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CHECK report for baySeq on tokay1

This page was generated on 2020-08-10 12:12:25 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE baySeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 120/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
baySeq 2.23.0
Thomas J. Hardcastle
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/baySeq
Branch: master
Last Commit: 2ea28df
Last Changed Date: 2020-04-27 14:20:16 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: baySeq
Version: 2.23.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:baySeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings baySeq_2.23.0.tar.gz
StartedAt: 2020-08-10 00:10:26 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 00:16:17 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 350.4 seconds
RetCode: 0
Status:  OK  
CheckDir: baySeq.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:baySeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings baySeq_2.23.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/baySeq.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '2.23.0'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
baySeq-package 44.71   0.20   44.90
getPriors      31.77   0.05   31.83
getLikelihoods 15.23   0.10   15.32
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
baySeq-package 52.28   0.03   52.31
getPriors      35.23   0.00   35.23
getLikelihoods 15.58   0.03   15.61
* 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


Installation output

baySeq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/baySeq_2.23.0.tar.gz && rm -rf baySeq.buildbin-libdir && mkdir baySeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=baySeq.buildbin-libdir baySeq_2.23.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL baySeq_2.23.0.zip && rm baySeq_2.23.0.tar.gz baySeq_2.23.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  278k  100  278k    0     0  6633k      0 --:--:-- --:--:-- --:--:-- 7336k

install for i386

* installing *source* package 'baySeq' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'baySeq'
    finding HTML links ... done
    CDPost                                  html  
    CDPriors                                html  
    allModels                               html  
    baySeq-classes                          html  
    baySeq-package                          html  
    bimodalSep                              html  
    densityFunction                         html  
    densityFunctions                        html  
    getLibsizes                             html  
    getLikelihoods                          html  
    getPosteriors                           html  
    getPriors                               html  
    getTPs                                  html  
    makeOrderings                           html  
    marginaliseEqual                        html  
    marginalisePairwise                     html  
    methObservables                         html  
    mobAnnotation                           html  
    mobData                                 html  
    pairData                                html  
    plotMA.CD                               html  
    plotNullPrior                           html  
    plotPosteriors                          html  
    plotPriors                              html  
    selectTop                               html  
    simData                                 html  
    summarisePosteriors                     html  
    topCounts                               html  
    zimData                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'baySeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'baySeq' as baySeq_2.23.0.zip
* DONE (baySeq)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'baySeq' successfully unpacked and MD5 sums checked

Tests output


Example timings

baySeq.Rcheck/examples_i386/baySeq-Ex.timings

nameusersystemelapsed
allModels0.350.000.34
baySeq-classes0.110.000.11
baySeq-package44.71 0.2044.90
bimodalSep000
densityFunction0.010.000.02
getLibsizes0.020.000.02
getLikelihoods15.23 0.1015.32
getPosteriors0.000.010.02
getPriors31.77 0.0531.83
getTPs0.010.000.01
makeOrderings0.030.010.05
marginaliseEqual0.320.020.33
marginalisePairwise0.320.000.33
plotMA.CD0.040.000.03
plotPosteriors0.060.020.08
plotPriors0.050.000.04
selectTop0.000.010.02
summarisePosteriors0.010.000.01
topCounts0.030.000.03

baySeq.Rcheck/examples_x64/baySeq-Ex.timings

nameusersystemelapsed
allModels0.420.000.42
baySeq-classes0.120.000.12
baySeq-package52.28 0.0352.31
bimodalSep000
densityFunction000
getLibsizes000
getLikelihoods15.58 0.0315.61
getPosteriors0.020.000.02
getPriors35.23 0.0035.23
getTPs0.020.000.02
makeOrderings0.030.020.04
marginaliseEqual0.420.010.44
marginalisePairwise0.420.000.42
plotMA.CD0.030.000.03
plotPosteriors0.060.000.07
plotPriors0.040.000.03
selectTop0.000.030.03
summarisePosteriors000
topCounts0.030.000.03