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This page was generated on 2022-08-15 13:22:39 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4365
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4118
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4183
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 CNVfilteR on merida1


To the developers/maintainers of the CNVfilteR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNVfilteR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 364/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVfilteR 1.10.0  (landing page)
Jose Marcos Moreno-Cabrera
Snapshot Date: 2022-08-14 13:55:13 -0400 (Sun, 14 Aug 2022)
git_url: https://git.bioconductor.org/packages/CNVfilteR
git_branch: RELEASE_3_15
git_last_commit: 67b24ff
git_last_commit_date: 2022-04-26 12:00:01 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CNVfilteR
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNVfilteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNVfilteR_1.10.0.tar.gz
StartedAt: 2022-08-15 00:33:19 -0400 (Mon, 15 Aug 2022)
EndedAt: 2022-08-15 00:42:40 -0400 (Mon, 15 Aug 2022)
EllapsedTime: 561.3 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVfilteR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNVfilteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNVfilteR_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/CNVfilteR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVfilteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVfilteR’ version ‘1.10.0’
* 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 ‘CNVfilteR’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
filterCNVs         10.312  0.942  12.059
plotVariantsForCNV  7.910  0.060   8.515
plotScoringModel    6.512  0.122   7.735
* 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: OK


Installation output

CNVfilteR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CNVfilteR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘CNVfilteR’ ...
** 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 (CNVfilteR)

Tests output


Example timings

CNVfilteR.Rcheck/CNVfilteR-Ex.timings

nameusersystemelapsed
filterCNVs10.312 0.94212.059
loadCNVcalls0.5600.0230.679
loadSNPsFromVCF0.8330.0110.957
loadVCFs3.5390.0564.214
plotAllCNVs1.0250.0271.232
plotScoringModel6.5120.1227.735
plotVariantsForCNV7.9100.0608.515