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Package 110/436HostnameOS / ArchBUILDCHECKBUILD BIN
DESeq 1.3.1
Simon Anders
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DESeq
Last Changed Rev: 50638 / Revision: 53255
Last Changed Date: 2010-11-02 14:40:45 -0700 (Tue, 02 Nov 2010)
lamb2 Linux (openSUSE 11.2) / 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 (10.6.4) / i386  OK  OK  OK 

Summary

Package: DESeq
Version: 1.3.1
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DESeq_1.3.1.tar.gz
StartedAt: 2011-02-24 18:59:18 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 19:02:45 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 207.1 seconds
RetCode: 0
Status:  OK 
CheckDir: DESeq.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/DESeq.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq/DESCRIPTION’ ... OK
* this is package ‘DESeq’ version ‘1.3.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘DESeq’ can be installed ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

DESeq.Rcheck/00install.out:

* installing *source* package ‘DESeq’ ...
** 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 pval.c -o pval.o
pval.c: In function ‘add_from_both_sides’:
pval.c:26: warning: unused variable ‘esttotalperlength’
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o DESeq.so pval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/DESeq.Rcheck/DESeq/libs/i386
** R
** 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: akima
Loading required package: lattice
locfit 1.5-6 	 2010-01-20 
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (DESeq)

DESeq.Rcheck/DESeq-Ex.timings:

nameusersystemelapsed
CountDataSet-class0.0000.0010.000
adjustScvForBias0.8530.0130.885
conditions4.2030.0434.259
counts4.0440.0304.086
estimateSizeFactors4.0330.0374.087
estimateSizeFactorsForMatrix4.0990.0444.173
estimateVarianceFunctionForMatrix4.6860.0634.787
estimateVarianceFunctions5.0480.0815.153
getBaseMeansAndVariances4.1880.0594.273
getRawScvDistanceMatrix9.3780.3979.827
getRawScvForSamplePair4.4490.0754.610
getVarianceStabilizedData5.3930.1295.596
makeExampleCountDataSet3.9420.0284.000
nbinomFitGLM000
nbinomGLMTest5.7330.0405.831
nbinomGLMsForMatrix000
nbinomTest20.523 0.17420.779
nbinomTestForMatrices20.998 0.15721.332
newCountDataSet4.1010.0374.162
rawVarFunc000
rawVarFuncTable4.8310.0844.954
residualsEcdfPlot5.0510.1105.208
residualsEcdfPlotFromDiagnostics5.1820.1255.351
scvPlot5.0060.1005.125
sizeFactors3.9290.0363.987
varianceFitDiagnostics4.9840.1035.125
varianceFitDiagnosticsForMatrix4.8900.1035.040