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Package 133/514HostnameOS / ArchBUILDCHECKBUILD BIN
DESeq 1.6.1
Simon Anders
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/DESeq
Last Changed Rev: 60544 / Revision: 64395
Last Changed Date: 2011-11-20 01:34:36 -0800 (Sun, 20 Nov 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: DESeq
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DESeq_1.6.1.tar.gz
StartedAt: 2012-03-24 00:37:29 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 00:42:04 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 275.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DESeq.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/DESeq.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 'DESeq/DESCRIPTION' ... OK
* this is package 'DESeq' version '1.6.1'
* 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 'DESeq' 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 ... 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 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

DESeq.Rcheck/00install.out:

* installing *source* package 'DESeq' ...
** 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 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-2.9-bioc/meat/DESeq.Rcheck/DESeq/libs/i386
** R
** inst
** preparing package for lazy loading
locfit 1.5-6 	 2010-01-20 
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'DESeq.Rnw' 
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 

* DONE (DESeq)

DESeq.Rcheck/DESeq-Ex.timings:

nameusersystemelapsed
CountDataSet-class000
adjustScvForBias0.7710.0190.796
conditions3.0520.0373.115
counts3.0800.0283.125
dispTable4.0410.2864.362
estimateDispersions3.9060.3104.243
estimateSizeFactors2.9560.0393.011
estimateSizeFactorsForMatrix2.8190.0382.876
fitInfo3.9090.2764.254
fitNbinomGLMs000
fitNbinomGLMsForMatrix0.0000.0000.001
getBaseMeansAndVariances2.9460.0573.066
getVarianceStabilizedData4.5170.4985.247
makeExampleCountDataSet2.7470.0262.868
nbinomGLMTest3.3520.0323.442
nbinomTest31.090 1.35333.531
nbinomTestForMatrices58.235 2.54361.367
newCountDataSet3.0090.0473.158
sizeFactors2.8700.0633.006