Package: phenoTest

Version: 1.1.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --force-multiarch --no-vignettes --timings phenoTest_1.1.0.tar.gz

StartedAt: 2011-06-16 01:32:34 -0700 (Thu, 16 Jun 2011)

EndedAt: 2011-06-16 01:35:38 -0700 (Thu, 16 Jun 2011)

EllapsedTime: 183.7 seconds

RetCode: 0

Status:  OK

CheckDir: phenoTest.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/phenoTest.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-05-30 r56020)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phenoTest/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phenoTest' version '1.1.0'
* 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 'phenoTest' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 ... OK
* 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 'phenoTest' ...
** libs

*** arch - i386
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c getEs.c -o getEs.o
gcc -shared -s -static-libgcc -o phenoTest.dll tmp.def getEs.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/phenoTest.Rcheck/phenoTest/libs/i386

*** arch - x64
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -c getEs.c -o getEs.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o phenoTest.dll tmp.def getEs.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/phenoTest.Rcheck/phenoTest/libs/x64
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

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

Loading required package: AnnotationDbi
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'phenoTest.Rnw' 
** testing if installed package can be loaded

* DONE (phenoTest)

name	user	system	elapsed
ClusterPhenoTest	0.1	0.0	0.1
ExpressionPhenoTest	6.38	0.00	6.38
epheno-class	0.01	0.00	0.01
epheno	0	0	0
epheno2html	0	0	0
eset	0.04	0.00	0.04
getVars2test	0.01	0.00	0.01
gseaSignatures-class	0	0	0
gseaSignatures	0	0	0
gseaSignaturesSign-class	0	0	0
gseaSignaturesVar-class	0.02	0.00	0.02
gseaSignificance	0	0	0
gseaSignificanceSign-class	0	0	0
gseaSignificanceVar-class	0	0	0
heatmapPhenoTest	0.26	0.00	0.26
pAdjust	0.02	0.00	0.02
plot.gseaSignatures	0	0	0
plots4epheno	0.04	0.00	0.04
smoothCoxph	0.07	0.00	0.07
summary.gseaSignificance	0	0	0