Back to Multiple platform build/check report for BioC 3.8 experimental data

CHECK report for curatedBreastData on malbec1

This page was generated on 2019-04-16 15:26:13 -0400 (Tue, 16 Apr 2019).

Package 74/360HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
curatedBreastData 2.10.0
Katie Planey
Snapshot Date: 2019-04-16 11:00:05 -0400 (Tue, 16 Apr 2019)
URL: https://git.bioconductor.org/packages/curatedBreastData
Branch: RELEASE_3_8
Last Commit: 62820e1
Last Changed Date: 2018-10-30 11:36:23 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: curatedBreastData
Version: 2.10.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:curatedBreastData.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings curatedBreastData_2.10.0.tar.gz
StartedAt: 2019-04-16 13:35:30 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 13:40:33 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 303.2 seconds
RetCode: 0
Status:  OK 
CheckDir: curatedBreastData.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:curatedBreastData.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings curatedBreastData_2.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-data-experiment/meat/curatedBreastData.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 ‘curatedBreastData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘curatedBreastData’ version ‘2.10.0’
* 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            61.368  0.756  62.413
processExpressionSet         37.148  0.216  37.384
filterAndImputeSamples       34.000  0.484  34.500
filterGenesByVariance        32.220  0.112  32.353
removeDuplicatedPatients     31.872  0.228  32.122
curatedBreastDataExprSetList 31.084  0.300  31.401
* 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-3.8-data-experiment/meat/curatedBreastData.Rcheck/00check.log’
for details.



Installation output

curatedBreastData.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL curatedBreastData
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘curatedBreastData’ ...
** 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
* DONE (curatedBreastData)

Tests output


Example timings

curatedBreastData.Rcheck/curatedBreastData-Ex.timings

nameusersystemelapsed
clinicalData0.0520.0000.058
collapseDupProbes61.368 0.75662.413
curatedBreastData-package000
curatedBreastDataExprSetList31.084 0.30031.401
filterAndImputeSamples34.000 0.48434.500
filterGenesByVariance32.220 0.11232.353
processExpressionSet37.148 0.21637.384
processExpressionSetList0.0000.0000.001
removeDuplicatedPatients31.872 0.22832.122