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Package 147/553HostnameOS / ArchBUILDCHECKBUILD BIN
DESeq 1.8.3
Simon Anders
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/DESeq
Last Changed Rev: 66208 / Revision: 69725
Last Changed Date: 2012-05-26 02:24:37 -0700 (Sat, 26 May 2012)
lamb2 Linux (openSUSE 11.4) / 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: 1.8.3
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings DESeq_1.8.3.tar.gz
StartedAt: 2012-09-24 00:25:11 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:28:54 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 223.5 seconds
RetCode: 0
Status:  OK 
CheckDir: DESeq.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/DESeq.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.8.3’
* 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 whether package ‘DESeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

DESeq.Rcheck/00install.out:

* installing *source* package ‘DESeq’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-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’
gcc -std=gnu99 -shared -L/usr/local/lib64 -o DESeq.so pval.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-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-class0.0000.0000.001
adjustScvForBias0.9080.0080.913
conditions2.0160.0082.024
counts2.3760.0042.378
dispTable3.6960.0123.706
estimateDispersions3.4450.0163.541
estimateSizeFactors1.9000.0041.944
estimateSizeFactorsForMatrix2.0960.0002.096
fitInfo3.1640.0043.168
fitNbinomGLMs000
fitNbinomGLMsForMatrix000
getBaseMeansAndVariances2.2320.0002.232
getVarianceStabilizedData4.0200.0044.022
makeExampleCountDataSet1.8210.0001.820
nbinomGLMTest2.2480.0002.332
nbinomTest20.757 0.00821.088
nbinomTestForMatrices39.198 0.00041.934
newCountDataSet1.9930.0002.279
sizeFactors2.2080.0042.638