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This page was generated on 2021-10-23 14:06:55 -0400 (Sat, 23 Oct 2021).

CHECK results for CNVRanger on merida1

To the developers/maintainers of the CNVRanger package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNVRanger.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 361/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVRanger 1.9.0  (landing page)
Ludwig Geistlinger
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/CNVRanger
git_branch: master
git_last_commit: ef39e51
git_last_commit_date: 2021-05-19 12:40:54 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  NO, package depends on 'GDSArray' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CNVRanger
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNVRanger.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNVRanger_1.9.0.tar.gz
StartedAt: 2021-10-23 02:12:20 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 02:17:25 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 304.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVRanger.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNVRanger.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNVRanger_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CNVRanger.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVRanger/DESCRIPTION’ ... OK
* this is package ‘CNVRanger’ version ‘1.9.0’
* package encoding: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CNVRanger’ 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
* 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 ... NOTE
Unexported object imported by a ':::' call: 'rappdirs:::get_os'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotRecurrentRegions: no visible binding for global variable ‘type’
plotRecurrentRegions: no visible binding for global variable ‘pvalue’
Undefined global functions or variables:
  pvalue type
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
plotRecurrentRegions 30.143  0.148  32.485
plotEQTL             22.771  0.635  27.740
plotManhattan        13.112  0.333  13.465
cnvGWAS              10.337  0.077  10.433
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/CNVRanger.Rcheck/00check.log’
for details.



Installation output

CNVRanger.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CNVRanger
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CNVRanger’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (CNVRanger)

Tests output


Example timings

CNVRanger.Rcheck/CNVRanger-Ex.timings

nameusersystemelapsed
cnvEQTL3.8190.1443.967
cnvGWAS10.337 0.07710.433
cnvOncoPrint2.3300.0372.370
generateGDS1.0640.0131.079
importLrrBaf0.0240.0040.028
plotEQTL22.771 0.63527.740
plotManhattan13.112 0.33313.465
plotRecurrentRegions30.143 0.14832.485
populationRanges2.6670.0072.678
setupCnvGWAS0.0120.0020.015