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CHECK report for cellbaseR on malbec1

This page was generated on 2021-01-25 11:48:11 -0500 (Mon, 25 Jan 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: 2021-01-24 14:40:16 -0500 (Sun, 24 Jan 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)
malbec1 Linux (Ubuntu 18.04.5 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
merida1 macOS 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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings cellbaseR_1.14.0.tar.gz
StartedAt: 2021-01-25 00:24:44 -0500 (Mon, 25 Jan 2021)
EndedAt: 2021-01-25 00:27:40 -0500 (Mon, 25 Jan 2021)
EllapsedTime: 176.2 seconds
RetCode: 0
Status:  OK 
CheckDir: cellbaseR.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:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings cellbaseR_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/cellbaseR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 7.424   2.12   9.969
* 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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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL cellbaseR
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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-method7.4242.1209.969
CellBaseParam0.0040.0000.002
CellBaseR0.0440.0000.410
createGeneModel0.1720.0040.842
getCaddScores0.0440.0080.540
getCellBase-CellBaseR-method0.0680.0000.697
getCellBaseResourceHelp0.3440.0080.939
getChromosomeInfo-CellBaseR-method0.0560.0000.584
getClinical-CellBaseR-method0.9040.0121.774
getClinicalByRegion1.7040.0083.061
getConservationByRegion0.0920.0000.829
getGene-CellBaseR-method0.5400.0001.345
getGeneInfo0.0720.0000.567
getMeta-CellBaseR-method0.0680.0000.555
getProtein-CellBaseR-method0.1560.0000.787
getProteinInfo0.1760.0000.811
getRegion-CellBaseR-method0.1360.0000.905
getRegulatoryByRegion0.1760.0001.111
getSnp-CellBaseR-method0.0720.0000.561
getSnpByGene0.0880.0040.626
getTf-CellBaseR-method0.0560.0042.925
getTfbsByRegion0.0800.0040.613
getTranscript-CellBaseR-method0.0600.0040.567
getTranscriptByGene0.0720.0000.569
getVariant-CellBaseR-method0.1680.0000.827
getVariantAnnotation0.1640.0000.848
getXref-CellBaseR-method0.0600.0000.552