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Package 53/609HostnameOS / ArchBUILDCHECKBUILD BIN
baySeq 1.12.0
Thomas J. Hardcastle
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/baySeq
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: baySeq
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch baySeq_1.12.0.tar.gz
StartedAt: 2013-03-24 22:38:36 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 22:43:21 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 285.6 seconds
RetCode: 0
Status:  OK 
CheckDir: baySeq.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/baySeq.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'baySeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'baySeq' version '1.12.0'
* 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 'baySeq' 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
baySeq-package 116.865  2.381 121.373
getPriors      102.362  0.306 116.024
getLikelihoods  13.324  1.959  16.196
* 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
  '/Users/biocbuild/bbs-2.11-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-classes0.0810.0110.097
baySeq-package116.865 2.381121.373
bimodalSep0.0000.0000.001
getLibsizes0.0090.0020.015
getLikelihoods13.324 1.95916.196
getPosteriors0.0470.0110.074
getPriors102.362 0.306116.024
getTPs0.0060.0040.010
plotMA.CD0.0190.0040.023
plotPosteriors0.0090.0040.014
plotPriors0.0120.0040.018
topCounts0.0220.0040.029