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BioC 3.5: CHECK report for baySeq on veracruz2

This page was generated on 2017-08-16 13:28:40 -0400 (Wed, 16 Aug 2017).

Package 93/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
baySeq 2.10.0
Thomas J. Hardcastle
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/baySeq
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: baySeq
Version: 2.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings baySeq_2.10.0.tar.gz
StartedAt: 2017-08-16 00:04:45 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:08:52 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 246.6 seconds
RetCode: 0
Status:  OK 
CheckDir: baySeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings baySeq_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/baySeq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.10.0’
* 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 ‘build’ 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 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
baySeq-package 53.909  0.170  55.639
getPriors      41.628  0.076  45.689
getLikelihoods 16.194  0.059  16.739
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

baySeq.Rcheck/00install.out:

* installing *source* package ‘baySeq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (baySeq)

baySeq.Rcheck/baySeq-Ex.timings:

nameusersystemelapsed
allModels0.4200.0060.443
baySeq-classes0.1550.0030.159
baySeq-package53.909 0.17055.639
bimodalSep0.0010.0000.002
densityFunction0.0010.0010.002
getLibsizes0.0060.0010.007
getLikelihoods16.194 0.05916.739
getPosteriors0.0100.0020.012
getPriors41.628 0.07645.689
getTPs0.0350.0040.038
makeOrderings0.0650.0030.102
marginaliseEqual0.5500.0040.574
marginalisePairwise0.4990.0020.525
plotMA.CD0.0130.0010.015
plotPosteriors0.0250.0010.027
plotPriors0.0130.0020.015
selectTop0.1040.0030.107
summarisePosteriors0.0190.0020.020
topCounts0.0970.0020.099