oligo 1.3.7
Benilton Carvalho
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo | | Last Changed Rev: 28222 / Revision: 29143 | | Last Changed Date: 2007-10-25 07:56:21 -0700 (Thu, 25 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | ERROR | skipped | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | ERROR | skipped | |
| wellington | Linux (openSUSE 10.3) / i686 | ERROR | skipped | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | [ ERROR ] | skipped | skipped |
| lemming | Windows Server 2003 (32-bit) / x64 | ERROR | skipped | skipped |
* checking for file 'oligo/DESCRIPTION' ... OK
* preparing 'oligo':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
installing R.css in E:/biocbld/bbs-2.2-bioc/tmpdir/Rinst145606506
---------- Making package oligo ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making baseProfile.d from baseProfile.c
making basecontent.d from basecontent.c
making rma2.d from rma2.c
making rma_background2.d from rma_background2.c
making rma_common.d from rma_common.c
making trimmed.d from trimmed.c
gcc-sjlj -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include" -O3 -Wall -c baseProfile.c -o baseProfile.o
gcc-sjlj -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include" -O3 -Wall -c basecontent.c -o basecontent.o
gcc-sjlj -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include" -O3 -Wall -c rma2.c -o rma2.o
gcc-sjlj -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include" -O3 -Wall -c rma_background2.c -o rma_background2.o
gcc-sjlj -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include" -O3 -Wall -c rma_common.c -o rma_common.o
gcc-sjlj -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include" -O3 -Wall -c trimmed.c -o trimmed.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include -i oligo_res.rc -o oligo_res.o
gcc-sjlj -std=gnu99 -shared -s -o oligo.dll oligo.def baseProfile.o basecontent.o rma2.o rma_background2.o rma_common.o trimmed.o oligo_res.o -Le:/biocbld/bbs-2.2-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
preparing package oligo for lazy loading
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: preprocessCore
Loading required package: AnnotationDbi
Loading required package: affxparser
Loading required package: oligoClasses
installing man source files
installing indices
installing help
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>>> Building/Updating help pages for package 'oligo'
Formats: text html latex example chm
DBPDInfo-class text html latex example chm
FeatureSet-class text html latex example chm
FeatureSetExtensions-class text html latex example chm
Index-methods text html latex chm
IntensityMatrix-methods text html latex chm
MAplot-methods text html latex chm
PDInfo-class text html latex example chm
PDInfo-methods text html latex chm
Sequences-methods text html latex chm
SnpCallSet-methods text html latex chm
SnpCopyNumberSet-methods text html latex chm
SnpQSet-class text html latex example chm
SnpQSet-methods text html latex chm
SnpSetExtensions-class text html latex example chm
basecontent text html latex example chm
boxplot text html latex chm
chromosome text html latex chm
crlmm text html latex example chm
featureIndex text html latex chm
featureNames-methods text html latex chm
genomeBuild text html latex chm
getPlatformDesign text html latex chm
hist text html latex chm
image text html latex chm
internals text html latex chm
justSNPRMA text html latex example chm
kind text html latex chm
list.celfiles text html latex chm
manufacturer text html latex chm
nProbes text html latex chm
ncol text html latex chm
oligo-package text html latex example chm
platform text html latex chm
platformDesign-class text html latex example chm
plotDensity text html latex chm
pmAllele text html latex chm
pmPosition text html latex chm
pmStrand text html latex chm
probeNames text html latex chm
read.celfiles text html latex chm
read.xysfiles text html latex chm
rma text html latex chm
sequenceDesignMatrix text html latex chm
snprma text html latex chm
snprmaSummaries text html latex chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.2-bioc\meat\oligo\chm\oligo.chm
Compile time: 0 minutes, 1 second
46 Topics
258 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.2-bioc\meat\oligo\chm\oligo.chm, 43,702 bytes
Compression decreased file by 102,964 bytes.
adding MD5 sums
* DONE (oligo)
* creating vignettes ... ERROR
entering extended mode
buildVignettes(dir = '.')
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: preprocessCore
Loading required package: AnnotationDbi
Loading required package: affxparser
Loading required package: oligoClasses
This is the oligo package
/-------------------------------------------\
| SAMPLE HAPMAP 100K XBA |
|-------------------------------------------|
| Data obtained from http://www.hapmap.org |
| This package is meant to be used only for |
| demonstration of BioConductor packages. |
| Access http://www.hapmap.org for details. |
|-------------------------------------------|
| The contents of this package are provided |
| in good faith and the maintainer does not |
| warrant their accuracy. |
\-------------------------------------------/
Loading required package: pd.mapping50k.xba240
Error: processing vignette 'oligo.Rnw' failed with diagnostics:
chunk 4 (label=crlmm)
Error in readCel(ff, indices = fid, readOutliers = FALSE, readMasked = FALSE, :
unused argument(s) (reorder = TRUE)
Execution halted