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CHECK report for brgedata on malbec2

This page was generated on 2021-01-18 15:58:31 -0500 (Mon, 18 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE brgedata PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 41/385HostnameOS / ArchINSTALLBUILDCHECK
brgedata 1.13.0
Carlos Ruiz-Arenas
Snapshot Date: 2021-01-18 09:00:15 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/brgedata
Branch: master
Last Commit: c9c7e98
Last Changed Date: 2020-10-27 10:23:31 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS 

Summary

Package: brgedata
Version: 1.13.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:brgedata.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings brgedata_1.13.0.tar.gz
StartedAt: 2021-01-18 11:42:20 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 11:46:43 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 263.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: brgedata.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:brgedata.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings brgedata_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/brgedata.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘brgedata/DESCRIPTION’ ... OK
* this is package ‘brgedata’ version ‘1.13.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘brgedata’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 638.3Mb
  sub-directories of 1Mb or more:
    data     184.2Mb
    extdata  454.0Mb
* 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 ... WARNING
  Warning: found non-ASCII strings
  'Average Brominated THM uptake (<b5>g/day)' in object 'brge_expo'
  'Average Chloroform uptake (<b5>g/day)' in object 'brge_expo'
  'Average total THM uptake (<b5>g/day)' in object 'brge_expo'
  'Benzene levels (<b5>g/m3)' in object 'brge_expo'
  'BPA (<b5>g/g creatine)' in object 'brge_expo'
  'Mercury (<b5>g/l)' in object 'brge_expo'
  'NO2 levels (<b5>g/m3)' in object 'brge_expo'
  'PFBS (<b5>g/l)' in object 'brge_expo'
  'PFHxS (<b5>g/l)' in object 'brge_expo'
  'PFOA (<b5>g/l)' in object 'brge_expo'
  '<b5>g/l' in object 'brge_expo'
* 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
brge_methy 12.854  0.585  14.176
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/brgedata.Rcheck/00check.log’
for details.



Installation output

brgedata.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL brgedata
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘brgedata’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (brgedata)

Tests output


Example timings

brgedata.Rcheck/brgedata-Ex.timings

nameusersystemelapsed
brge_gexp1.7620.0961.858
brge_methy12.854 0.58514.176
brge_prot0.0000.0020.003