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This page was generated on 2025-09-01 12:05 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 2164/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFEA.ChIP 1.29.2  (landing page)
Yosra Berrouayel
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 2025)
git_url: https://git.bioconductor.org/packages/TFEA.ChIP
git_branch: devel
git_last_commit: 249fa53
git_last_commit_date: 2025-08-25 05:23:25 -0400 (Mon, 25 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for TFEA.ChIP on lconway

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: 2025-09-01 00:14:42 -0400 (Mon, 01 Sep 2025)
EndedAt: 2025-09-01 00:20:37 -0400 (Mon, 01 Sep 2025)
EllapsedTime: 354.4 seconds
RetCode: 0
Status:   OK  
CheckDir: TFEA.ChIP.Rcheck
Warnings: 0

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
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/TFEA.ChIP.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TFEA.ChIP/DESCRIPTION’ ... OK
* 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  6.2Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
* 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 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 LazyData ... OK
* 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
rankTFs  14.077  0.670  14.863
GSEA_run 12.450  1.705  14.245
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


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-x86_64/Resources/library’
* installing *source* package ‘TFEA.ChIP’ ...
** this is package ‘TFEA.ChIP’ version ‘1.29.2’
** 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 (TFEA.ChIP)

Tests output


Example timings

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

nameusersystemelapsed
GSEA_ESpermutations0.0010.0000.001
GSEA_EnrichmentScore0.0000.0010.000
GSEA_run12.450 1.70514.245
GeneID2entrez0.6410.0230.666
Select_genes0.0390.0140.053
analysis_from_table3.3830.2783.680
contingency_matrix2.0550.2032.275
getCMstats3.6120.2804.080
get_chip_index0.0440.0340.078
makeChIPGeneDB0.1010.0020.103
matrixDB_to_listDB0.0000.0000.001
metaanalysis_fx0.7060.0730.788
plot_RES3.6440.1893.863
preprocessInputData1.1980.2701.480
rankTFs14.077 0.67014.863
set_user_data1.4120.0331.455
txt2GR0.0250.0010.026