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BioC 3.1: CHECK report for DESeq2 on zin2

This page was generated on 2015-10-09 09:25:22 -0700 (Fri, 09 Oct 2015).

Package 256/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DESeq2 1.8.2
Michael Love
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/DESeq2
Last Changed Rev: 109165 / Revision: 109384
Last Changed Date: 2015-10-04 07:53:30 -0700 (Sun, 04 Oct 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DESeq2
Version: 1.8.2
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.8.2.tar.gz
StartedAt: 2015-10-09 00:28:28 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:33:14 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 285.8 seconds
RetCode: 0
Status:  OK 
CheckDir: DESeq2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/DESeq2.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.8.2’
* 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 ... [25s/39s] 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/45s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
results 4.826  0.019   6.997
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [43s/60s]
 [43s/60s] 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
* DONE

Status: OK

DESeq2.Rcheck/00install.out:

* installing *source* package ‘DESeq2’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c DESeq2.cpp -o DESeq2.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.1-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/DESeq2.Rcheck/DESeq2/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (DESeq2)

DESeq2.Rcheck/DESeq2-Ex.timings:

nameusersystemelapsed
DESeq1.3770.0102.414
DESeqDataSet0.0370.0000.065
coef1.9220.0093.366
collapseReplicates0.0970.0000.149
counts0.0720.0000.088
design0.0540.0000.066
dispersionFunction1.5390.0012.462
estimateDispersions0.7240.0001.316
estimateDispersionsGeneEst0.7800.0001.392
estimateSizeFactors0.1250.0000.242
estimateSizeFactorsForMatrix0.0680.0000.147
fpkm0.2130.0000.449
fpm0.1210.0000.241
makeExampleDESeqDataSet0.0620.0000.125
nbinomLRT1.1390.0011.826
nbinomWaldTest1.5270.0002.419
normalizationFactors1.4920.0082.228
plotCounts0.1280.0000.169
plotDispEsts0.7530.0000.968
plotMA1.5100.0012.209
plotPCA1.2830.0002.158
plotSparsity0.0710.0000.072
results4.8260.0196.997
rlog1.3580.0002.070
summary2.0100.0012.443
varianceStabilizingTransformation0.9050.0041.298