| Back to Build/check report for BioC 3.21 experimental data |
|
This page was generated on 2025-10-16 15:01 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| 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 55/432 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| chipenrich.data 2.32.0 (landing page) Kai Wang
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||
|
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. |
| Package: chipenrich.data |
| Version: 2.32.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:chipenrich.data.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings chipenrich.data_2.32.0.tar.gz |
| StartedAt: 2025-10-16 12:03:07 -0400 (Thu, 16 Oct 2025) |
| EndedAt: 2025-10-16 12:08:05 -0400 (Thu, 16 Oct 2025) |
| EllapsedTime: 297.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: chipenrich.data.Rcheck |
| Warnings: 3 |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:chipenrich.data.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings chipenrich.data_2.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/chipenrich.data.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘chipenrich.data/DESCRIPTION’ ... OK
* this is package ‘chipenrich.data’ version ‘2.32.0’
* 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-3.21-data-experiment/meat/chipenrich.data.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
installed size is 221.7Mb
sub-directories of 1Mb or more:
data 221.0Mb
* 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
BUG FIXES
* checking code 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 223.0 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.21-data-experiment/meat/chipenrich.data.Rcheck/00check.log’
for details.
chipenrich.data.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL chipenrich.data ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘chipenrich.data’ ... ** this is package ‘chipenrich.data’ version ‘2.32.0’ ** 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)
chipenrich.data.Rcheck/chipenrich.data-Ex.timings
| name | user | system | elapsed | |
| GeneSet-class | 0.148 | 0.033 | 0.182 | |
| LocusDefinition-class | 0.077 | 0.008 | 0.086 | |
| peaks_E2F4 | 0.003 | 0.000 | 0.004 | |
| peaks_H3K4me3_GM12878 | 0.005 | 0.001 | 0.006 | |