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CHECK report for cellbaseR on malbec2

This page was generated on 2018-10-17 08:30:12 -0400 (Wed, 17 Oct 2018).

Package 200/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.4.0
Mohammed OE Abdallah
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/cellbaseR
Branch: RELEASE_3_7
Last Commit: 5403267
Last Changed Date: 2018-04-30 10:35:46 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: cellbaseR
Version: 1.4.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings cellbaseR_1.4.0.tar.gz
StartedAt: 2018-10-15 23:02:43 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:04:32 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 108.5 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-3.7-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings cellbaseR_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/cellbaseR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.4.0’
* 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 6.292   1.48  10.375
* 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-3.7-bioc/R/bin/R CMD INSTALL cellbaseR
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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 6.292 1.48010.375
CellBaseParam0.0040.0000.002
CellBaseR0.0360.0120.341
createGeneModel0.3280.0120.963
getCaddScores0.0640.0000.547
getCellBase-CellBaseR-method0.0600.0040.559
getCellBaseResourceHelp0.3160.0160.913
getChromosomeInfo-CellBaseR-method0.0520.0000.533
getClinical-CellBaseR-method0.5200.0041.352
getClinicalByRegion1.0840.0522.283
getConservationByRegion0.0920.0040.815
getGene-CellBaseR-method0.1480.0000.868
getGeneInfo0.0720.0000.574
getMeta-CellBaseR-method0.0800.0040.562
getProtein-CellBaseR-method0.1640.0000.741
getProteinInfo0.1560.0001.759
getRegion-CellBaseR-method0.1480.0000.866
getRegulatoryByRegion0.1320.0000.984
getSnp-CellBaseR-method0.0760.0040.578
getSnpByGene0.0720.0000.612
getTf-CellBaseR-method0.0520.0002.792
getTfbsByRegion0.0880.0000.618
getTranscript-CellBaseR-method0.0560.0000.552
getTranscriptByGene0.0560.0001.554
getVariant-CellBaseR-method0.1120.0000.758
getVariantAnnotation0.1520.0000.810
getXref-CellBaseR-method0.0640.0040.563