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This page was generated on 2021-12-03 13:04:44 -0500 (Fri, 03 Dec 2021).

CHECK results for cellbaseR on nebbiolo2

To the developers/maintainers of the cellbaseR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellbaseR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 264/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.18.0  (landing page)
Mohammed OE Abdallah
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/cellbaseR
git_branch: RELEASE_3_14
git_last_commit: 5598bf6
git_last_commit_date: 2021-10-26 12:35:00 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cellbaseR
Version: 1.18.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings cellbaseR_1.18.0.tar.gz
StartedAt: 2021-12-02 06:30:16 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 06:32:20 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 124.3 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-3.14-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings cellbaseR_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/cellbaseR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.18.0’
* 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 4.564  1.014   9.711
* 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-3.14-bioc/R/bin/R CMD INSTALL cellbaseR
###
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* installing to library ‘/home/biocbuild/bbs-3.14-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-method4.5641.0149.711
CellBaseParam0.0020.0000.001
CellBaseR0.0430.0000.349
createGeneModel0.1730.0081.010
getCaddScores0.0590.0000.557
getCellBase-CellBaseR-method0.0710.0000.582
getCellBaseResourceHelp0.1600.0160.791
getChromosomeInfo-CellBaseR-method0.0430.0080.546
getClinical-CellBaseR-method0.5430.0401.708
getClinicalByRegion0.8810.0123.176
getConservationByRegion0.0800.0000.918
getGene-CellBaseR-method0.1320.0120.964
getGeneInfo0.0660.0000.572
getMeta-CellBaseR-method0.0610.0000.556
getProtein-CellBaseR-method0.0960.0000.697
getProteinInfo0.1060.0000.708
getRegion-CellBaseR-method0.1670.0001.832
getRegulatoryByRegion0.2120.0002.465
getSnp-CellBaseR-method0.0800.0040.586
getSnpByGene0.0970.0000.608
getTf-CellBaseR-method0.0710.0002.916
getTfbsByRegion0.0760.0000.615
getTranscript-CellBaseR-method0.0600.0040.569
getTranscriptByGene0.0650.0000.570
getVariant-CellBaseR-method0.1230.0120.884
getVariantAnnotation0.1410.0000.888
getXref-CellBaseR-method0.0630.0040.569