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CHECK report for CNVfilteR on malbec1

This page was generated on 2021-05-06 12:27:10 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the CNVfilteR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 339/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVfilteR 1.4.2  (landing page)
Jose Marcos Moreno-Cabrera
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/CNVfilteR
Branch: RELEASE_3_12
Last Commit: 0cb32a5
Last Changed Date: 2021-04-16 08:46:56 -0400 (Fri, 16 Apr 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: CNVfilteR
Version: 1.4.2
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CNVfilteR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CNVfilteR_1.4.2.tar.gz
StartedAt: 2021-05-06 00:16:00 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:22:21 -0400 (Thu, 06 May 2021)
EllapsedTime: 380.3 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVfilteR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CNVfilteR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CNVfilteR_1.4.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CNVfilteR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.2’
* 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       7.180  0.268   7.831
plotScoringModel 4.996  0.012   5.017
* 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:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CNVfilteR
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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
filterCNVs7.1800.2687.831
loadCNVcalls0.4520.0080.463
loadSNPsFromVCF0.6280.0080.639
loadVCFs2.4520.0002.455
plotAllCNVs0.5600.0040.566
plotScoringModel4.9960.0125.017
plotVariantsForCNV4.7960.0164.821