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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: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch DESeq_1.4.1.tar.gz
StartedAt: 2011-10-20 14:02:57 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 14:05:22 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 145.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: DESeq.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/DESeq.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... 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 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 examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   DESeq.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/DESeq.Rcheck/00check.log'
for details

DESeq.Rcheck/00install.out:

* installing *source* package 'DESeq' ...
** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -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'
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o DESeq.dll tmp.def pval.o -LD:/biocbld/BBS-2˜1.8-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.8-bioc/meat/DESeq.Rcheck/DESeq/libs/x64
** 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
adjustScvForBias0.610.000.60
conditions3.040.023.07
counts3.170.003.17
estimateSizeFactors3.180.003.17
estimateSizeFactorsForMatrix2.760.002.77
estimateVarianceFunctionForMatrix3.420.003.42
estimateVarianceFunctions3.550.003.58
getBaseMeansAndVariances2.860.002.87
getRawScvDistanceMatrix6.600.006.65
getRawScvForSamplePair3.210.003.21
getVarianceStabilizedData3.920.003.95
makeExampleCountDataSet2.840.002.84
nbinomFitGLM0.020.000.02
nbinomGLMTest4.010.014.03
nbinomGLMsForMatrix000
nbinomTest12.84 0.0012.86
nbinomTestForMatrices12.79 0.0012.79
newCountDataSet2.780.002.78
rawVarFunc000
rawVarFuncTable3.470.003.49
residualsEcdfPlot3.580.003.58
residualsEcdfPlotFromDiagnostics3.510.003.51
scvPlot3.400.003.39
sizeFactors2.760.002.77
varianceFitDiagnostics3.470.003.47
varianceFitDiagnosticsForMatrix3.520.003.51