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Package 100/389HostnameOS / ArchBUILDCHECKBUILD BIN
DESeq 1.0.6
Simon Anders
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/DESeq
Last Changed Rev: 49240 / Revision: 49923
Last Changed Date: 2010-09-06 05:18:28 -0700 (Mon, 06 Sep 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: DESeq
Version: 1.0.6
Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings DESeq_1.0.6.tar.gz
StartedAt: 2010-10-04 17:48:14 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 17:51:18 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 184.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: DESeq.Rcheck
Warnings: 1

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/DESeq.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DESeq/DESCRIPTION' ... OK
* this is package 'DESeq' version '1.0.6'
* 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 ... WARNING
Invalid citation information in 'inst/CITATION':
  citEntry 1 (techreport): missing required field(s) 'institution'
* 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 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

WARNING: There was 1 warning, see
  E:/biocbld/bbs-2.6-bioc/meat/DESeq.Rcheck/00check.log
for details

DESeq.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'DESeq' ...
** libs
  making DLL ...
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"         -O3 -Wall  -std=gnu99 -c pval.c -o pval.o
gcc -shared -s -static-libgcc -o DESeq.dll tmp.def pval.o -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/meat/DESeq.Rcheck/DESeq/libs
  ... done
** 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-class000
adjustScvForBias0.610.000.62
conditions2.810.002.83
counts2.750.022.78
estimateSizeFactors2.830.012.87
estimateSizeFactorsForMatrix2.710.022.74
estimateVarianceFunctionForMatrix3.590.003.59
estimateVarianceFunctions4.110.004.19
getBaseMeansAndVariances2.830.002.89
getVarianceStabilizedData5.010.005.03
makeExampleCountDataSet2.710.002.72
nbinomTest25.84 0.0026.19
nbinomTestForMatrices25.41 0.0025.45
newCountDataSet2.790.002.80
rawVarFunc000
rawVarFuncTable3.910.003.92
residualsEcdfPlot3.970.003.97
residualsEcdfPlotFromDiagnostics3.920.003.92
scvPlot4.030.004.04
sizeFactors2.660.002.65
varianceFitDiagnostics3.900.003.92
varianceFitDiagnosticsForMatrix3.890.003.91