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BioC 2.13: CHECK report for DESeq2 on zin1

This page was generated on 2014-04-05 09:48:34 -0700 (Sat, 05 Apr 2014).

Package 200/750HostnameOS / ArchBUILDCHECKBUILD BIN
DESeq2 1.2.10
Michael Love
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/DESeq2
Last Changed Rev: 86057 / Revision: 88450
Last Changed Date: 2014-02-04 10:03:14 -0800 (Tue, 04 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: DESeq2
Version: 1.2.10
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.2.10.tar.gz
StartedAt: 2014-04-05 00:45:49 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:48:37 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 167.8 seconds
RetCode: 0
Status:  OK 
CheckDir: DESeq2.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/DESeq2.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.2.10’
* 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 ... [21s/22s] 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘DESeq2.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [30s/30s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [17s/17s]
 [17s/17s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/DESeq2.Rcheck/00check.log’
for details.

DESeq2.Rcheck/00install.out:

* installing *source* package ‘DESeq2’ ...
** libs
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.13-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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
DESeq3.2840.0083.318
DESeqDataSet0.0640.0000.067
counts0.0840.0000.084
design0.0920.0000.091
dispersionFunction0.8440.0000.848
dispersions0.8160.0000.836
estimateDispersions0.9560.0000.960
estimateDispersionsGeneEst0.8440.0080.852
estimateSizeFactors0.1400.0000.139
estimateSizeFactorsForMatrix0.1040.0000.105
makeExampleDESeqDataSet0.0960.0000.094
nbinomLRT1.3880.0081.400
nbinomWaldTest1.6840.0001.688
normalizationFactors1.7730.0001.792
plotDispEsts0.9440.0040.950
plotMA1.4800.0081.489
plotPCA1.4520.0001.454
replaceOutliersWithTrimmedMean0.5600.0000.558
results3.1280.0003.131
rlogTransformation2.4000.0002.404
sizeFactors0.1120.0000.112
varianceStabilizingTransformation1.2800.0001.282