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CHECK report for curatedBreastData on malbec1

This page was generated on 2018-04-12 12:49:54 -0400 (Thu, 12 Apr 2018).

Package 65/326HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
curatedBreastData 2.6.0
Katie Planey
Snapshot Date: 2018-04-12 07:35:06 -0400 (Thu, 12 Apr 2018)
URL: https://git.bioconductor.org/packages/curatedBreastData
Branch: RELEASE_3_6
Last Commit: 1ca2f11
Last Changed Date: 2017-10-30 11:58:30 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: curatedBreastData
Version: 2.6.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings curatedBreastData_2.6.0.tar.gz
StartedAt: 2018-04-12 09:51:04 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 09:56:04 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 299.7 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-3.6-bioc/R/bin/R CMD check --no-vignettes --timings curatedBreastData_2.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/curatedBreastData.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘2.6.0’
* 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 283.1Mb
  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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
collapseDupProbes            61.140  0.588  61.793
processExpressionSet         33.480  0.236  33.743
filterAndImputeSamples       32.120  0.448  32.596
filterGenesByVariance        29.648  0.204  29.872
curatedBreastDataExprSetList 28.988  0.316  29.337
removeDuplicatedPatients     29.136  0.160  29.314
* 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-3.6-data-experiment/meat/curatedBreastData.Rcheck/00check.log’
for details.



Installation output

curatedBreastData.Rcheck/00install.out

* installing *source* package ‘curatedBreastData’ ...
** R
** data
** inst
** preparing 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
clinicalData0.0720.0000.069
collapseDupProbes61.140 0.58861.793
curatedBreastData-package000
curatedBreastDataExprSetList28.988 0.31629.337
filterAndImputeSamples32.120 0.44832.596
filterGenesByVariance29.648 0.20429.872
processExpressionSet33.480 0.23633.743
processExpressionSetList0.0000.0000.001
removeDuplicatedPatients29.136 0.16029.314