Package: sigPathway

Version: 1.4.0

Command: D:\biocbld\bbs-2.0-bioc\R\bin\R.exe CMD check sigPathway_1.4.0.tar.gz

RetCode: 0

Time: 83.1 seconds

Status: OK

CheckDir: sigPathway.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.0-bioc/meat/sigPathway.Rcheck'
* using R version 2.5.0 (2007-04-23)
* 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 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 R.css in D:/biocbld/bbs-2.0-bioc/meat/sigPathway.Rcheck


---------- Making package sigPathway ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making calc_gene_set_internal.d from calc_gene_set_internal.c
making calc_gene_set_stat.d from calc_gene_set_stat.c
making calc_probe_stat.d from calc_probe_stat.c
making calc_weights.d from calc_weights.c
making matrix_fn.d from matrix_fn.c
making permute.d from permute.c
making shuffle.d from shuffle.c
making sigPathway.d from sigPathway.c
gcc   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c calc_gene_set_internal.c -o calc_gene_set_internal.o
gcc   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c calc_gene_set_stat.c -o calc_gene_set_stat.o
gcc   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c calc_probe_stat.c -o calc_probe_stat.o
gcc   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c calc_weights.c -o calc_weights.o
gcc   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c matrix_fn.c -o matrix_fn.o
gcc   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c permute.c -o permute.o
gcc   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c shuffle.c -o shuffle.o
gcc   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c sigPathway.c -o sigPathway.o
windres -I d:/biocbld/bbs-2.0-bioc/R/include  -i sigPathway_res.rc -o sigPathway_res.o
gcc  -shared -s  -o sigPathway.dll sigPathway.def 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 sigPathway_res.o  -Ld:/biocbld/bbs-2.0-bioc/R/bin -Ld:/biocbld/bbs-2.0-bioc/R/bin -lRlapack -Ld:/biocbld/bbs-2.0-bioc/R/bin -lRblas -lg2c   -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'sigPathway'
     Formats: text html latex example chm 
  MuscleExample                     text    html    latex           chm
  calcTNullFast                     text    html    latex           chm
  calcTStatFast                     text    html    latex   example chm
  calculate.GSEA                    text    html    latex           chm
  calculate.NGSk                    text    html    latex   example chm
  calculatePathwayStatistics        text    html    latex   example chm
  estimateNumPerm                   text    html    latex   example chm
  getPathwayStatistics.NGSk         text    html    latex           chm
  getPathwayStatistics              text    html    latex           chm
  rankPathways.NGSk                 text    html    latex           chm
  rankPathways                      text    html    latex           chm
  runSigPathway                     text    html    latex   example chm
  selectGeneSets                    text    html    latex           chm
  writeSigPathway                   text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.0-bioc\meat\sigPathway.Rcheck\00_pkg_src\sigPathway\chm\sigPathway.chm


Compile time: 0 minutes, 0 seconds
15	Topics
33	Local links
10	Internet links
1	Graphic


Created d:\biocbld\bbs-2.0-bioc\meat\sigPathway.Rcheck\00_pkg_src\sigPathway\chm\sigPathway.chm, 37,517 bytes
Compression decreased file by 28,728 bytes.
  preparing package sigPathway for lazy loading
  adding MD5 sums

* DONE (sigPathway)