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Package 207/319HostnameOS / ArchBUILDCHECKBUILD BIN
oligo 1.8.3
Benilton Carvalho
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/oligo
Last Changed Rev: 41241 / Revision: 42512
Last Changed Date: 2009-08-19 19:22:00 -0700 (Wed, 19 Aug 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: oligo
Version: 1.8.3
Command: /home/biocbuild/bbs-2.4-bioc/R/bin/R CMD check --no-vignettes oligo_1.8.3.tar.gz
StartedAt: 2009-10-20 17:13:09 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 17:15:17 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 127.6 seconds
RetCode: 0
Status: OK
CheckDir: oligo.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.4-bioc/meat/oligo.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.8.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'oligo' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

oligo.Rcheck/00install.out:

* Installing *source* package 'oligo' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c baseProfile.c -o baseProfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c basecontent.c -o basecontent.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o oligo.so baseProfile.o basecontent.o rma2.o rma_background2.o rma_common.o trimmed.o -L/home/biocbuild/bbs-2.4-bioc/R/lib -lR
** 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)'.

** help
*** installing help indices
 >>> Building/Updating help pages for package 'oligo'
     Formats: text html latex example 
  IntensityMatrix-methods           text    html    latex   example
  MAplot-methods                    text    html    latex
  basecontent                       text    html    latex   example
  basicRMA                          text    html    latex   example
  boxplot                           text    html    latex
  coordinates                       text    html    latex   example
  crlmm                             text    html    latex
  getContainer                      text    html    latex
  getCrlmmSummaries                 text    html    latex
  getNgsColorsInfo                  text    html    latex
  hist                              text    html    latex
  image                             text    html    latex
  justSNPRMA                        text    html    latex   example
  list.celfiles                     text    html    latex   example
  oligo-package                     text    html    latex
  plotM-methods                     text    html    latex
  read.celfiles                     text    html    latex   example
  read.xysfiles                     text    html    latex   example
  readSummaries                     text    html    latex
  rma                               text    html    latex   example
  sequenceDesignMatrix              text    html    latex   example
  snprma                            text    html    latex
** building package indices ...
* DONE (oligo)