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CHECK report for cellbaseR on merida2

This page was generated on 2019-04-02 13:27:30 -0400 (Tue, 02 Apr 2019).

Package 220/1696HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.7.0
Mohammed OE Abdallah
Snapshot Date: 2019-04-01 17:01:00 -0400 (Mon, 01 Apr 2019)
URL: https://git.bioconductor.org/packages/cellbaseR
Branch: master
Last Commit: 4852c72
Last Changed Date: 2018-10-30 11:54:37 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: cellbaseR
Version: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2019-04-01 23:41:52 -0400 (Mon, 01 Apr 2019)
EndedAt: 2019-04-01 23:45:13 -0400 (Mon, 01 Apr 2019)
EllapsedTime: 201.6 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_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cellbaseR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.7.0’
* 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 or elapsed time > 5s
                              user system elapsed
AnnotateVcf-CellBaseR-method 9.667  3.826  12.642
* 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/3.6/Resources/library’
* installing *source* package ‘cellbaseR’ ...
** 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
* DONE (cellbaseR)

Tests output


Example timings

cellbaseR.Rcheck/cellbaseR-Ex.timings

nameusersystemelapsed
AnnotateVcf-CellBaseR-method 9.667 3.82612.642
CellBaseParam0.0020.0010.003
CellBaseR0.0440.0080.358
createGeneModel0.3030.0421.015
getCaddScores0.0570.0080.608
getCellBase-CellBaseR-method0.0720.0090.637
getCellBaseResourceHelp0.3130.0421.012
getChromosomeInfo-CellBaseR-method0.0570.0030.608
getClinical-CellBaseR-method0.7790.0361.679
getClinicalByRegion1.9320.1143.421
getConservationByRegion0.0750.0050.781
getGene-CellBaseR-method0.1250.0060.786
getGeneInfo0.0690.0030.603
getMeta-CellBaseR-method0.0770.0030.626
getProtein-CellBaseR-method0.1510.0060.773
getProteinInfo0.1370.0040.769
getRegion-CellBaseR-method0.1100.0040.845
getRegulatoryByRegion0.1550.0071.066
getSnp-CellBaseR-method0.0770.0030.602
getSnpByGene0.0970.0080.638
getTf-CellBaseR-method0.0500.0033.789
getTfbsByRegion0.0790.0030.639
getTranscript-CellBaseR-method0.0620.0030.589
getTranscriptByGene0.0560.0030.577
getVariant-CellBaseR-method0.1380.0040.838
getVariantAnnotation0.1280.0040.795
getXref-CellBaseR-method0.0550.0030.591