Package: gcrma

Version: 2.20.0

Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings gcrma_2.20.0.tar.gz

StartedAt: 2010-10-04 18:11:32 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 18:14:56 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 204.5 seconds

RetCode: 0

Status:  OK

CheckDir: gcrma.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/gcrma.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gcrma/DESCRIPTION' ... OK
* this is package 'gcrma' version '2.20.0'
* checking package name space information ... OK
* 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 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
compute.affinities: no visible binding for global variable
  'affinity.spline.coefs'
compute.affinities.nomm: no visible binding for global variable
  'affinity.spline.coefs'
compute.affinities2: no visible binding for global variable
  'affinity.spline.coefs'
just.gcrma: possible error in gsub("^/?([^/]*/)*", "",
  unlist(filenames), extended = TRUE): unused argument(s) (extended =
  TRUE)
* checking Rd files ... NOTE
prepare_Rd: gcrma.engine.Rd:59-61: Dropping empty section \examples
prepare_Rd: gcrma.engine2.Rd:62-63: Dropping empty section \examples
prepare_Rd: justGCRMA.Rd:109-111: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... 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

* install options are ' --no-html'

* installing *source* package 'gcrma' ...
** libs
  making DLL ...
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"         -O3 -Wall  -std=gnu99 -c baseProfile.c -o baseProfile.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"         -O3 -Wall  -std=gnu99 -c computeAffinities.c -o computeAffinities.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"         -O3 -Wall  -std=gnu99 -c postmean.c -o postmean.o
gcc -shared -s -static-libgcc -o gcrma.dll tmp.def baseProfile.o computeAffinities.o postmean.o -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/meat/gcrma.Rcheck/gcrma/libs
  ... done
** R
** data
** 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 package indices ...
** testing if installed package can be loaded

* DONE (gcrma)

name	user	system	elapsed
bg.adjust.gcrma	56.52	0.43	57.67
gcrma	49.98	0.50	50.72