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Package 162/609HostnameOS / ArchBUILDCHECKBUILD BIN
DESeq 1.10.1
Simon Anders
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/DESeq
Last Changed Rev: 70293 / Revision: 74773
Last Changed Date: 2012-10-08 13:51:48 -0700 (Mon, 08 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: DESeq
Version: 1.10.1
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings DESeq_1.10.1.tar.gz
StartedAt: 2013-03-25 00:40:26 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 00:44:22 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 236.5 seconds
RetCode: 0
Status:  OK 
CheckDir: DESeq.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/DESeq.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq/DESCRIPTION’ ... OK
* this is package ‘DESeq’ version ‘1.10.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... NOTE
plotMA: no visible binding for global variable ‘baseMean’
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
nbinomTestForMatrices 38.158  0.032  39.107
nbinomTest            20.781  0.024  20.986
* 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/DESeq.Rcheck/00check.log’
for details.

DESeq.Rcheck/00install.out:

* installing *source* package ‘DESeq’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c pval.c -o pval.o
pval.c: In function ‘add_from_both_sides’:
pval.c:26:11: warning: unused variable ‘esttotalperlength’ [-Wunused-variable]
gcc -std=gnu99 -shared -L/usr/local/lib64 -o DESeq.so pval.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/DESeq.Rcheck/DESeq/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘DESeq.Rnw’ 
** testing if installed package can be loaded

* DONE (DESeq)

DESeq.Rcheck/DESeq-Ex.timings:

nameusersystemelapsed
CountDataSet-class000
adjustScvForBias0.8120.0080.821
conditions1.8400.0001.859
counts1.9840.0082.066
dispTable3.7040.0003.702
estimateDispersions2.8170.0042.820
estimateSizeFactors1.9840.0001.987
estimateSizeFactorsForMatrix1.7200.0161.736
fitInfo2.8440.0002.847
fitNbinomGLMs000
fitNbinomGLMsForMatrix000
getBaseMeansAndVariances1.9960.0001.995
getVarianceStabilizedData3.8760.0003.879
makeExampleCountDataSet2.4600.0002.461
nbinomGLMTest2.7170.0042.719
nbinomTest20.781 0.02420.986
nbinomTestForMatrices38.158 0.03239.107
newCountDataSet2.0040.0002.091
plotDispEsts3.0130.0123.351
plotMA0.0000.0000.001
plotPCA3.9560.0163.986
sizeFactors1.9720.0081.986