Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:00 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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? 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 274/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.22.0  (landing page)
Mohammed OE Abdallah
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/cellbaseR
git_branch: RELEASE_3_16
git_last_commit: 03e6b83
git_last_commit_date: 2022-11-01 11:15:37 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cellbaseR
Version: 1.22.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings cellbaseR_1.22.0.tar.gz
StartedAt: 2023-04-10 19:34:26 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:37:10 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 163.6 seconds
RetCode: 0
Status:   OK  
CheckDir: cellbaseR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings cellbaseR_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/cellbaseR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘cellbaseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellbaseR’ version ‘1.22.0’
* 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 loading without being on the library search path ... 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 3.592  1.213   8.114
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘cellbaseR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

cellbaseR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL cellbaseR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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-method3.5921.2138.114
CellBaseParam0.0020.0000.002
CellBaseR0.0310.0050.264
createGeneModel0.4870.1040.874
getCaddScores0.0510.0040.387
getCellBase-CellBaseR-method0.0610.0000.302
getCellBaseResourceHelp0.1690.0122.512
getChromosomeInfo-CellBaseR-method0.0540.0000.387
getClinical-CellBaseR-method0.4420.0601.113
getClinicalByRegion0.8650.0561.890
getConservationByRegion0.0660.0110.387
getGene-CellBaseR-method0.0990.0000.384
getGeneInfo0.0690.0040.313
getMeta-CellBaseR-method0.0480.0120.287
getProtein-CellBaseR-method0.0830.0080.342
getProteinInfo0.0950.0000.336
getRegion-CellBaseR-method0.0900.0190.400
getRegulatoryByRegion0.1430.0120.575
getSnp-CellBaseR-method0.0590.0000.293
getSnpByGene0.0640.0000.310
getTf-CellBaseR-method0.0620.0032.602
getTfbsByRegion0.0660.0010.427
getTranscript-CellBaseR-method0.0490.0030.295
getTranscriptByGene0.0620.0010.305
getVariant-CellBaseR-method0.1100.0040.437
getVariantAnnotation0.1100.0080.437
getXref-CellBaseR-method0.0590.0160.310