Package: Biobase

Version: 2.13.7

Command: mkdir Biobase.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Biobase.buildbin-libdir Biobase_2.13.7.tar.gz >Biobase-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=Biobase.buildbin-libdir --install="check:Biobase-install.out" --force-multiarch --no-vignettes --timings Biobase_2.13.7.tar.gz && mv Biobase.buildbin-libdir/* Biobase.Rcheck/ && rmdir Biobase.buildbin-libdir

StartedAt: 2011-07-07 04:18:33 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:20:55 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 142.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biobase.Rcheck

Warnings: 3

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/Biobase.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* 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 '2.13.7'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
Undocumented code objects:
  'estimateDispersions' 'estimateSizeFactors'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                           old_size new_size compress
  SW.rda                      338Kb    261Kb       xz
  sample.ExpressionSet.rda    271Kb     72Kb       xz
  sample.MultiSet.rda          25Kb     19Kb       xz
  seD.rda                      28Kb     18Kb    bzip2
* 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 ...
** running examples for arch 'i386' ... 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.
** running examples for arch 'x64' ... 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 tests for arch 'i386'
  Running 'test-rowMedians.R'
 OK
** running tests for arch 'x64'
  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 were 3 warnings, see
  'D:/biocbld/bbs-2.9-bioc/meat/Biobase.Rcheck/00check.log'
for details

install for i386

* installing *source* package 'Biobase' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c Rinit.c -o Rinit.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c anyMissing.c -o anyMissing.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c envir.c -o envir.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c matchpt.c -o matchpt.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c rowMedians.c -o rowMedians.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -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 -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/Biobase.buildbin-libdir/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

add DLL for x64

* installing *source* package 'Biobase' ...
** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c Rinit.c -o Rinit.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c anyMissing.c -o anyMissing.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c envir.c -o envir.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c matchpt.c -o matchpt.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c rowMedians.c -o rowMedians.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c sublist_extract.c -o sublist_extract.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o Biobase.dll tmp.def Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/Biobase.buildbin-libdir/Biobase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Biobase' as Biobase_2.13.7.zip

* DONE (Biobase)

name	user	system	elapsed
Aggregate	0	0	0
ScalarObject-class	0.03	0.00	0.03
addVig2Menu	0	0	0
anyMissing	0.01	0.00	0.02
biocReposList	0.00	0.00	0.01
cache	0	0	0
channel	0.22	0.00	0.24
channelNames	0.05	0.00	0.05
class.AnnotatedDataFrame	0.05	0.00	0.04
class.ExpressionSet	0.39	0.00	0.39
class.MIAxE	0.01	0.00	0.02
class.MultiSet	0.06	0.00	0.06
class.NChannelSet	0.33	0.00	0.33
class.Versioned	0.11	0.00	0.11
class.VersionedBiobase	0.04	0.00	0.05
class.Versions	0.02	0.00	0.01
class.VersionsNull	0	0	0
class.container	0.01	0.00	0.02
class.eSet	0.18	0.00	0.17
classVersion	0.01	0.00	0.02
combine	0.08	0.00	0.08
contents	0	0	0
copyEnv	0	0	0
copySubstitute	0.01	0.02	0.04
createPackage	0	0	0
data.aaMap	0	0	0
data.geneData	0.02	0.01	0.03
data.reporter	0	0	0
data.sample.ExpressionSet	0.01	0.00	0.01
data.sample.MultiSet	0.00	0.02	0.02
dumpPackTxt	0	0	0
esApply	2.64	0.00	2.64
getPkgVigs	0.04	0.00	0.04
isCurrent	0.07	0.00	0.07
isUnique	0	0	0
isVersioned	0.01	0.00	0.02
lcSuffix	0	0	0
listLen	0	0	0
makeDataPackage	0.09	0.00	0.10
matchpt	0	0	0
multiassign	0	0	0
note	0	0	0
openPDF	0	0	0
openVignette	0	0	0
package.version	0	0	0
read.AnnotatedDataFrame	0.02	0.02	0.03
read.MIAME	0	0	0
readExpressionSet	0.14	0.00	0.14
reverseSplit	0	0	0
rowMedians	0.06	0.00	0.06
rowQ	0.03	0.00	0.03
selectChannels	0.08	0.00	0.08
selectSome	0	0	0
strbreak	0	0	0
subListExtract	1.58	0.00	1.57
testBioCConnection	0.00	0.00	0.02
updateObject	0.22	0.00	0.21
updateOldESet	0	0	0
validMsg	0	0	0