Package: oligo

Version: 1.12.2

Command: chmod a+r oligo -R && E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD build oligo

StartedAt: 2010-10-04 14:05:35 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 14:05:57 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 22.3 seconds

RetCode: 0

Status:  OK

PackageFile: oligo_1.12.2.tar.gz

PackageFileSize: 2.316 MiB

* checking for file 'oligo/DESCRIPTION' ... OK
* preparing 'oligo':
* checking DESCRIPTION meta-information ... OK
* cleaning src
make: Nothing to be done for `clean'.
* installing the package to re-build vignettes
* installing *source* package 'oligo' ...
** libs
  making DLL ...
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function 'read_one_xys':
ParserXYS.c:105: warning: unused variable 'token'
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c baseProfile.c -o baseProfile.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c basecontent.c -o basecontent.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma2.c -o rma2.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma_common.c -o rma_common.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c trimmed.c -o trimmed.o
gcc -shared -s -static-libgcc -o oligo.dll tmp.def ParserXYS.o baseProfile.o basecontent.o chipbackground.o rma2.o rma_common.o trimmed.o -lRzlib -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/tmpdir/Rinst662488882/oligo/libs
  ... done
** R
** inst
** preparing package for lazy loading
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)'.

================================================================================
Welcome to oligoClasses version 1.10.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
in method for 'backgroundCorrect' with signature '"ff_matrix"': no definition for class "ff_matrix"
in method for 'normalize' with signature '"ff_matrix"': no definition for class "ff_matrix"
in method for 'normalizeToTarget' with signature '"ff_matrix"': no definition for class "ff_matrix"
in method for 'summarize' with signature '"ff_matrix"': no definition for class "ff_matrix"
Creating a new generic function for "boxplot" in "oligo"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
================================================================================
Welcome to oligo version 1.12.2
================================================================================

* DONE (oligo)
* creating vignettes ... OK
* cleaning src
make: Nothing to be done for `clean'.
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'oligo_1.12.2.tar.gz'