Back to Build/check report for BioC 3.17 experimental data
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This page was generated on 2023-10-12 14:51:35 -0400 (Thu, 12 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
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

Package 56/421HostnameOS / ArchINSTALLBUILDCHECK
chipenrich.data 2.24.0  (landing page)
Kai Wang
Snapshot Date: 2023-10-12 07:30:02 -0400 (Thu, 12 Oct 2023)
git_url: https://git.bioconductor.org/packages/chipenrich.data
git_branch: RELEASE_3_17
git_last_commit: 6bbc9b9
git_last_commit_date: 2023-04-25 10:34:04 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

CHECK results for chipenrich.data on nebbiolo1


To the developers/maintainers of the chipenrich.data package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: chipenrich.data
Version: 2.24.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:chipenrich.data.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings chipenrich.data_2.24.0.tar.gz
StartedAt: 2023-10-12 11:05:39 -0400 (Thu, 12 Oct 2023)
EndedAt: 2023-10-12 11:10:27 -0400 (Thu, 12 Oct 2023)
EllapsedTime: 288.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: chipenrich.data.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:chipenrich.data.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings chipenrich.data_2.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-data-experiment/meat/chipenrich.data.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘chipenrich.data/DESCRIPTION’ ... OK
* this is package ‘chipenrich.data’ version ‘2.24.0’
* 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 ... OK
* 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-3.17-data-experiment/meat/chipenrich.data.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 228.4Mb
  sub-directories of 1Mb or more:
    data  227.7Mb
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    BUG FIXES
* 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 ... WARNING
Undocumented code objects:
  ‘enhancer.hg19’ ‘enhancer.hg38’ ‘gene.enh.desc.hg19’
  ‘geneset.cellType.hsa’ ‘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’
  ‘geneset.cellType.hsa’ ‘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 230.8 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 ...
  ‘chipenrich.data-vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-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-3.17-bioc/R/bin/R CMD INSTALL chipenrich.data
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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-class0.1620.0040.166
LocusDefinition-class0.0650.0000.065
peaks_E2F40.0040.0000.005
peaks_H3K4me3_GM128780.0030.0040.007