Back to Build/check report for BioC 3.15 experimental data
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This page was generated on 2022-06-30 14:50:08 -0400 (Thu, 30 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for curatedBreastData on nebbiolo1


To the developers/maintainers of the curatedBreastData package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 80/410HostnameOS / ArchINSTALLBUILDCHECK
curatedBreastData 2.24.0  (landing page)
Katie Planey
Snapshot Date: 2022-06-30 07:30:02 -0400 (Thu, 30 Jun 2022)
git_url: https://git.bioconductor.org/packages/curatedBreastData
git_branch: RELEASE_3_15
git_last_commit: f21a7f3
git_last_commit_date: 2022-04-26 13:16:30 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: curatedBreastData
Version: 2.24.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:curatedBreastData.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings curatedBreastData_2.24.0.tar.gz
StartedAt: 2022-06-30 11:16:07 -0400 (Thu, 30 Jun 2022)
EndedAt: 2022-06-30 11:20:41 -0400 (Thu, 30 Jun 2022)
EllapsedTime: 274.0 seconds
RetCode: 0
Status:   OK  
CheckDir: curatedBreastData.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:curatedBreastData.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings curatedBreastData_2.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/curatedBreastData.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘2.24.0’
* 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 283.0Mb
  sub-directories of 1Mb or more:
    data  282.9Mb
* 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 (user + system) or elapsed time > 5s
                               user system elapsed
collapseDupProbes            48.538  1.015  49.555
processExpressionSet         28.396  0.476  28.872
filterAndImputeSamples       26.327  0.863  27.192
filterGenesByVariance        24.587  0.284  24.872
removeDuplicatedPatients     24.118  0.308  24.427
curatedBreastDataExprSetList 23.833  0.544  24.377
* 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-3.15-data-experiment/meat/curatedBreastData.Rcheck/00check.log’
for details.



Installation output

curatedBreastData.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL curatedBreastData
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.15-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
clinicalData0.0330.0030.037
collapseDupProbes48.538 1.01549.555
curatedBreastData-package0.0010.0000.000
curatedBreastDataExprSetList23.833 0.54424.377
filterAndImputeSamples26.327 0.86327.192
filterGenesByVariance24.587 0.28424.872
processExpressionSet28.396 0.47628.872
processExpressionSetList000
removeDuplicatedPatients24.118 0.30824.427