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Package 379/436HostnameOS / ArchBUILDCHECKBUILD BIN
segmentSeq 1.3.1
Thomas J. Hardcastle
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/segmentSeq
Last Changed Rev: 51302 / Revision: 53255
Last Changed Date: 2010-12-07 02:41:46 -0800 (Tue, 07 Dec 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: segmentSeq
Version: 1.3.1
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch segmentSeq_1.3.1.tar.gz
StartedAt: 2011-02-24 21:22:24 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 21:34:19 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 715.0 seconds
RetCode: 0
Status:  OK 
CheckDir: segmentSeq.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/segmentSeq.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘segmentSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘segmentSeq’ version ‘1.3.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘segmentSeq’ 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
getCounts : <anonymous>: no visible binding for global variable ‘tag’
lociLikelihoods: no visible binding for global variable ‘chr’
* 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 examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

segmentSeq.Rcheck/00install.out:

* installing *source* package ‘segmentSeq’ ...
** R
** data
** inst
** preparing package for lazy loading

Attaching package: 'baySeq'

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

    rbind

Loading required package: IRanges

Attaching package: 'IRanges'

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

    rbind

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: GenomicRanges
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 (segmentSeq)

segmentSeq.Rcheck/segmentSeq-Ex.timings:

nameusersystemelapsed
alignmentData-class6.4980.4556.985
classifySeg453.248 6.668462.879
clustSeg18.175 1.99420.404
filterSegments 9.870 1.88211.950
getCounts3.8410.5114.394
getOverlaps4.0130.5284.603
lociLikelihoods21.374 2.26423.895
plotGenome3.7760.4844.364
processAD8.0940.9999.164
processTags3.4450.4583.924
segData-class8.5971.0459.731
segmentSeq-package 9.147 1.15910.446