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oligo

1.0.2-6

Benilton Carvalho
Last Changed Date: 2007-06-13 23:59:58 -0700
Last Changed Rev: 25367
lamb1 Linux (SUSE 10.1) x86_64  OK  OK 
wellington Linux (SUSE 9.2) i686  ERROR skipped
lemming Windows Server 2003 (32-bit) x64 [ ERROR ]skippedskipped
Package: oligo
Version: 1.0.2-6
Command: D:\biocbld\bbs-2.0-bioc\R\bin\R.exe CMD build oligo
RetCode: 1
Time: 189.5 seconds
Status: ERROR
PackageFile: None

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-2.0-bioc/tmpdir/Rinst354486911


---------- Making package oligo ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making M_estimator2.d from M_estimator2.c
making baseProfile.d from baseProfile.c
making basecontent.d from basecontent.c
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c M_estimator2.c -o M_estimator2.o
M_estimator2.c: In function `R_HuberMatrixRows2':
M_estimator2.c:129: warning: 'scale1' might be used uninitialized in this function
M_estimator2.c:129: warning: 'scale2' might be used uninitialized in this function
M_estimator2.c:129: warning: 'scale3' might be used uninitialized in this function
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c baseProfile.c -o baseProfile.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c basecontent.c -o basecontent.o
windres -I d:/biocbld/bbs-2.0-bioc/R/include  -i oligo_res.rc -o oligo_res.o
gcc  -shared -s  -o oligo.dll oligo.def M_estimator2.o baseProfile.o basecontent.o oligo_res.o  -Ld:/biocbld/bbs-2.0-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  save image
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: affyio
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: BufferedMatrix
Loading required package: BufferedMatrixMethods
  installing inst files
  installing man source files
  installing indices
  installing help
 >>> 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
     missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
  FeatureSetExtensions-class        text    html    latex   example chm
     missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
  Index-methods                     text    html    latex   example chm
  IntensityMatrix-methods           text    html    latex   example chm
  PDInfo-class                      text    html    latex   example chm
  PDInfo-methods                    text    html    latex   example chm
  Sequences-methods                 text    html    latex   example chm
  SnpCallSet-methods                text    html    latex   example chm
  SnpCopyNumberSet-methods          text    html    latex   example chm
  SnpQSet-class                     text    html    latex   example chm
     missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
  SnpQSet-methods                   text    html    latex   example chm
  SnpSetExtensions-class            text    html    latex   example chm
     missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
  basecontent                       text    html    latex   example chm
  boxplot                           text    html    latex   example chm
  chromosome                        text    html    latex   example chm
  crlmm                             text    html    latex   example chm
  featureIndex                      text    html    latex   example chm
  genomeBuild                       text    html    latex   example chm
  getPlatformDesign                 text    html    latex   example chm
  hist                              text    html    latex   example chm
  image                             text    html    latex   example chm
  internals                         text    html    latex   example chm
  kind                              text    html    latex   example chm
  list.celfiles                     text    html    latex   example chm
  manufacturer                      text    html    latex   example chm
  nProbes                           text    html    latex   example chm
  ncol                              text    html    latex   example chm
  oligo-package                     text    html    latex   example chm
  platform                          text    html    latex   example chm
  platformDesign-class              text    html    latex   example chm
  plotDensity                       text    html    latex   example chm
  pmAllele                          text    html    latex   example chm
  pmPosition                        text    html    latex   example chm
  pmStrand                          text    html    latex   example chm
  probeNames                        text    html    latex   example chm
  read.celfiles                     text    html    latex   example chm
  read.xysfiles                     text    html    latex   example chm
  rma                               text    html    latex   example chm
  sequenceDesignMatrix              text    html    latex   example chm
  snprma                            text    html    latex   example chm
  snprmaSummaries                   text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702



Compiling d:\biocbld\bbs-2.0-bioc\meat\oligo\chm\oligo.chm





Compile time: 0 minutes, 0 seconds

43	Topics

215	Local links

0	Internet links

1	Graphic





Created d:\biocbld\bbs-2.0-bioc\meat\oligo\chm\oligo.chm, 41,578 bytes

Compression decreased file by 89,529 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: affyio
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: BufferedMatrix
Loading required package: BufferedMatrixMethods
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.                   |
\-------------------------------------------/
Platform design info loaded.

Error: processing vignette 'oligo.Rnw' failed with diagnostics:
 chunk 4 (label=snprma) 
Error : cannot allocate vector of size 683.7 Mb
Execution halted