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CHECK report for IMPCdata on malbec1

This page was generated on 2019-04-16 11:50:56 -0400 (Tue, 16 Apr 2019).

Package 771/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IMPCdata 1.18.0
Jeremy Mason
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/IMPCdata
Branch: RELEASE_3_8
Last Commit: 16b3b95
Last Changed Date: 2018-10-30 11:41:56 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IMPCdata
Version: 1.18.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:IMPCdata.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings IMPCdata_1.18.0.tar.gz
StartedAt: 2019-04-16 00:48:06 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:50:13 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 127.9 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-3.8-bioc/R/bin/R CMD check --install=check:IMPCdata.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings IMPCdata_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/IMPCdata.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.18.0’
* 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 ‘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 or elapsed time > 5s
                 user system elapsed
getPhenCenters  1.236  0.116  15.909
getStrains      0.940  0.080  10.242
printStrains    0.920  0.088  12.134
printProcedures 0.624  0.028   8.109
getAlleles      0.580  0.048   5.470
printAlleles    0.588  0.036   5.566
getGenes        0.584  0.032   5.163
printGenes      0.580  0.028   5.378
getProcedures   0.548  0.052   6.196
printParameters 0.576  0.024   5.250
getParameters   0.564  0.028   5.224
getPipelines    0.476  0.032   5.311
printPipelines  0.472  0.032   6.753
* 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-3.8-bioc/R/bin/R CMD INSTALL IMPCdata
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘IMPCdata’ ...
** 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 (IMPCdata)

Tests output


Example timings

IMPCdata.Rcheck/IMPCdata-Ex.timings

nameusersystemelapsed
getAlleles0.5800.0485.470
getGenes0.5840.0325.163
getIMPCDataset0.6880.0083.664
getIMPCTable0.3960.0404.239
getName0.0680.0081.113
getParameters0.5640.0285.224
getPhenCenters 1.236 0.11615.909
getPipelines0.4760.0325.311
getProcedures0.5480.0526.196
getStrains 0.940 0.08010.242
getZygosities0.1040.0040.853
printAlleles0.5880.0365.566
printGenes0.5800.0285.378
printParameters0.5760.0245.250
printPhenCenters0.2080.0084.123
printPipelines0.4720.0326.753
printProcedures0.6240.0288.109
printStrains 0.920 0.08812.134