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Package 124/462HostnameOS / ArchBUILDCHECKBUILD BIN
DESeq 1.5.1
Simon Anders
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DESeq
Last Changed Rev: 54998 / Revision: 55359
Last Changed Date: 2011-04-20 13:19:15 -0700 (Wed, 20 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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: 1.5.1
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings DESeq_1.5.1.tar.gz
StartedAt: 2011-05-09 13:16:52 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 13:19:43 -0700 (Mon, 09 May 2011)
EllapsedTime: 170.5 seconds
RetCode: 0
Status:  OK  
CheckDir: DESeq.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/DESeq.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DESeq/DESCRIPTION' ... OK
* this is package 'DESeq' version '1.5.1'
* 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 installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
* checking package directory ... OK
* checking for portable file names ... 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 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
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c pval.c -o pval.o
pval.c: In function 'add_from_both_sides':
pval.c:26:11: warning: unused variable 'esttotalperlength'
gcc -shared -s -static-libgcc -o DESeq.dll tmp.def pval.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-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 ...
*** 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
adjustScvForBias0.610.000.63
conditions2.650.002.68
counts2.570.002.57
estimateSizeFactors2.70.02.7
estimateSizeFactorsForMatrix2.580.012.59
estimateVarianceFunctionForMatrix3.290.003.32
estimateVarianceFunctions3.580.003.64
getBaseMeansAndVariances2.670.002.67
getRawScvDistanceMatrix7.910.008.03
getRawScvForSamplePair3.140.003.16
getVarianceStabilizedData4.140.024.15
makeExampleCountDataSet2.540.002.57
nbinomFitGLM000
nbinomGLMTest3.680.003.70
nbinomGLMsForMatrix000
nbinomTest20.98 0.0021.01
nbinomTestForMatrices21.06 0.0321.21
newCountDataSet2.640.002.64
rawVarFunc000
rawVarFuncTable3.720.003.74
residualsEcdfPlot3.650.003.67
residualsEcdfPlotFromDiagnostics3.630.003.64
scvPlot3.700.013.75
sizeFactors2.560.002.59
varianceFitDiagnostics3.660.003.69
varianceFitDiagnosticsForMatrix3.720.003.72