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Package 370/514HostnameOS / ArchBUILDCHECKBUILD BIN
phenoTest 1.2.0
Evarist Planet
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/phenoTest
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: phenoTest
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phenoTest_1.2.0.tar.gz
StartedAt: 2012-03-24 03:12:50 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 03:19:22 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 391.8 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 2.14.2 (2012-02-29)
* 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 '1.2.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.gseaSignatures':
  'plot.gseaSignaturesSign' 'plot.gseaSignaturesVar'

S3 methods shown with full name in documentation object 'summary.gseaSignificance':
  'summary.gseaSignificanceSign' 'summary.gseaSignificanceVar'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
             old_size new_size compress
  eset.RData    664Kb    382Kb       xz
* 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 compiled code ... 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 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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-2.9-bioc/meat/phenoTest.Rcheck/phenoTest/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
** 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
ClusterPhenoTest0.1470.0100.190
ExpressionPhenoTest8.1610.0768.474
epheno-class0.0020.0000.002
epheno0.0110.0020.030
epheno2html000
eset0.0570.0030.068
findCopyNumber000
genesInArea0.5890.0600.918
getEsPositions0.3100.0180.343
getVars2test0.0150.0010.017
gseaSignatures-class0.0010.0000.002
gseaSignatures0.0160.0020.017
gseaSignaturesSign-class0.0010.0010.001
gseaSignaturesVar-class0.0010.0000.001
gseaSignificance0.0000.0000.001
gseaSignificanceSign-class0.0000.0000.001
gseaSignificanceVar-class0.0000.0000.001
heatmapPhenoTest0.3770.0160.482
pAdjust0.0200.0030.025
plot.gseaSignatures0.0000.0000.001
plots4epheno0.0580.0030.061
smoothCoxph0.1080.0070.131
summary.gseaSignificance000