BioC 3.5: CHECK report for baySeq on oaxaca
This page was generated on 2017-03-04 16:38:31 -0500 (Sat, 04 Mar 2017).
baySeq 2.9.1 Thomas J. Hardcastle
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/baySeq | Last Changed Rev: 125692 / Revision: 127142 | Last Changed Date: 2017-01-05 07:31:15 -0500 (Thu, 05 Jan 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
Summary
Package: baySeq |
Version: 2.9.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings baySeq_2.9.1.tar.gz |
StartedAt: 2017-03-03 23:26:58 -0800 (Fri, 03 Mar 2017) |
EndedAt: 2017-03-03 23:31:14 -0800 (Fri, 03 Mar 2017) |
EllapsedTime: 255.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: baySeq.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings baySeq_2.9.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/baySeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.9.1’
* 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 70.483 0.262 70.837
getPriors 52.940 0.081 53.058
getLikelihoods 17.474 0.057 17.541
* 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:
name | user | system | elapsed
|
allModels | 0.642 | 0.007 | 0.650 |
|
baySeq-classes | 0.223 | 0.003 | 0.227 |
|
baySeq-package | 70.483 | 0.262 | 70.837 |
|
bimodalSep | 0.001 | 0.000 | 0.001 |
|
densityFunction | 0.002 | 0.000 | 0.002 |
|
getLibsizes | 0.009 | 0.002 | 0.009 |
|
getLikelihoods | 17.474 | 0.057 | 17.541 |
|
getPosteriors | 0.009 | 0.001 | 0.009 |
|
getPriors | 52.940 | 0.081 | 53.058 |
|
getTPs | 0.039 | 0.004 | 0.043 |
|
makeOrderings | 0.071 | 0.003 | 0.073 |
|
marginaliseEqual | 0.605 | 0.002 | 0.608 |
|
marginalisePairwise | 0.551 | 0.002 | 0.555 |
|
plotMA.CD | 0.015 | 0.001 | 0.017 |
|
plotPosteriors | 0.035 | 0.002 | 0.037 |
|
plotPriors | 0.018 | 0.002 | 0.019 |
|
selectTop | 0.157 | 0.003 | 0.160 |
|
summarisePosteriors | 0.025 | 0.002 | 0.027 |
|
topCounts | 0.120 | 0.003 | 0.123 |
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