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Package 123/467HostnameOS / ArchBUILDCHECKBUILD BIN
DESeq 1.4.1
Simon Anders
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/DESeq
Last Changed Rev: 54999 / Revision: 59457
Last Changed Date: 2011-04-20 13:23:23 -0700 (Wed, 20 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: DESeq
Version: 1.4.1
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DESeq_1.4.1.tar.gz
StartedAt: 2011-10-20 14:32:20 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 14:35:58 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 218.3 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 2.13.2 (2011-09-30)
* 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 '1.4.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'DESeq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
* 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 sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'DESeq.pdf' from 4847Kb to 940Kb
  consider running tools::compactPDF() on these files
* 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-4.2 -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-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 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
locfit 1.5-6 	 2010-01-20 
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 

* DONE (DESeq)

DESeq.Rcheck/DESeq-Ex.timings:

nameusersystemelapsed
CountDataSet-class000
adjustScvForBias0.8490.0130.867
conditions4.1400.0374.218
counts4.1530.0394.232
estimateSizeFactors4.1040.0414.163
estimateSizeFactorsForMatrix3.9340.0454.036
estimateVarianceFunctionForMatrix4.4860.0644.587
estimateVarianceFunctions4.9280.0835.039
getBaseMeansAndVariances4.0010.0504.076
getRawScvDistanceMatrix8.9690.4019.433
getRawScvForSamplePair4.4800.0724.573
getVarianceStabilizedData5.5290.1275.755
makeExampleCountDataSet3.9270.0304.049
nbinomFitGLM000
nbinomGLMTest5.6120.0325.688
nbinomGLMsForMatrix000
nbinomTest20.402 0.18321.126
nbinomTestForMatrices21.065 0.14821.393
newCountDataSet3.9630.0374.081
rawVarFunc0.0010.0000.000
rawVarFuncTable4.9300.0865.126
residualsEcdfPlot4.9560.1185.147
residualsEcdfPlotFromDiagnostics5.0010.1275.319
scvPlot5.0380.1115.172
sizeFactors3.9520.0444.061
varianceFitDiagnostics4.9370.1085.164
varianceFitDiagnosticsForMatrix4.9380.1095.302