Biobase 1.16.3
Biocore Team c/o BioC user list
| Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/Biobase | | Last Changed Rev: 29763 / Revision: 30966 | | Last Changed Date: 2008-01-30 11:30:24 -0800 (Wed, 30 Jan 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/Biobase.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'Biobase/DESCRIPTION' ... OK
* this is package 'Biobase' version '1.16.3'
* 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 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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 ... OK
* creating Biobase-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-2.1-bioc/meat/Biobase.Rcheck/tests'
Running 'test-rowMedians.R'
make[1]: Leaving directory `/cygdrive/d/biocbld/bbs-2.1-bioc/meat/Biobase.Rcheck/tests'
OK
* checking package vignettes in 'inst/doc' ... OK
* creating Biobase-manual.tex ... OK
* checking Biobase-manual.tex ... OK
installing R.css in D:/biocbld/bbs-2.1-bioc/meat/Biobase.Rcheck
---------- Making package Biobase ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making Rinit.d from Rinit.c
making anyMissing.d from anyMissing.c
making envir.d from envir.c
making matchpt.d from matchpt.c
making rowMedians.d from rowMedians.c
making sublist_extract.d from sublist_extract.c
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c Rinit.c -o Rinit.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c anyMissing.c -o anyMissing.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c envir.c -o envir.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c matchpt.c -o matchpt.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c rowMedians.c -o rowMedians.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c sublist_extract.c -o sublist_extract.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.1-bioc/R/include -i Biobase_res.rc -o Biobase_res.o
gcc-sjlj -std=gnu99 -shared -s -o Biobase.dll Biobase.def Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o Biobase_res.o -Ld:/biocbld/bbs-2.1-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
preparing package Biobase for lazy loading
Loading required package: tools
installing man source files
installing indices
Loading required package: methods
not zipping data
installing help
>>> Building/Updating help pages for package 'Biobase'
Formats: text html latex example chm
Aggregate text html latex example chm
Biobase-package text html latex chm
ScalarObject-class text html latex example chm
abstract text html latex chm
addVig2Menu text html latex example chm
annotatedDataFrameFrom-methods text html latex chm
annotation text html latex chm
anyMissing text html latex example chm
assayData text html latex chm
biocReposList text html latex example chm
cache text html latex example chm
channel text html latex example chm
channelNames text html latex example chm
class.AnnotatedDataFrame text html latex example chm
class.AssayData text html latex chm
class.ExpressionSet text html latex example chm
class.MIAME text html latex chm
class.MultiSet text html latex example chm
class.NChannelSet text html latex example chm
class.SnpSet text html latex chm
class.Versioned text html latex example chm
class.VersionedBiobase text html latex example chm
class.Versions text html latex example chm
class.VersionsNull text html latex example chm
class.aggregator text html latex chm
class.annotatedDataset text html latex chm
class.characterORmiame text html latex chm
class.container text html latex example chm
class.eSet text html latex example chm
class.exprList text html latex example chm
class.exprMatrix text html latex chm
class.exprSet text html latex example chm
class.phenoData text html latex example chm
classVersion text html latex example chm
combine text html latex example chm
contents text html latex example chm
copyEnv text html latex example chm
copySubstitute text html latex example chm
createPackage text html latex example chm
data.aaMap text html latex example chm
data.eset text html latex example chm
data.geneData text html latex example chm
data.reporter text html latex example chm
data.sample.ExpressionSet text html latex example chm
data.sample.eSet text html latex example chm
data.sample.exprSet.1 text html latex example chm
data.sample.exprSet text html latex example chm
defunct text html latex chm
description text html latex chm
dims text html latex chm
dumpPackTxt text html latex example chm
esApply text html latex example chm
exprs text html latex chm
featureData text html latex chm
featureNames text html latex chm
getPkgVigs text html latex example chm
internals text html latex chm
isCurrent text html latex example chm
isUnique text html latex example chm
isVersioned text html latex example chm
lcSuffix text html latex example chm
listLen text html latex example chm
makeDataPackage text html latex example chm
matchpt text html latex example chm
multiassign text html latex example chm
note text html latex example chm
notes text html latex chm
openPDF text html latex example chm
openVignette text html latex example chm
package.version text html latex example chm
phenoData text html latex chm
read.AnnotatedDataFrame text html latex example chm
read.MIAME text html latex example chm
read.exprSet text html latex example chm
read.phenoData text html latex example chm
readExpressionSet text html latex example chm
reporterInfo text html latex chm
reverseSplit text html latex example chm
rowMedians text html latex example chm
rowQ text html latex example chm
selectChannels text html latex example chm
selectSome text html latex example chm
storageMode text html latex chm
strbreak text html latex example chm
subListExtract text html latex example chm
testBioCConnection text html latex example chm
updateObject text html latex example chm
updateOldESet text html latex example chm
userQuery text html latex example chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "les\Windows Resource Kits\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\bbs-2.1-bioc\meat\Biobase.Rcheck\00_pkg_src\Biobase\chm\Biobase.chm
HHC4016: Warning: Cannot open "les\Windows Resource Kits\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
The following files were not compiled:
adding MD5 sums
* DONE (Biobase)