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Package 153/251HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: oligo
Version: 1.3.7
Command: D:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD build oligo
StartedAt: 2007-12-11 03:51:47 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 03:53:06 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 78.4 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA

Command output

* 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 D:/biocbld/bbs-2.2-bioc/tmpdir/Rinst582882690


---------- 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  -std=gnu99 -Id:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.2-bioc/R/include -I"d:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c baseProfile.c -o baseProfile.o
gcc  -std=gnu99 -Id:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.2-bioc/R/include -I"d:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c basecontent.c -o basecontent.o
gcc  -std=gnu99 -Id:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.2-bioc/R/include -I"d:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rma2.c -o rma2.o
gcc  -std=gnu99 -Id:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.2-bioc/R/include -I"d:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rma_background2.c -o rma_background2.o
gcc  -std=gnu99 -Id:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.2-bioc/R/include -I"d:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rma_common.c -o rma_common.o
gcc  -std=gnu99 -Id:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.2-bioc/R/include -I"d:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c trimmed.c -o trimmed.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.2-bioc/R/include  -i oligo_res.rc -o oligo_res.o
gcc  -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  -Ld:/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
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  installing help
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 >>> Building/Updating help pages for package 'oligo'
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Created d:\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
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