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This page was generated on 2025-08-21 11:43 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 2182/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFEA.ChIP 1.28.0  (landing page)
Laura Puente Santamaría
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/TFEA.ChIP
git_branch: RELEASE_3_21
git_last_commit: 129c11f
git_last_commit_date: 2025-04-15 11:16:46 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for TFEA.ChIP on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: TFEA.ChIP
Version: 1.28.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:TFEA.ChIP.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TFEA.ChIP_1.28.0.tar.gz
StartedAt: 2025-08-19 14:53:52 -0000 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 15:02:46 -0000 (Tue, 19 Aug 2025)
EllapsedTime: 533.7 seconds
RetCode: 0
Status:   OK  
CheckDir: TFEA.ChIP.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:TFEA.ChIP.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TFEA.ChIP_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/TFEA.ChIP.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 ‘1.28.0’
* 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 ‘TFEA.ChIP’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
* 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 loading without being on the library search path ... 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 ... NOTE
rankTFs: no visible binding for global variable ‘arg.ES’
rankTFs: no visible binding for global variable ‘ES’
rankTFs: no visible binding for global variable ‘TF’
Undefined global functions or variables:
  ES TF arg.ES
* 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’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
rankTFs            24.230  0.196  24.482
GSEA_run           17.615  0.232  17.893
plot_CM            11.493  0.164  11.682
getCMstats         11.141  0.040  11.204
contingency_matrix  9.195  0.123   9.340
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/TFEA.ChIP.Rcheck/00check.log’
for details.


Installation output

TFEA.ChIP.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL TFEA.ChIP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘TFEA.ChIP’ ...
** this is package ‘TFEA.ChIP’ version ‘1.28.0’
** 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

TFEA.ChIP.Rcheck/tests/runTests.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage(pkgname = "TFEA.ChIP")

Because of space limitations, TFEA.ChIPs internal database only includes ChIP-seq experiments from cell types in ENCODE's tiers 1, 2, and 2.5. 
To download the full ReMap2022 database, as well as other ready-to-use databases, visit https://github.com/LauraPS1/TFEA.ChIP_downloads

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Done! 2 genes of 2 successfully converted.

Done! 1 genes of 1 successfully converted.

Done! 1 genes of 1 successfully converted.

Done! 2 genes of 2 successfully converted.

Done! 16532 genes of 17527 successfully converted.

Couldn't find Entrez IDs for 995 genes.

Loading required namespace: DESeq2
Done! 10444 genes of 11667 successfully converted.

Couldn't find Entrez IDs for 1223 genes.

Done! 16532 genes of 17527 successfully converted.

Couldn't find Entrez IDs for 995 genes.

Done! 10444 genes of 11667 successfully converted.

Couldn't find Entrez IDs for 1223 genes.



RUNIT TEST PROTOCOL -- Tue Aug 19 15:02:42 2025 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TFEA.ChIP RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
Warning message:
Some genes returned 1:many mapping to ENTREZ ID. Genes were assigned the first ENTREZ ID match found.
 
> 
> proc.time()
   user  system elapsed 
 72.800   1.780  74.728 

Example timings

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

nameusersystemelapsed
GSEA_EnrichmentScore0.0010.0000.001
GSEA_run17.615 0.23217.893
GeneID2entrez0.7240.0160.742
Select_genes0.1100.0040.114
contingency_matrix9.1950.1239.340
getCMstats11.141 0.04011.204
get_chip_index0.0290.0000.029
makeChIPGeneDB0.1270.0000.127
matrixDB_to_listDB0.0000.0000.001
plot_CM11.493 0.16411.682
plot_ES0.5190.0240.544
plot_RES0.7730.0360.807
preprocessInputData1.7210.0791.804
rankTFs24.230 0.19624.482
set_user_data2.3240.0002.330
txt2GR0.0400.0000.039