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BioC 3.5: CHECK report for baySeq on tokay2

This page was generated on 2017-10-18 14:20:31 -0400 (Wed, 18 Oct 2017).

Package 93/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
baySeq 2.10.0
Thomas J. Hardcastle
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/baySeq
Branch: RELEASE_3_5
Last Commit: 23f68a1
Last Changed Date: 2017-04-24 15:45:44 -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: rm -rf baySeq.buildbin-libdir baySeq.Rcheck && mkdir baySeq.buildbin-libdir baySeq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=baySeq.buildbin-libdir baySeq_2.10.0.tar.gz >baySeq.Rcheck\00install.out 2>&1 && cp baySeq.Rcheck\00install.out baySeq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=baySeq.buildbin-libdir --install="check:baySeq-install.out" --force-multiarch --no-vignettes --timings baySeq_2.10.0.tar.gz
StartedAt: 2017-10-17 22:12:03 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:17:32 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 329.1 seconds
RetCode: 0
Status:  OK  
CheckDir: baySeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf baySeq.buildbin-libdir baySeq.Rcheck && mkdir baySeq.buildbin-libdir baySeq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=baySeq.buildbin-libdir baySeq_2.10.0.tar.gz >baySeq.Rcheck\00install.out 2>&1 && cp baySeq.Rcheck\00install.out baySeq-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=baySeq.buildbin-libdir --install="check:baySeq-install.out" --force-multiarch --no-vignettes --timings baySeq_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/baySeq.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
baySeq-package 41.86   0.09   41.95
getPriors      27.86   0.01   27.87
getLikelihoods 13.97   0.02   13.98
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
baySeq-package 56.31   0.00   56.33
getPriors      34.44   0.00   34.45
getLikelihoods 17.20   0.05   17.25
* 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:


install for i386

* 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

install for x64

* installing *source* package 'baySeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'baySeq' as baySeq_2.10.0.zip
* DONE (baySeq)

baySeq.Rcheck/examples_i386/baySeq-Ex.timings:

nameusersystemelapsed
allModels0.350.020.36
baySeq-classes0.110.020.12
baySeq-package41.86 0.0941.95
bimodalSep000
densityFunction000
getLibsizes0.020.000.02
getLikelihoods13.97 0.0213.98
getPosteriors0.010.000.02
getPriors27.86 0.0127.87
getTPs0.050.000.05
makeOrderings0.080.000.08
marginaliseEqual0.770.020.78
marginalisePairwise0.550.000.54
plotMA.CD0.010.010.04
plotPosteriors0.050.020.06
plotPriors0.020.010.03
selectTop0.140.000.14
summarisePosteriors0.010.000.02
topCounts0.080.020.09

baySeq.Rcheck/examples_x64/baySeq-Ex.timings:

nameusersystemelapsed
allModels0.580.000.58
baySeq-classes0.170.000.17
baySeq-package56.31 0.0056.33
bimodalSep000
densityFunction0.020.000.02
getLibsizes000
getLikelihoods17.20 0.0517.25
getPosteriors0.030.000.03
getPriors34.44 0.0034.45
getTPs0.030.000.03
makeOrderings0.050.000.05
marginaliseEqual0.420.000.42
marginalisePairwise0.370.000.38
plotMA.CD0.010.000.02
plotPosteriors0.020.000.01
plotPriors0.000.010.02
selectTop0.110.000.11
summarisePosteriors0.020.000.01
topCounts0.060.020.08