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CHECK report for BadRegionFinder on tokay1

This page was generated on 2020-09-21 11:14:09 -0400 (Mon, 21 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BadRegionFinder PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 104/1912HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BadRegionFinder 1.17.0
Sarah Sandmann
Snapshot Date: 2020-09-20 14:41:51 -0400 (Sun, 20 Sep 2020)
URL: https://git.bioconductor.org/packages/BadRegionFinder
Branch: master
Last Commit: 5297ff3
Last Changed Date: 2020-04-27 14:56:28 -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
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BadRegionFinder
Version: 1.17.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BadRegionFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BadRegionFinder_1.17.0.tar.gz
StartedAt: 2020-09-21 03:16:18 -0400 (Mon, 21 Sep 2020)
EndedAt: 2020-09-21 03:22:53 -0400 (Mon, 21 Sep 2020)
EllapsedTime: 395.0 seconds
RetCode: 0
Status:  OK  
CheckDir: BadRegionFinder.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:BadRegionFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BadRegionFinder_1.17.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BadRegionFinder.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 'BadRegionFinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BadRegionFinder' version '1.17.0'
* 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 'BadRegionFinder' 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 ... NOTE
determineCoverage: no visible global function definition for 'path'
Undefined global functions or variables:
  path
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plotDetailed     16.08   0.52   20.00
plotSummaryGenes  9.28   0.26   12.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plotDetailed     13.04   0.16   14.84
plotSummaryGenes  5.86   0.07    7.58
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BadRegionFinder.Rcheck/00check.log'
for details.



Installation output

BadRegionFinder.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/BadRegionFinder_1.17.0.tar.gz && rm -rf BadRegionFinder.buildbin-libdir && mkdir BadRegionFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BadRegionFinder.buildbin-libdir BadRegionFinder_1.17.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BadRegionFinder_1.17.0.zip && rm BadRegionFinder_1.17.0.tar.gz BadRegionFinder_1.17.0.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  565k  100  565k    0     0  11.8M      0 --:--:-- --:--:-- --:--:-- 12.8M

install for i386

* installing *source* package 'BadRegionFinder' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BadRegionFinder'
    finding HTML links ... done
    BadRegionFinder-package                 html  
    determineCoverage                       html  
    determineCoverageQuality                html  
    determineQuantiles                      html  
    determineRegionsOfInterest              html  
    plotDetailed                            html  
    plotSummary                             html  
    plotSummaryGenes                        html  
    reportBadRegionsDetailed                html  
    reportBadRegionsGenes                   html  
    reportBadRegionsSummary                 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 'BadRegionFinder' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BadRegionFinder' as BadRegionFinder_1.17.0.zip
* DONE (BadRegionFinder)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BadRegionFinder' successfully unpacked and MD5 sums checked

Tests output


Example timings

BadRegionFinder.Rcheck/examples_i386/BadRegionFinder-Ex.timings

nameusersystemelapsed
BadRegionFinder-package0.290.090.39
determineCoverage0.020.000.02
determineCoverageQuality000
determineQuantiles0.270.080.34
determineRegionsOfInterest000
plotDetailed16.08 0.5220.00
plotSummary0.260.050.31
plotSummaryGenes 9.28 0.2612.03
reportBadRegionsDetailed0.240.050.28
reportBadRegionsGenes0.250.010.27
reportBadRegionsSummary0.250.020.27

BadRegionFinder.Rcheck/examples_x64/BadRegionFinder-Ex.timings

nameusersystemelapsed
BadRegionFinder-package0.280.040.31
determineCoverage000
determineCoverageQuality0.000.010.01
determineQuantiles0.220.060.28
determineRegionsOfInterest0.020.000.02
plotDetailed13.04 0.1614.84
plotSummary0.190.020.20
plotSummaryGenes5.860.077.58
reportBadRegionsDetailed0.170.000.17
reportBadRegionsGenes0.140.050.19
reportBadRegionsSummary0.150.000.15