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CHECK report for cellbaseR on merida1

This page was generated on 2020-09-18 10:25:54 -0400 (Fri, 18 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cellbaseR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 241/1912HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.13.0
Mohammed OE Abdallah
Snapshot Date: 2020-09-17 14:41:56 -0400 (Thu, 17 Sep 2020)
URL: https://git.bioconductor.org/packages/cellbaseR
Branch: master
Last Commit: e14a517
Last Changed Date: 2020-04-27 15:07:27 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cellbaseR
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cellbaseR_1.13.0.tar.gz
StartedAt: 2020-09-18 03:21:27 -0400 (Fri, 18 Sep 2020)
EndedAt: 2020-09-18 03:24:24 -0400 (Fri, 18 Sep 2020)
EllapsedTime: 177.5 seconds
RetCode: 0
Status:  OK 
CheckDir: cellbaseR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cellbaseR_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/cellbaseR.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellbaseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellbaseR’ version ‘1.13.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cellbaseR’ 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
AnnotateVcf-CellBaseR-method 8.969  1.762  11.252
* 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

cellbaseR.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cellbaseR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘cellbaseR’ ...
** 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 (cellbaseR)

Tests output


Example timings

cellbaseR.Rcheck/cellbaseR-Ex.timings

nameusersystemelapsed
AnnotateVcf-CellBaseR-method 8.969 1.76211.252
CellBaseParam0.0030.0010.004
CellBaseR0.0510.0060.361
createGeneModel0.2610.0180.921
getCaddScores0.0550.0030.559
getCellBase-CellBaseR-method0.0650.0040.576
getCellBaseResourceHelp0.2640.0170.878
getChromosomeInfo-CellBaseR-method0.0610.0050.560
getClinical-CellBaseR-method1.6870.1182.630
getClinicalByRegion1.8010.0473.111
getConservationByRegion0.0970.0040.758
getGene-CellBaseR-method0.1680.0040.810
getGeneInfo0.0680.0030.580
getMeta-CellBaseR-method0.0650.0020.576
getProtein-CellBaseR-method0.1510.0020.761
getProteinInfo0.1410.0040.756
getRegion-CellBaseR-method0.1530.0050.896
getRegulatoryByRegion0.1830.0051.055
getSnp-CellBaseR-method0.0820.0030.589
getSnpByGene0.0950.0020.611
getTf-CellBaseR-method0.0580.0023.154
getTfbsByRegion0.0870.0010.623
getTranscript-CellBaseR-method0.0610.0010.571
getTranscriptByGene0.0570.0020.565
getVariant-CellBaseR-method0.1510.0030.813
getVariantAnnotation0.1400.0030.796
getXref-CellBaseR-method0.0640.0020.564