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Package 339/469HostnameOS / ArchBUILDCHECKBUILD BIN
phenoTest 1.1.0
Evarist Planet
Snapshot Date: 2011-06-15 19:55:29 -0700 (Wed, 15 Jun 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/phenoTest
Last Changed Rev: 54802 / Revision: 56217
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: phenoTest
Version: 1.1.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phenoTest_1.1.0.tar.gz
StartedAt: 2011-06-16 04:31:08 -0700 (Thu, 16 Jun 2011)
EndedAt: 2011-06-16 04:34:25 -0700 (Thu, 16 Jun 2011)
EllapsedTime: 196.9 seconds
RetCode: 0
Status:  OK 
CheckDir: phenoTest.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/phenoTest.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* 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 ... 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 sizes of PDF files under ‘inst/doc’ ... 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

phenoTest.Rcheck/00install.out:

* installing *source* package ‘phenoTest’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c getEs.c -o getEs.o
gcc-4.2 -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-2.9-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 ...
*** tangling vignette sources ...
   ‘phenoTest.Rnw’ 
** testing if installed package can be loaded

* DONE (phenoTest)

phenoTest.Rcheck/phenoTest-Ex.timings:

nameusersystemelapsed
ClusterPhenoTest0.1490.0070.156
ExpressionPhenoTest 9.938 0.06410.258
epheno-class0.0020.0010.003
epheno0.0110.0010.014
epheno2html0.0000.0000.001
eset0.0580.0040.072
getVars2test0.0170.0020.024
gseaSignatures-class0.0010.0000.002
gseaSignatures0.0220.0020.028
gseaSignaturesSign-class0.0020.0000.004
gseaSignaturesVar-class0.0020.0000.002
gseaSignificance0.0000.0000.001
gseaSignificanceSign-class0.0020.0000.002
gseaSignificanceVar-class0.0020.0000.001
heatmapPhenoTest0.4140.0130.452
pAdjust0.0220.0020.024
plot.gseaSignatures0.0010.0000.001
plots4epheno0.0670.0020.077
smoothCoxph0.1050.0050.112
summary.gseaSignificance000