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Package 109/419HostnameOS / ArchBUILDCHECKBUILD BIN
DESeq 1.2.1
Simon Anders
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/DESeq
Last Changed Rev: 50639 / Revision: 54281
Last Changed Date: 2010-11-02 14:41:53 -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 

Summary

Package: DESeq
Version: 1.2.1
Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DESeq_1.2.1.tar.gz
StartedAt: 2011-03-31 05:27:10 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 05:31:00 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 230.2 seconds
RetCode: 0
Status:  OK 
CheckDir: DESeq.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/DESeq.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* 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 ‘1.2.1’
* 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) and $(LAPACK_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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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-2.7-bioc/meat/DESeq.Rcheck/DESeq/libs/i386
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. 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-class0.0000.0000.001
adjustScvForBias0.8590.0151.013
conditions4.1080.0474.472
counts3.9970.0434.336
estimateSizeFactors4.0160.0524.679
estimateSizeFactorsForMatrix4.0030.0424.779
estimateVarianceFunctionForMatrix4.5410.0825.374
estimateVarianceFunctions5.0540.0995.887
getBaseMeansAndVariances4.0310.0614.145
getRawScvDistanceMatrix9.0550.3989.553
getRawScvForSamplePair4.4080.0784.538
getVarianceStabilizedData5.3900.1235.605
makeExampleCountDataSet3.9400.0464.137
nbinomFitGLM0.0010.0000.000
nbinomGLMTest5.6900.0476.136
nbinomGLMsForMatrix000
nbinomTest20.284 0.18220.743
nbinomTestForMatrices20.200 0.15720.719
newCountDataSet3.9890.0484.289
rawVarFunc000
rawVarFuncTable4.8990.0855.047
residualsEcdfPlot4.9280.1265.115
residualsEcdfPlotFromDiagnostics5.0200.1365.298
scvPlot5.0810.1215.408
sizeFactors4.0000.0524.374
varianceFitDiagnostics4.9910.1175.319
varianceFitDiagnosticsForMatrix4.8960.1085.217