Package: sigPathway

Version: 1.4.0

Command: /loc/biocbuild/bbs-2.0-bioc/R/bin/R CMD check sigPathway_1.4.0.tar.gz

RetCode: 0

Time: 131.8 seconds

Status: OK

CheckDir: sigPathway.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.0-bioc/meat/sigPathway.Rcheck'
* using R version 2.5.1 (2007-06-27)
* checking for file 'sigPathway/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigPathway' version '1.4.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'sigPathway' 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 ... NOTE
  Note: found 1 marked Latin-1 string(s)
Portable packages use only ASCII characters in their datasets.
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating sigPathway-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating sigPathway-manual.tex ... OK
* checking sigPathway-manual.tex ... OK

* Installing *source* package 'sigPathway' ...
** 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 calc_gene_set_internal.c -o calc_gene_set_internal.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 calc_gene_set_stat.c -o calc_gene_set_stat.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 calc_probe_stat.c -o calc_probe_stat.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 calc_weights.c -o calc_weights.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 matrix_fn.c -o matrix_fn.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 permute.c -o permute.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 shuffle.c -o shuffle.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 sigPathway.c -o sigPathway.o
gcc -std=gnu99 -shared -L/usr/local/lib -o sigPathway.so calc_gene_set_internal.o calc_gene_set_stat.o calc_probe_stat.o calc_weights.o matrix_fn.o permute.o shuffle.o sigPathway.o -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lRlapack -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lRblas -lg2c -lm -lgcc_s  -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'sigPathway'
     Formats: text html latex example 
  MuscleExample                     text    html    latex
  calcTNullFast                     text    html    latex
  calcTStatFast                     text    html    latex   example
  calculate.GSEA                    text    html    latex
  calculate.NGSk                    text    html    latex   example
  calculatePathwayStatistics        text    html    latex   example
  estimateNumPerm                   text    html    latex   example
  getPathwayStatistics.NGSk         text    html    latex
  getPathwayStatistics              text    html    latex
  rankPathways.NGSk                 text    html    latex
  rankPathways                      text    html    latex
  runSigPathway                     text    html    latex   example
  selectGeneSets                    text    html    latex
  writeSigPathway                   text    html    latex
** building package indices ...
* DONE (sigPathway)