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Package 317/444HostnameOS / ArchBUILDCHECKBUILD BIN
phenoTest 0.99.3
Evarist Planet
Snapshot Date: 2011-03-16 11:16:24 -0700 (Wed, 16 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/phenoTest
Last Changed Rev: 53247 / Revision: 53799
Last Changed Date: 2011-02-24 01:24:54 -0800 (Thu, 24 Feb 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 (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ OK ] OK 

Summary

Package: phenoTest
Version: 0.99.3
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phenoTest_0.99.3.tar.gz
StartedAt: 2011-03-16 16:58:11 -0700 (Wed, 16 Mar 2011)
EndedAt: 2011-03-16 17:00:30 -0700 (Wed, 16 Mar 2011)
EllapsedTime: 139.5 seconds
RetCode: 0
Status:  OK 
CheckDir: phenoTest.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/phenoTest.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'phenoTest/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phenoTest' version '0.99.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* 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 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 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 ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

phenoTest.Rcheck/00install.out:

* installing *source* package 'phenoTest' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c getEs.c -o getEs.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o phenoTest.so getEs.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/phenoTest.Rcheck/phenoTest/libs/i386
** 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 ...
** testing if installed package can be loaded

* DONE (phenoTest)

phenoTest.Rcheck/phenoTest-Ex.timings:

nameusersystemelapsed
ClusterPhenoTest0.0980.0030.101
ExpressionPhenoTest5.7650.0165.781
epheno-class0.0010.0000.002
epheno0.0070.0000.008
epheno2html0.0000.0010.001
eset0.0360.0010.037
getVars2test0.0100.0010.011
gseaSignatures-class0.0010.0000.001
gseaSignatures0.0110.0010.012
gseaSignaturesSign-class0.0010.0010.001
gseaSignaturesVar-class0.0000.0000.001
gseaSignificance000
gseaSignificanceSign-class0.0010.0000.001
gseaSignificanceVar-class0.0010.0000.001
heatmapPhenoTest0.3150.0040.320
pAdjust0.0160.0000.016
plot.gseaSignatures000
plots4epheno0.0530.0010.054
smoothCoxph0.0640.0020.085
summary.gseaSignificance000