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CHECK report for cellbaseR on merida1

This page was generated on 2021-02-22 12:42:04 -0500 (Mon, 22 Feb 2021).

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 250/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.14.0
Mohammed OE Abdallah
Snapshot Date: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 2021)
URL: https://git.bioconductor.org/packages/cellbaseR
Branch: RELEASE_3_12
Last Commit: 6ecfb00
Last Changed Date: 2020-10-27 11:23:55 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    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: cellbaseR
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2021-02-22 00:08:40 -0500 (Mon, 22 Feb 2021)
EndedAt: 2021-02-22 00:11:30 -0500 (Mon, 22 Feb 2021)
EllapsedTime: 170.0 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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/cellbaseR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.14.0’
* 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 8.126  3.716  10.549
* 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 8.126 3.71610.549
CellBaseParam0.0020.0000.002
CellBaseR0.0410.0060.357
createGeneModel0.1580.0180.827
getCaddScores0.0470.0030.560
getCellBase-CellBaseR-method0.0530.0050.572
getCellBaseResourceHelp0.2200.0260.903
getChromosomeInfo-CellBaseR-method0.0520.0040.560
getClinical-CellBaseR-method0.9430.0431.834
getClinicalByRegion1.6740.0553.015
getConservationByRegion0.4090.0091.081
getGene-CellBaseR-method0.1240.0060.782
getGeneInfo0.0630.0020.577
getMeta-CellBaseR-method0.0600.0020.567
getProtein-CellBaseR-method0.1420.0030.758
getProteinInfo0.1410.0030.755
getRegion-CellBaseR-method0.1410.0040.882
getRegulatoryByRegion0.1740.0041.065
getSnp-CellBaseR-method0.0760.0020.632
getSnpByGene0.0800.0020.607
getTf-CellBaseR-method0.0550.0022.933
getTfbsByRegion0.0720.0020.619
getTranscript-CellBaseR-method0.0570.0020.651
getTranscriptByGene0.0480.0010.562
getVariant-CellBaseR-method0.1640.0040.838
getVariantAnnotation0.1480.0020.831
getXref-CellBaseR-method0.0630.0020.570