sigPathway 1.6.0
Weil Lai
| Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/sigPathway | | Last Changed Rev: 27709 / Revision: 30966 | | Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/sigPathway.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'sigPathway/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigPathway' version '1.6.0'
* checking package name space information ... OK
* 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 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 ... 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-2.1-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-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c calc_gene_set_internal.c -o calc_gene_set_internal.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c calc_gene_set_stat.c -o calc_gene_set_stat.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c calc_probe_stat.c -o calc_probe_stat.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c calc_weights.c -o calc_weights.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c matrix_fn.c -o matrix_fn.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c permute.c -o permute.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c shuffle.c -o shuffle.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c sigPathway.c -o sigPathway.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.1-bioc/R/include -i sigPathway_res.rc -o sigPathway_res.o
gcc-sjlj -std=gnu99 -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-2.1-bioc/R/bin -Ld:/biocbld/bbs-2.1-bioc/R/bin -lRlapack -Ld:/biocbld/bbs-2.1-bioc/R/bin -lRblas -lgfortran -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
importGeneSets 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
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "its\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\bbs-2.1-bioc\meat\sigPathway.Rcheck\00_pkg_src\sigPathway\chm\sigPathway.chm
HHC4016: Warning: Cannot open "its\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
The following files were not compiled:
preparing package sigPathway for lazy loading
adding MD5 sums
* DONE (sigPathway)