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This page was generated on 2021-09-22 15:05:08 -0400 (Wed, 22 Sep 2021).

CHECK results for BadRegionFinder on tokay2

To the developers/maintainers of the BadRegionFinder package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BadRegionFinder.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 110/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BadRegionFinder 1.20.0  (landing page)
Sarah Sandmann
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/BadRegionFinder
git_branch: RELEASE_3_13
git_last_commit: 833821c
git_last_commit_date: 2021-05-19 12:19:30 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BadRegionFinder
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BadRegionFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BadRegionFinder_1.20.0.tar.gz
StartedAt: 2021-09-21 19:23:58 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 19:30:57 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 418.9 seconds
RetCode: 0
Status:   OK  
CheckDir: BadRegionFinder.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BadRegionFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BadRegionFinder_1.20.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BadRegionFinder.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.20.0'
* 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     11.80   0.92   14.11
plotSummaryGenes  6.61   0.07    7.70
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plotDetailed     11.47   0.26   12.86
plotSummaryGenes  6.14   0.08    7.39
* 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-3.13-bioc/meat/BadRegionFinder.Rcheck/00check.log'
for details.



Installation output

BadRegionFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BadRegionFinder_1.20.0.tar.gz && rm -rf BadRegionFinder.buildbin-libdir && mkdir BadRegionFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BadRegionFinder.buildbin-libdir BadRegionFinder_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BadRegionFinder_1.20.0.zip && rm BadRegionFinder_1.20.0.tar.gz BadRegionFinder_1.20.0.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  566k  100  566k    0     0  1256k      0 --:--:-- --:--:-- --:--:-- 1259k

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_1.20.0.zip
* DONE (BadRegionFinder)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BadRegionFinder' successfully unpacked and MD5 sums checked

Tests output


Example timings

BadRegionFinder.Rcheck/examples_i386/BadRegionFinder-Ex.timings

nameusersystemelapsed
BadRegionFinder-package0.310.010.33
determineCoverage0.020.000.02
determineCoverageQuality0.020.000.02
determineQuantiles0.250.040.28
determineRegionsOfInterest0.010.000.02
plotDetailed11.80 0.9214.11
plotSummary0.160.010.17
plotSummaryGenes6.610.077.70
reportBadRegionsDetailed0.230.010.25
reportBadRegionsGenes0.260.030.29
reportBadRegionsSummary0.200.050.25

BadRegionFinder.Rcheck/examples_x64/BadRegionFinder-Ex.timings

nameusersystemelapsed
BadRegionFinder-package0.180.050.23
determineCoverage0.020.000.02
determineCoverageQuality0.000.010.01
determineQuantiles0.160.020.17
determineRegionsOfInterest000
plotDetailed11.47 0.2612.86
plotSummary0.180.020.21
plotSummaryGenes6.140.087.39
reportBadRegionsDetailed0.210.010.22
reportBadRegionsGenes0.180.020.21
reportBadRegionsSummary0.180.010.18