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CHECK report for BadRegionFinder on tokay1

This page was generated on 2020-04-15 12:26:29 -0400 (Wed, 15 Apr 2020).

Package 105/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BadRegionFinder 1.14.0
Sarah Sandmann
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/BadRegionFinder
Branch: RELEASE_3_10
Last Commit: 49af136
Last Changed Date: 2019-10-29 13:09:37 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 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
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BadRegionFinder
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BadRegionFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BadRegionFinder_1.14.0.tar.gz
StartedAt: 2020-04-15 01:23:49 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:29:28 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 339.7 seconds
RetCode: 0
Status:  OK  
CheckDir: BadRegionFinder.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BadRegionFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BadRegionFinder_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/BadRegionFinder.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.14.0'
* 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 or elapsed time > 5s
             user system elapsed
plotDetailed 7.92   0.69   10.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotDetailed     7.10   0.14    9.72
plotSummaryGenes 3.42   0.11    5.28
* 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-3.10-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/3.10/bioc/src/contrib/BadRegionFinder_1.14.0.tar.gz && rm -rf BadRegionFinder.buildbin-libdir && mkdir BadRegionFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BadRegionFinder.buildbin-libdir BadRegionFinder_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL BadRegionFinder_1.14.0.zip && rm BadRegionFinder_1.14.0.tar.gz BadRegionFinder_1.14.0.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  14.1M      0 --:--:-- --:--:-- --:--:-- 15.7M

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_1.14.0.zip
* DONE (BadRegionFinder)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'BadRegionFinder' successfully unpacked and MD5 sums checked

Tests output


Example timings

BadRegionFinder.Rcheck/examples_i386/BadRegionFinder-Ex.timings

nameusersystemelapsed
BadRegionFinder-package0.280.000.28
determineCoverage000
determineCoverageQuality000
determineQuantiles0.130.020.14
determineRegionsOfInterest0.010.000.02
plotDetailed 7.92 0.6910.08
plotSummary0.160.000.15
plotSummaryGenes3.190.124.25
reportBadRegionsDetailed0.220.030.25
reportBadRegionsGenes0.240.000.23
reportBadRegionsSummary0.230.000.24

BadRegionFinder.Rcheck/examples_x64/BadRegionFinder-Ex.timings

nameusersystemelapsed
BadRegionFinder-package0.190.000.19
determineCoverage000
determineCoverageQuality000
determineQuantiles0.130.040.15
determineRegionsOfInterest0.010.000.02
plotDetailed7.100.149.72
plotSummary0.170.000.17
plotSummaryGenes3.420.115.28
reportBadRegionsDetailed0.110.060.17
reportBadRegionsGenes0.130.030.15
reportBadRegionsSummary0.140.020.16