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CHECK report for cellbaseR on malbec2

This page was generated on 2019-10-16 12:11:05 -0400 (Wed, 16 Oct 2019).

Package 225/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.8.1
Mohammed OE Abdallah
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/cellbaseR
Branch: RELEASE_3_9
Last Commit: f6fa465
Last Changed Date: 2019-09-22 11:02:36 -0400 (Sun, 22 Sep 2019)
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  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cellbaseR
Version: 1.8.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cellbaseR_1.8.1.tar.gz
StartedAt: 2019-10-16 00:19:54 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:22:20 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 145.9 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-3.9-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cellbaseR_1.8.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/cellbaseR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.8.1’
* 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 10.552  1.754  12.911
getTf-CellBaseR-method        0.059  0.004   5.012
* 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-3.9-bioc/R/bin/R CMD INSTALL cellbaseR
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* installing to library ‘/home/biocbuild/bbs-3.9-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-method10.552 1.75412.911
CellBaseParam0.0010.0000.002
CellBaseR0.0390.0110.346
createGeneModel0.1790.0160.816
getCaddScores0.0530.0040.549
getCellBase-CellBaseR-method0.0570.0080.563
getCellBaseResourceHelp0.3450.0040.937
getChromosomeInfo-CellBaseR-method0.0590.0000.548
getClinical-CellBaseR-method0.8910.0081.712
getClinicalByRegion1.5940.0203.020
getConservationByRegion0.0990.0000.833
getGene-CellBaseR-method0.1530.0000.867
getGeneInfo0.0690.0030.570
getMeta-CellBaseR-method0.0720.0000.562
getProtein-CellBaseR-method0.1190.0000.707
getProteinInfo0.1520.0050.746
getRegion-CellBaseR-method0.1410.0080.863
getRegulatoryByRegion0.1770.0001.074
getSnp-CellBaseR-method0.1000.0000.592
getSnpByGene0.0920.0070.604
getTf-CellBaseR-method0.0590.0045.012
getTfbsByRegion0.0960.0000.626
getTranscript-CellBaseR-method0.0640.0000.562
getTranscriptByGene0.0610.0000.558
getVariant-CellBaseR-method0.1540.0000.815
getVariantAnnotation0.1500.0000.835
getXref-CellBaseR-method0.0560.0030.552