Package: GSVA

Version: 1.1.1

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings GSVA_1.1.1.tar.gz

StartedAt: 2011-05-09 14:05:46 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:07:00 -0700 (Mon, 09 May 2011)

EllapsedTime: 74.7 seconds

RetCode: 0

Status:  OK

CheckDir: GSVA.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/GSVA.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GSVA/DESCRIPTION' ... OK
* this is package 'GSVA' version '1.1.1'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: multicore
* checking if this is a source package ... OK
* checking whether package 'GSVA' can be installed ... OK
* checking installed package size ... 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.geneset.es: no visible binding for global variable
  'rank_scores'
* checking Rd files ... OK
* 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 for unstated dependencies in examples ... 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) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'GSVA' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"       -I/src/include -IC:/gsl/include   -O3 -Wall  -std=gnu99 -c assess_density_test.c -o assess_density_test.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"       -I/src/include -IC:/gsl/include   -O3 -Wall  -std=gnu99 -c ks_test.c -o ks_test.o
ks_test.c: In function 'ks_sample':
ks_test.c:22:9: warning: unused variable 'mx_value'
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"       -I/src/include -IC:/gsl/include   -O3 -Wall  -std=gnu99 -c register_cmethods.c -o register_cmethods.o
gcc -shared -s -static-libgcc -o GSVA.dll tmp.def assess_density_test.o ks_test.o register_cmethods.o -LC:/gsl/bin -lgsl -lgslcblas -lm -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/GSVA.Rcheck/GSVA/libs/i386
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'GSVA.Rnw' 
** testing if installed package can be loaded

* DONE (GSVA)

name	user	system	elapsed
computeGeneSetsOverlap	0.02	0.00	0.02
filterGeneSets	0	0	0
gsva	0.79	0.03	1.03