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CHECK report for cellbaseR on merida1

This page was generated on 2019-04-16 12:00:38 -0400 (Tue, 16 Apr 2019).

Package 214/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.6.1
Mohammed OE Abdallah
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/cellbaseR
Branch: RELEASE_3_8
Last Commit: f01f468
Last Changed Date: 2019-04-08 16:09:41 -0400 (Mon, 08 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  ERROR 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cellbaseR
Version: 1.6.1
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_1.6.1.tar.gz
StartedAt: 2019-04-15 22:49:30 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:52:58 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 208.0 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_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/cellbaseR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.6.1’
* 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 10.814  3.994  13.441
* 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/3.5/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-method10.814 3.99413.441
CellBaseParam0.0030.0010.005
CellBaseR0.0390.0060.373
createGeneModel0.3420.0401.050
getCaddScores0.0560.0060.596
getCellBase-CellBaseR-method0.0660.0070.605
getCellBaseResourceHelp0.2660.0300.916
getChromosomeInfo-CellBaseR-method0.0550.0030.574
getClinical-CellBaseR-method0.7620.0341.674
getClinicalByRegion1.8000.1083.084
getConservationByRegion0.0810.0050.770
getGene-CellBaseR-method0.1410.0050.850
getGeneInfo0.0520.0020.586
getMeta-CellBaseR-method0.0640.0020.572
getProtein-CellBaseR-method0.1380.0020.773
getProteinInfo0.1410.0050.780
getRegion-CellBaseR-method0.1220.0040.875
getRegulatoryByRegion0.1540.0051.064
getSnp-CellBaseR-method0.0750.0020.608
getSnpByGene0.0840.0020.636
getTf-CellBaseR-method0.0580.0023.431
getTfbsByRegion0.0770.0030.633
getTranscript-CellBaseR-method0.0680.0030.621
getTranscriptByGene0.0620.0020.652
getVariant-CellBaseR-method0.1380.0070.831
getVariantAnnotation0.1270.0040.874
getXref-CellBaseR-method0.0510.0020.559