Back to Build/check report for BioC 3.13 experimental data
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This page was generated on 2021-10-16 15:58:39 -0400 (Sat, 16 Oct 2021).

CHECK results for chipenrich.data on malbec2

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

raw results

Package 61/406HostnameOS / ArchINSTALLBUILDCHECK
chipenrich.data 2.16.0  (landing page)
Raymond G. Cavalcante
Snapshot Date: 2021-10-16 09:30:07 -0400 (Sat, 16 Oct 2021)
git_url: https://git.bioconductor.org/packages/chipenrich.data
git_branch: RELEASE_3_13
git_last_commit: 7bbcf41
git_last_commit_date: 2021-05-19 11:43:46 -0400 (Wed, 19 May 2021)
malbec2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: chipenrich.data
Version: 2.16.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:chipenrich.data.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings chipenrich.data_2.16.0.tar.gz
StartedAt: 2021-10-16 12:56:23 -0400 (Sat, 16 Oct 2021)
EndedAt: 2021-10-16 13:01:17 -0400 (Sat, 16 Oct 2021)
EllapsedTime: 294.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: chipenrich.data.Rcheck
Warnings: 3

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:chipenrich.data.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings chipenrich.data_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/chipenrich.data.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chipenrich.data/DESCRIPTION’ ... OK
* this is package ‘chipenrich.data’ version ‘2.16.0’
* 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 ‘chipenrich.data’ can be installed ... WARNING
Found the following significant warnings:
  Warning: objects ‘gene.enh.desc’, ‘gene.enh.desc’ are created by more than one data call
See ‘/home/biocbuild/bbs-3.13-data-experiment/meat/chipenrich.data.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 233.6Mb
  sub-directories of 1Mb or more:
    data  232.9Mb
* 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 ... WARNING
Undocumented code objects:
  ‘enhancer.hg19’ ‘enhancer.hg38’ ‘gene.enh.desc.hg19’
  ‘locusdef.hg19.enhancer’ ‘locusdef.hg19.enhancer_plus5kb’
  ‘locusdef.hg38.enhancer’ ‘locusdef.hg38.enhancer_plus5kb’ ‘mm10’
  ‘mm9’
Undocumented data sets:
  ‘enhancer.hg19’ ‘enhancer.hg38’ ‘mm10’ ‘mm9’ ‘gene.enh.desc.hg19’
  ‘locusdef.hg19.enhancer’ ‘locusdef.hg19.enhancer_plus5kb’
  ‘locusdef.hg38.enhancer’ ‘locusdef.hg38.enhancer_plus5kb’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 LazyData ... WARNING
  LazyData DB of 232.8 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/chipenrich.data.Rcheck/00check.log’
for details.



Installation output

chipenrich.data.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL chipenrich.data
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘chipenrich.data’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Warning: objects ‘gene.enh.desc’, ‘gene.enh.desc’ are created by more than one data call
** 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 (chipenrich.data)

Tests output


Example timings

chipenrich.data.Rcheck/chipenrich.data-Ex.timings

nameusersystemelapsed
GeneSet-class0.1760.0080.184
LocusDefinition-class0.0780.0040.081
peaks_E2F40.0040.0000.004
peaks_H3K4me3_GM128780.0800.0000.079