Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:05:54 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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 107/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BadRegionFinder 1.22.0  (landing page)
Sarah Sandmann
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/BadRegionFinder
git_branch: RELEASE_3_14
git_last_commit: e9d52d0
git_last_commit_date: 2021-10-26 12:26:51 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.22.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BadRegionFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BadRegionFinder_1.22.0.tar.gz
StartedAt: 2022-01-23 15:32:38 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 15:40:00 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 441.8 seconds
RetCode: 0
Status:   OK  
CheckDir: BadRegionFinder.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BadRegionFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BadRegionFinder_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BadRegionFinder.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.22.0'
* 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     12.14   0.75   46.93
plotSummaryGenes  5.90   0.06   27.83
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plotDetailed     10.10   0.20   11.42
plotSummaryGenes  5.18   0.05    6.36
* 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-3.14-bioc/meat/BadRegionFinder.Rcheck/00check.log'
for details.



Installation output

BadRegionFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BadRegionFinder_1.22.0.tar.gz && rm -rf BadRegionFinder.buildbin-libdir && mkdir BadRegionFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BadRegionFinder.buildbin-libdir BadRegionFinder_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BadRegionFinder_1.22.0.zip && rm BadRegionFinder_1.22.0.tar.gz BadRegionFinder_1.22.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 27  566k   27  157k    0     0   704k      0 --:--:-- --:--:-- --:--:--  705k
100  566k  100  566k    0     0  1677k      0 --:--:-- --:--:-- --:--:-- 1676k

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_1.22.0.zip
* DONE (BadRegionFinder)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'BadRegionFinder' successfully unpacked and MD5 sums checked

Tests output


Example timings

BadRegionFinder.Rcheck/examples_i386/BadRegionFinder-Ex.timings

nameusersystemelapsed
BadRegionFinder-package0.080.090.17
determineCoverage0.020.000.02
determineCoverageQuality0.000.020.01
determineQuantiles0.140.030.17
determineRegionsOfInterest000
plotDetailed12.14 0.7546.93
plotSummary0.110.010.12
plotSummaryGenes 5.90 0.0627.83
reportBadRegionsDetailed0.250.000.25
reportBadRegionsGenes0.170.040.21
reportBadRegionsSummary0.150.010.17

BadRegionFinder.Rcheck/examples_x64/BadRegionFinder-Ex.timings

nameusersystemelapsed
BadRegionFinder-package0.240.030.27
determineCoverage0.000.020.02
determineCoverageQuality000
determineQuantiles0.200.030.24
determineRegionsOfInterest000
plotDetailed10.10 0.2011.42
plotSummary0.130.020.14
plotSummaryGenes5.180.056.36
reportBadRegionsDetailed0.110.030.14
reportBadRegionsGenes0.120.010.14
reportBadRegionsSummary0.110.030.14