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BioC 2.14: CHECK report for DESeq2 on zin2

This page was generated on 2014-10-08 08:49:52 -0700 (Wed, 08 Oct 2014).

Package 222/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DESeq2 1.4.5
Michael Love
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/DESeq2
Last Changed Rev: 90186 / Revision: 95116
Last Changed Date: 2014-05-10 20:36:13 -0700 (Sat, 10 May 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: DESeq2
Version: 1.4.5
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.4.5.tar.gz
StartedAt: 2014-10-07 23:07:43 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:10:59 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 195.7 seconds
RetCode: 0
Status:  OK 
CheckDir: DESeq2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.4.5.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/DESeq2.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DESeq2’ version ‘1.4.5’
* 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 ‘DESeq2’ can be installed ... [23s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/31s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [29s/29s]
 [29s/29s] OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

DESeq2.Rcheck/00install.out:

* installing *source* package ‘DESeq2’ ...
** libs
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c DESeq2.cpp -o DESeq2.o
DESeq2.cpp: In function ‘SEXPREC* fitDisp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
DESeq2.cpp:210:26: warning: ‘change’ may be used uninitialized in this function [-Wuninitialized]
g++ -shared -L/usr/local/lib -o DESeq2.so DESeq2.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.14-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/DESeq2.Rcheck/DESeq2/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DESeq2)

DESeq2.Rcheck/DESeq2-Ex.timings:

nameusersystemelapsed
DESeq1.7160.0081.785
DESeqDataSet0.0760.0000.074
coef1.4480.0041.454
collapseReplicates0.1480.0000.146
counts0.0840.0000.087
design0.0920.0000.094
dispersionFunction1.1560.0121.173
dispersions0.9440.0080.952
estimateDispersions0.9440.0000.946
estimateDispersionsGeneEst1.1520.0001.150
estimateSizeFactors0.1360.0040.139
estimateSizeFactorsForMatrix0.1040.0000.103
fpkm0.3520.0000.353
fpm0.1920.0000.190
makeExampleDESeqDataSet0.1000.0000.099
nbinomLRT1.6560.0001.658
nbinomWaldTest1.6130.0081.621
normalizationFactors1.5200.0001.522
plotDispEsts1.2440.0001.245
plotMA1.8400.0001.843
plotPCA0.7080.0000.710
replaceOutliers0.7040.0000.701
results3.9720.0123.990
rlog1.8320.0001.833
sizeFactors0.1080.0000.107
varianceStabilizingTransformation1.3840.0081.397