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Package 53/631HostnameOS / ArchBUILDCHECKBUILD BIN
baySeq 1.13.0
Thomas J. Hardcastle
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/baySeq
Last Changed Rev: 70052 / Revision: 72575
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
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: baySeq
Version: 1.13.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings baySeq_1.13.0.tar.gz
StartedAt: 2013-01-16 00:48:53 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 00:53:40 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 287.2 seconds
RetCode: 0
Status:  OK 
CheckDir: baySeq.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/baySeq.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘baySeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘baySeq’ version ‘1.13.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘baySeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
getPosteriors: no visible binding for global variable ‘clustAssign’
getPosteriors: no visible binding for global variable ‘getPostsEnv’
getPriors.NB: no visible global function definition for
  ‘newSeqCountSet’
getPriors.NB: no visible global function definition for ‘estDispersion’
getTPs: no visible binding for global variable ‘logsum’
topCounts: no visible global function definition for ‘seqnames’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
baySeq-package 129.264  0.024 129.351
getPriors      110.255  0.008 110.313
getLikelihoods  18.585  0.004  18.595
* 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/baySeq.Rcheck/00check.log’
for details.

baySeq.Rcheck/00install.out:

* installing *source* package ‘baySeq’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘rbind’ in package ‘baySeq’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘baySeq.Rnw’ 
** testing if installed package can be loaded

* DONE (baySeq)

baySeq.Rcheck/baySeq-Ex.timings:

nameusersystemelapsed
baySeq-classes0.1360.0000.136
baySeq-package129.264 0.024129.351
bimodalSep0.0080.0000.009
getLibsizes0.0240.0000.025
getLikelihoods18.585 0.00418.595
getPosteriors0.0280.0000.027
getPriors110.255 0.008110.313
getTPs0.0160.0000.019
plotMA.CD0.0360.0000.038
plotPosteriors0.0240.0000.022
plotPriors0.0200.0000.021
topCounts0.0320.0000.031