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BioC 3.0: CHECK report for DESeq2 on perceval

This page was generated on 2015-04-10 09:57:50 -0700 (Fri, 10 Apr 2015).

Package 238/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DESeq2 1.6.3
Michael Love
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/DESeq2
Last Changed Rev: 97702 / Revision: 102249
Last Changed Date: 2014-12-16 12:26:29 -0800 (Tue, 16 Dec 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: DESeq2
Version: 1.6.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DESeq2_1.6.3.tar.gz
StartedAt: 2015-04-10 00:44:40 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:51:20 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 399.6 seconds
RetCode: 0
Status:  OK 
CheckDir: DESeq2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DESeq2_1.6.3.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/DESeq2.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.6.3’
* 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 ... [41s/45s] 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 ... [47s/47s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
results 5.298  0.033   5.341
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [71s/71s]
 [71s/72s] 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

DESeq2.Rcheck/00install.out:

* installing *source* package ‘DESeq2’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c DESeq2.cpp -o DESeq2.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c RcppExports.cpp -o RcppExports.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-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
DESeq2.6450.0282.673
DESeqDataSet0.0720.0000.073
coef1.7390.0111.761
collapseReplicates0.1900.0040.194
counts0.1140.0010.116
design0.1200.0020.121
dispersionFunction1.0280.0151.052
dispersions1.0270.0041.037
estimateDispersions1.3690.0031.372
estimateDispersionsGeneEst1.0060.0101.017
estimateSizeFactors0.2430.0030.247
estimateSizeFactorsForMatrix0.1270.0010.128
fpkm0.3390.0030.343
fpm0.2280.0030.231
makeExampleDESeqDataSet0.1000.0020.102
nbinomLRT1.6090.0091.621
nbinomWaldTest2.4040.0112.420
normalizationFactors1.7480.0051.758
plotCounts0.2290.0050.254
plotDispEsts1.0510.0041.070
plotMA2.5640.0072.596
plotPCA1.5750.0061.588
replaceOutliers1.3720.0031.376
results5.2980.0335.341
rlog2.5860.0202.612
sizeFactors0.1220.0010.124
summary1.5970.0071.612
varianceStabilizingTransformation1.3790.0051.391