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
/tmp/Rinst1502564099
* Installing *source* package 'oligo' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c basecontent.c -o basecontent.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c baseProfile.c -o baseProfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc -std=gnu99 -shared -L/usr/local/lib -o oligo.so basecontent.o baseProfile.o rma2.o rma_background2.o rma_common.o trimmed.o -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** inst
** preparing package 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
** help
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>>> Building/Updating help pages for package 'oligo'
Formats: text html latex example
DBPDInfo-class text html latex example
FeatureSet-class text html latex example
FeatureSetExtensions-class text html latex example
Index-methods text html latex
IntensityMatrix-methods text html latex
MAplot-methods text html latex
PDInfo-class text html latex example
PDInfo-methods text html latex
Sequences-methods text html latex
SnpCallSet-methods text html latex
SnpCopyNumberSet-methods text html latex
SnpQSet-class text html latex example
SnpQSet-methods text html latex
SnpSetExtensions-class text html latex example
basecontent text html latex example
boxplot text html latex
chromosome text html latex
crlmm text html latex example
featureIndex text html latex
featureNames-methods text html latex
genomeBuild text html latex
getPlatformDesign text html latex
hist text html latex
image text html latex
internals text html latex
justSNPRMA text html latex example
kind text html latex
list.celfiles text html latex
manufacturer text html latex
nProbes text html latex
ncol text html latex
oligo-package text html latex example
platform text html latex
platformDesign-class text html latex example
plotDensity text html latex
pmAllele text html latex
pmPosition text html latex
pmStrand text html latex
probeNames text html latex
read.celfiles text html latex
read.xysfiles text html latex
rma text html latex
sequenceDesignMatrix text html latex
snprma text html latex
snprmaSummaries text html latex
** building package indices ...
* DONE (oligo)
* creating vignettes ... ERROR
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './ClassesUsedInOligo.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './ClassesUsedInOligo.tex' ...
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
Attaching package: 'oligo'
The following object(s) are masked from package:oligoClasses :
calls,
calls<-,
callsConfidence,
callsConfidence<-,
cnConfidence,
cnConfidence<-,
copyNumber,
copyNumber<-
/-------------------------------------------\
| 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