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BioC 3.6: CHECK report for baySeq on tokay1

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

Package 92/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
baySeq 2.11.0
Thomas J. Hardcastle
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/baySeq
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: baySeq
Version: 2.11.0
Command: rm -rf baySeq.buildbin-libdir baySeq.Rcheck && mkdir baySeq.buildbin-libdir baySeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=baySeq.buildbin-libdir baySeq_2.11.0.tar.gz >baySeq.Rcheck\00install.out 2>&1 && cp baySeq.Rcheck\00install.out baySeq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=baySeq.buildbin-libdir --install="check:baySeq-install.out" --force-multiarch --no-vignettes --timings baySeq_2.11.0.tar.gz
StartedAt: 2017-08-15 21:52:48 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:58:00 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 312.0 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-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=baySeq.buildbin-libdir baySeq_2.11.0.tar.gz >baySeq.Rcheck\00install.out 2>&1 && cp baySeq.Rcheck\00install.out baySeq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=baySeq.buildbin-libdir --install="check:baySeq-install.out" --force-multiarch --no-vignettes --timings baySeq_2.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/baySeq.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '2.11.0'
* 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 41.57   0.16   41.74
getPriors      24.33   0.00   24.33
getLikelihoods 16.27   0.00   16.27
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
baySeq-package 48.53   0.00   48.53
getPriors      39.30   0.01   39.31
getLikelihoods 16.81   0.02   16.83
* 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_2.11.0.zip
* DONE (baySeq)

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

nameusersystemelapsed
allModels0.330.010.35
baySeq-classes0.120.000.12
baySeq-package41.57 0.1641.74
bimodalSep000
densityFunction000
getLibsizes0.010.000.01
getLikelihoods16.27 0.0016.27
getPosteriors000
getPriors24.33 0.0024.33
getTPs0.030.000.03
makeOrderings0.030.020.04
marginaliseEqual0.340.000.35
marginalisePairwise0.310.010.33
plotMA.CD0.000.020.01
plotPosteriors0.020.010.03
plotPriors0.020.020.03
selectTop0.090.000.10
summarisePosteriors0.020.000.02
topCounts0.060.000.06

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

nameusersystemelapsed
allModels0.450.000.46
baySeq-classes0.140.040.17
baySeq-package48.53 0.0048.53
bimodalSep000
densityFunction000
getLibsizes0.000.010.02
getLikelihoods16.81 0.0216.83
getPosteriors000
getPriors39.30 0.0139.31
getTPs0.010.000.02
makeOrderings0.050.000.05
marginaliseEqual0.400.020.42
marginalisePairwise0.380.000.38
plotMA.CD0.010.000.01
plotPosteriors0.020.010.03
plotPriors0.000.020.02
selectTop0.090.020.11
summarisePosteriors0.020.000.01
topCounts0.060.010.08