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Package 79/436HostnameOS / ArchBUILDCHECKBUILD BIN
chipseq 1.1.2
Biocore Team c/o BioC user list
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chipseq
Last Changed Rev: 51113 / Revision: 53255
Last Changed Date: 2010-11-29 13:21:02 -0800 (Mon, 29 Nov 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: chipseq
Version: 1.1.2
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings chipseq_1.1.2.tar.gz
StartedAt: 2011-02-24 18:46:15 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 18:49:06 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 170.7 seconds
RetCode: 0
Status:  OK 
CheckDir: chipseq.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/chipseq.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.1.2’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘chipseq’ can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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’
diffPeakSummaryRef: no visible global function definition for
  ‘laneCoverage’
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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

chipseq.Rcheck/00install.out:

* installing *source* package ‘chipseq’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/chipseq.Rcheck/chipseq/libs
** R
** data
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (chipseq)

chipseq.Rcheck/chipseq-Ex.timings:

nameusersystemelapsed
chipseqFilter0.8160.0200.881
combineLanes16.297 0.14016.460
copyIRangesbyChr0.0160.0000.016
coverageplot0.1240.0000.121
cstest0.2880.0000.290
diffPeakSummary8.1560.0448.203
estimate.mean.fraglen1.9490.0041.955
extendReads1.4240.0041.426
islandDepthPlot4.1120.0084.120
peakCutoff3.5600.0003.562
readReads000
subsetSummary2.6280.0042.641