Back to Multiple platform build/check report for BioC 3.9 experimental data

CHECK report for curatedBreastData on malbec2

This page was generated on 2019-10-17 16:51:30 -0400 (Thu, 17 Oct 2019).

Package 80/371HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
curatedBreastData 2.12.0
Katie Planey
Snapshot Date: 2019-10-17 09:00:12 -0400 (Thu, 17 Oct 2019)
URL: https://git.bioconductor.org/packages/curatedBreastData
Branch: RELEASE_3_9
Last Commit: 4086734
Last Changed Date: 2019-05-02 11:56:42 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: curatedBreastData
Version: 2.12.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:curatedBreastData.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings curatedBreastData_2.12.0.tar.gz
StartedAt: 2019-10-17 13:01:42 -0400 (Thu, 17 Oct 2019)
EndedAt: 2019-10-17 13:07:15 -0400 (Thu, 17 Oct 2019)
EllapsedTime: 332.8 seconds
RetCode: 0
Status:  OK 
CheckDir: curatedBreastData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:curatedBreastData.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings curatedBreastData_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/curatedBreastData.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 ‘curatedBreastData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘curatedBreastData’ version ‘2.12.0’
* 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 ‘curatedBreastData’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 282.8Mb
  sub-directories of 1Mb or more:
    data  282.7Mb
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
collapseDupProbes            55.781  0.527  56.308
processExpressionSet         33.813  0.208  34.067
filterAndImputeSamples       30.799  0.659  31.459
filterGenesByVariance        28.386  0.165  28.549
removeDuplicatedPatients     28.077  0.136  28.213
curatedBreastDataExprSetList 27.582  0.297  27.879
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-data-experiment/meat/curatedBreastData.Rcheck/00check.log’
for details.



Installation output

curatedBreastData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL curatedBreastData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘curatedBreastData’ ...
** using staged installation
** R
** data
** 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 (curatedBreastData)

Tests output


Example timings

curatedBreastData.Rcheck/curatedBreastData-Ex.timings

nameusersystemelapsed
clinicalData0.0430.0040.046
collapseDupProbes55.781 0.52756.308
curatedBreastData-package000
curatedBreastDataExprSetList27.582 0.29727.879
filterAndImputeSamples30.799 0.65931.459
filterGenesByVariance28.386 0.16528.549
processExpressionSet33.813 0.20834.067
processExpressionSetList0.0000.0000.001
removeDuplicatedPatients28.077 0.13628.213