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Package 414/467HostnameOS / ArchBUILDCHECKBUILD BIN
sigPathway 1.20.0
Weil Lai
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/sigPathway
Last Changed Rev: 54808 / Revision: 59457
Last Changed Date: 2011-04-13 18:03:42 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: sigPathway
Version: 1.20.0
Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch sigPathway_1.20.0.tar.gz
StartedAt: 2011-10-20 16:59:20 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 17:00:04 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 44.3 seconds
RetCode: 0
Status:  OK  
CheckDir: sigPathway.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/sigPathway.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sigPathway/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigPathway' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'sigPathway' 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 1 marked Latin-1 string
* checking data for ASCII and uncompressed saves ... 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

sigPathway.Rcheck/00install.out:

* installing *source* package 'sigPathway' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c calc_gene_set_internal.c -o calc_gene_set_internal.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c calc_gene_set_stat.c -o calc_gene_set_stat.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c calc_probe_stat.c -o calc_probe_stat.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c calc_weights.c -o calc_weights.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c matrix_fn.c -o matrix_fn.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c permute.c -o permute.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c shuffle.c -o shuffle.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c sigPathway.c -o sigPathway.o
gcc -shared -s -static-libgcc -o sigPathway.dll tmp.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 -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lRlapack -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lRblas -lgfortran -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/sigPathway.Rcheck/sigPathway/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (sigPathway)

sigPathway.Rcheck/sigPathway-Ex.timings:

nameusersystemelapsed
calcTStatFast0.140.000.14
calculate.NGSk3.790.164.71
calculatePathwayStatistics5.290.085.74
estimateNumPerm000
runSigPathway5.090.095.18