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CHECK report for IMPCdata on malbec2

This page was generated on 2020-10-17 11:54:58 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE IMPCdata PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 871/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IMPCdata 1.24.0
Jeremy Mason
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/IMPCdata
Branch: RELEASE_3_11
Last Commit: c4af55b
Last Changed Date: 2020-04-27 14:44:52 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IMPCdata
Version: 1.24.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:IMPCdata.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings IMPCdata_1.24.0.tar.gz
StartedAt: 2020-10-17 02:21:11 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:22:43 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 92.8 seconds
RetCode: 0
Status:  OK 
CheckDir: IMPCdata.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:IMPCdata.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings IMPCdata_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/IMPCdata.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IMPCdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IMPCdata’ version ‘1.24.0’
* 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 ‘IMPCdata’ 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
getPhenCenters  0.985  0.065  13.982
getPipelines    0.474  0.013   5.137
printProcedures 0.458  0.028   5.014
getProcedures   0.442  0.044   6.140
getStrains      0.405  0.016   5.025
* 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

IMPCdata.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL IMPCdata
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘IMPCdata’ ...
** 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 (IMPCdata)

Tests output


Example timings

IMPCdata.Rcheck/IMPCdata-Ex.timings

nameusersystemelapsed
getAlleles0.5120.0204.081
getGenes0.5190.0203.839
getIMPCDataset0.0760.0121.114
getIMPCTable0.3000.0242.593
getName0.0700.0040.800
getParameters0.4220.0123.982
getPhenCenters 0.985 0.06513.982
getPipelines0.4740.0135.137
getProcedures0.4420.0446.140
getStrains0.4050.0165.025
getZygosities0.0760.0080.521
printAlleles0.4390.0293.401
printGenes0.4750.0233.504
printParameters0.4460.0404.240
printPhenCenters0.1510.0084.545
printPipelines0.4390.0284.450
printProcedures0.4580.0285.014
printStrains0.3970.0243.985