Package: gcrma

Version: 2.8.0

Command: /loc/biocbuild/bbs-2.0-bioc/R/bin/R CMD check gcrma_2.8.0.tar.gz

RetCode: 0

Time: 689.9 seconds

Status: OK

CheckDir: gcrma.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/loc/biocbuild/bbs-2.0-bioc/meat/gcrma.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'gcrma/DESCRIPTION' ... OK
* this is package 'gcrma' version '2.8.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'gcrma' 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating gcrma-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating gcrma-manual.tex ... OK
* checking gcrma-manual.tex ... OK

* Installing *source* package 'gcrma' ...
** libs
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c baseProfile.c -o baseProfile.o
baseProfile.c: In function 'gcrma_getSeq2':
baseProfile.c:14: warning: unused variable 'nx'
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c computeAffinities.c -o computeAffinities.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c postmean.c -o postmean.o
gcc -std=gnu99 -G -L/usr/local/lib -o gcrma.so baseProfile.o computeAffinities.o postmean.o   -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lR
** R
** data
** 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: affy
Loading required package: affyio
Loading required package: matchprobes
Loading required package: splines
** help
 >>> Building/Updating help pages for package 'gcrma'
     Formats: text html latex example 
  affinity.spline.coefs             text    html    latex
  bg.adjust.affinities              text    html    latex
  bg.adjust.gcrma                   text    html    latex   example
  bg.parameters.ns                  text    html    latex
  compute.affinities                text    html    latex
  fast.bkg                          text    html    latex
  gcrma                             text    html    latex   example
  gcrma.engine                      text    html    latex   example
  gcrma.engine2                     text    html    latex   example
  getCDF                            text    html    latex
  justGCRMA                         text    html    latex   example
** building package indices ...
* DONE (gcrma)