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BioC experimental data: CHECK report for curatedBreastData on malbec1

This page was generated on 2017-04-15 16:49:43 -0400 (Sat, 15 Apr 2017).

Package 63/310HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
curatedBreastData 2.0.1
Katie Planey
Snapshot Date: 2017-04-15 09:20:05 -0400 (Sat, 15 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_4/experiment/pkgs/curatedBreastData
Last Changed Rev: 3980 / Revision: 4141
Last Changed Date: 2016-10-28 11:06:39 -0400 (Fri, 28 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: curatedBreastData
Version: 2.0.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings curatedBreastData_2.0.1.tar.gz
StartedAt: 2017-04-15 10:47:51 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 10:52:57 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 306.1 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-3.4-bioc/R/bin/R CMD check --no-vignettes --timings curatedBreastData_2.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/curatedBreastData.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.0.1’
* 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  282.6Mb
* 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            65.164  0.864  66.065
processExpressionSet         36.780  0.628  37.430
filterAndImputeSamples       34.316  1.932  36.267
filterGenesByVariance        31.692  0.428  32.136
curatedBreastDataExprSetList 30.216  0.880  31.111
removeDuplicatedPatients     30.320  0.552  30.886
* 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-3.4-data-experiment/meat/curatedBreastData.Rcheck/00check.log’
for details.


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)

curatedBreastData.Rcheck/curatedBreastData-Ex.timings:

nameusersystemelapsed
clinicalData0.0600.0000.061
collapseDupProbes65.164 0.86466.065
curatedBreastData-package0.0000.0000.001
curatedBreastDataExprSetList30.216 0.88031.111
filterAndImputeSamples34.316 1.93236.267
filterGenesByVariance31.692 0.42832.136
processExpressionSet36.780 0.62837.430
processExpressionSetList0.0040.0000.001
removeDuplicatedPatients30.320 0.55230.886