Versions0.030.000.03
class.VersionsNull000
class.container000
class.eSet0.180.000.19
classVersion0.020.000.02
combine0.080.000.08
contents000
copyEnv000
copySubstitute0.020.000.02
createPackage000
data.aaMap0.010.000.02
data.geneData0.040.000.03
data.reporter0.010.000.01
data.sample.ExpressionSet0.030.000.04
data.sample.MultiSet000
dumpPackTxt0.000.000.04
esApply2.670.002.69
getPkgVigs0.040.000.08
isCurrent0.060.000.09
isUnique000
isVersioned0.010.000.02
lcSuffix000
listLen0.000.020.01
makeDataPackage0.10.00.1
matchpt0.010.000.01
multiassign000
note000
openPDF000
openVignette000
package.version000
read.AnnotatedDataFrame0.020.000.03
read.MIAME0.010.000.02
readExpressionSet0.110.000.11
reverseSplit000
rowMedians0.080.000.08
rowQ0.030.000.03
selectChannels0.100.000.09
selectSome000
strbreak0.010.000.02
subListExtract1.820.001.83
testBioCConnection0.000.000.01
updateObject0.230.000.24
updateOldESet000
validMsg000