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Package 405/462HostnameOS / ArchBUILDCHECKBUILD BIN
segmentSeq 1.5.0
Thomas J. Hardcastle
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/segmentSeq
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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 

Summary

Package: segmentSeq
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch segmentSeq_1.5.0.tar.gz
StartedAt: 2011-05-09 16:59:26 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 17:12:48 -0700 (Mon, 09 May 2011)
EllapsedTime: 802.0 seconds
RetCode: 0
Status:  OK 
CheckDir: segmentSeq.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/segmentSeq.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* 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 ‘1.5.0’
* 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 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 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 ... 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 sizes of PDF files under ‘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

segmentSeq.Rcheck/00install.out:

* installing *source* package ‘segmentSeq’ ...
** R
** 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
Creating a generic for ‘cbind’ in package ‘segmentSeq’
    (the supplied definition differs from and overrides the implicit generic
    in package ‘base’: Signatures differ:  (...), (deparse.level))
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘segmentSeq.Rnw’ 
** testing if installed package can be loaded

* DONE (segmentSeq)

segmentSeq.Rcheck/segmentSeq-Ex.timings:

nameusersystemelapsed
alignmentData-class4.8120.3165.223
classifySeg 97.943 3.135101.355
filterSegments51.935 2.12254.437
findChunks4.2560.4774.752
getCounts4.4560.4084.868
getOverlaps4.7290.4215.159
heuristicSeg64.798 2.53967.635
lociLikelihoods65.608 2.62969.820
mergeSD106.618 4.226114.181
plotGenome4.9790.3995.418
processAD53.048 1.99455.544
processTags4.6360.4685.170
segData-class53.542 2.09056.695
segmentSeq-package53.247 2.10955.804