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Package 173/658HostnameOS / ArchBUILDCHECKBUILD BIN
DESeq 1.11.6
Simon Anders
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DESeq
Last Changed Rev: 73717 / Revision: 74774
Last Changed Date: 2013-02-24 15:13:24 -0800 (Sun, 24 Feb 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: DESeq
Version: 1.11.6
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings DESeq_1.11.6.tar.gz
StartedAt: 2013-03-25 01:10:32 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:16:23 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 350.5 seconds
RetCode: 0
Status:  OK 
CheckDir: DESeq.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/DESeq.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.11.6’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DESeq’ can be installed ... [21s/23s] OK
* checking installed package size ... OK
* checking package directory ... 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’ ... NOTE
The following files should probably not be installed:
  ‘whbiocvignette.sty’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... [150s/159s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
nbinomTestForMatrices     49.843  0.024  52.676
nbinomTest                26.530  0.040  27.099
getVarianceStabilizedData  6.781  0.004   6.855
plotPCA                    6.669  0.004   7.430
dispTable                  6.420  0.044   6.954
fitInfo                    5.072  0.064   5.522
estimateDispersions        4.804  0.072   5.399
plotDispEsts               4.760  0.008   5.554
* 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 were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/DESeq.Rcheck/00check.log’
for details.

DESeq.Rcheck/00install.out:

* installing *source* package ‘DESeq’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-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/lib -o DESeq.so pval.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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-class0.0120.0000.013
adjustScvForBias0.7320.0000.745
conditions3.6200.0083.627
counts3.5450.0163.813
dispTable6.4200.0446.954
estimateDispersions4.8040.0725.399
estimateSizeFactors3.2240.0163.260
estimateSizeFactorsForMatrix2.8050.0523.199
fitInfo5.0720.0645.522
fitNbinomGLMs0.0120.0000.014
fitNbinomGLMsForMatrix0.0120.0000.014
getBaseMeansAndVariances2.8080.0483.186
getVarianceStabilizedData6.7810.0046.855
makeExampleCountDataSet2.6360.0002.637
nbinomGLMTest3.5880.0123.615
nbinomTest26.530 0.04027.099
nbinomTestForMatrices49.843 0.02452.676
newCountDataSet2.7160.0002.902
plotDispEsts4.7600.0085.554
plotMA0.0160.0000.013
plotPCA6.6690.0047.430
sizeFactors2.9080.0003.203