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CHECK report for cellbaseR on nebbiolo1

This page was generated on 2021-02-22 12:33:22 -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: /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: 2021-02-21 20:31:56 -0500 (Sun, 21 Feb 2021)
EndedAt: 2021-02-21 20:36:59 -0500 (Sun, 21 Feb 2021)
EllapsedTime: 303.2 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 6.283  2.613  11.524
* 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-method 6.283 2.61311.524
CellBaseParam0.0020.0000.001
CellBaseR0.0290.0000.361
createGeneModel0.1240.0001.031
getCaddScores0.0450.0000.594
getCellBase-CellBaseR-method0.0560.0080.630
getCellBaseResourceHelp0.2160.0170.893
getChromosomeInfo-CellBaseR-method0.0480.0040.593
getClinical-CellBaseR-method0.4740.0441.713
getClinicalByRegion0.9490.0713.465
getConservationByRegion0.0770.0000.986
getGene-CellBaseR-method0.5510.0161.463
getGeneInfo0.0780.0000.631
getMeta-CellBaseR-method0.0700.0000.609
getProtein-CellBaseR-method0.1390.0000.796
getProteinInfo0.1320.0000.792
getRegion-CellBaseR-method0.1010.0001.099
getRegulatoryByRegion0.1300.0001.173
getSnp-CellBaseR-method0.0580.0000.603
getSnpByGene0.0710.0000.635
getTf-CellBaseR-method0.0550.0002.840
getTfbsByRegion0.0880.0000.674
getTranscript-CellBaseR-method0.0710.0030.625
getTranscriptByGene0.0680.0000.621
getVariant-CellBaseR-method0.1730.0001.012
getVariantAnnotation0.1740.0000.989
getXref-CellBaseR-method0.0610.0000.606