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Package 91/514HostnameOS / ArchBUILDCHECKBUILD BIN
chipseq 1.4.0
Bioconductor Package Maintainer
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/chipseq
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: chipseq
Version: 1.4.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings chipseq_1.4.0.tar.gz
StartedAt: 2012-03-23 23:42:27 -0700 (Fri, 23 Mar 2012)
EndedAt: 2012-03-23 23:46:46 -0700 (Fri, 23 Mar 2012)
EllapsedTime: 259.6 seconds
RetCode: 0
Status:  OK 
CheckDir: chipseq.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/chipseq.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chipseq/DESCRIPTION’ ... OK
* this is package ‘chipseq’ version ‘1.4.0’
* 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 ‘chipseq’ 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 ... NOTE
correlation.estimate: no visible binding for global variable ‘mu’
correlation.estimate: no visible binding for global variable ‘corr’
coverage.estimate: no visible binding for global variable ‘mu’
coverage.estimate: no visible binding for global variable ‘covered’
islandDepthPlot: no visible binding for global variable ‘depth’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 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

chipseq.Rcheck/00install.out:

* installing *source* package ‘chipseq’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c rlesumprod.c -o rlesumprod.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o chipseq.so rlesumprod.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/chipseq.Rcheck/chipseq/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘Workflow.Rnw’ 
** testing if installed package can be loaded

* DONE (chipseq)

chipseq.Rcheck/chipseq-Ex.timings:

nameusersystemelapsed
chipseqFilter0.4280.0120.461
coverageplot0.1160.0000.120
cstest2.6880.0282.771
diffPeakSummary20.782 0.23221.084
estimate.mean.fraglen2.0200.0362.060
islandDepthPlot5.0200.0165.060
laneSubsample7.5010.0647.627
peakCutoff3.7640.0283.841
subsetSummary3.2800.0203.426