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This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 2161/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFEA.ChIP 1.29.2  (landing page)
Yosra Berrouayel
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/TFEA.ChIP
git_branch: devel
git_last_commit: fbe5cd3
git_last_commit_date: 2025-08-07 07:01:45 -0400 (Thu, 07 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    ERROR  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    ERROR  


CHECK results for TFEA.ChIP on kjohnson3

To the developers/maintainers of the TFEA.ChIP package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TFEA.ChIP.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: TFEA.ChIP
Version: 1.29.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TFEA.ChIP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TFEA.ChIP_1.29.2.tar.gz
StartedAt: 2025-08-08 22:00:10 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 22:02:21 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 131.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TFEA.ChIP.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TFEA.ChIP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TFEA.ChIP_1.29.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/TFEA.ChIP.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TFEA.ChIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TFEA.ChIP’ version ‘1.29.2’
* 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 ‘TFEA.ChIP’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   9.2Mb
    doc    1.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... WARNING
Output(s) listed in 'build/vignette.rds' but not in package:
  ‘inst/doc/TFEA.ChIP.html’
Source(s) listed in 'build/vignette.rds' but not in package:
  ‘TFEA.ChIP.Rmd’
R code(s) listed in 'build/vignette.rds' but not in package:
  ‘TFEA.ChIP.R’
* 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 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 whether startup messages can be suppressed ... 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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘CMplot1.png’ ‘CMplot2.png’ ‘GSEAplot1.png’ ‘GSEAplot2.png’
  ‘TFEA.ChIP.Rmd’ ‘meta_hif1a.png’ ‘meta_table.png’ ‘rankTFplot.png’
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
GSEA_run 5.561  0.822   6.397
rankTFs  5.144  0.614   5.776
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... WARNING
Directory 'inst/doc' does not exist.
Package vignette without corresponding single PDF/HTML:
  ‘TFEA.ChIP.Rmd’
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/TFEA.ChIP.Rcheck/00check.log’
for details.


Installation output

TFEA.ChIP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TFEA.ChIP
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘TFEA.ChIP’ ...
** this is package ‘TFEA.ChIP’ version ‘1.29.2’
** 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 (TFEA.ChIP)

Tests output


Example timings

TFEA.ChIP.Rcheck/TFEA.ChIP-Ex.timings

nameusersystemelapsed
GSEA_ESpermutations000
GSEA_EnrichmentScore000
GSEA_run5.5610.8226.397
GeneID2entrez0.2370.0090.247
Select_genes0.0450.0050.051
analysis_from_table2.0120.1262.143
contingency_matrix1.0060.1271.137
getCMstats1.4560.1751.651
get_chip_index0.0320.0120.044
makeChIPGeneDB0.0300.0000.031
matrixDB_to_listDB000
metaanalysis_fx0.1950.0210.220
plot_RES1.1300.0561.196
preprocessInputData0.4990.0890.598
rankTFs5.1440.6145.776
set_user_data0.6780.0180.696
txt2GR0.0110.0040.015