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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: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings DESeq_1.3.1.tar.gz
StartedAt: 2011-02-24 17:46:44 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 17:49:30 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 165.8 seconds
RetCode: 0
Status:  OK  
CheckDir: DESeq.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/DESeq.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 '1.3.1'
* 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 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
gcc -I"E:/biocbld/BBS-2˜1.8-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˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/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-class000
adjustScvForBias0.550.020.57
conditions2.680.002.70
counts2.690.002.69
estimateSizeFactors2.730.012.78
estimateSizeFactorsForMatrix2.550.002.55
estimateVarianceFunctionForMatrix3.270.003.26
estimateVarianceFunctions3.580.003.58
getBaseMeansAndVariances2.600.002.62
getRawScvDistanceMatrix7.880.038.13
getRawScvForSamplePair3.080.023.16
getVarianceStabilizedData4.190.004.18
makeExampleCountDataSet2.590.002.60
nbinomFitGLM000
nbinomGLMTest3.760.003.78
nbinomGLMsForMatrix000
nbinomTest20.97 0.0021.12
nbinomTestForMatrices21.19 0.0021.28
newCountDataSet2.740.002.74
rawVarFunc000
rawVarFuncTable3.600.003.61
residualsEcdfPlot3.750.003.78
residualsEcdfPlotFromDiagnostics3.550.013.58
scvPlot3.610.003.61
sizeFactors2.750.002.79
varianceFitDiagnostics3.610.003.64
varianceFitDiagnosticsForMatrix3.700.003.71