Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 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 2161/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TFEA.ChIP 1.29.2 (landing page) Yosra Berrouayel
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | ERROR | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | ERROR | |||||||||
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. |
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 |
############################################################################## ############################################################################## ### ### 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.
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)
TFEA.ChIP.Rcheck/TFEA.ChIP-Ex.timings
name | user | system | elapsed | |
GSEA_ESpermutations | 0 | 0 | 0 | |
GSEA_EnrichmentScore | 0 | 0 | 0 | |
GSEA_run | 5.561 | 0.822 | 6.397 | |
GeneID2entrez | 0.237 | 0.009 | 0.247 | |
Select_genes | 0.045 | 0.005 | 0.051 | |
analysis_from_table | 2.012 | 0.126 | 2.143 | |
contingency_matrix | 1.006 | 0.127 | 1.137 | |
getCMstats | 1.456 | 0.175 | 1.651 | |
get_chip_index | 0.032 | 0.012 | 0.044 | |
makeChIPGeneDB | 0.030 | 0.000 | 0.031 | |
matrixDB_to_listDB | 0 | 0 | 0 | |
metaanalysis_fx | 0.195 | 0.021 | 0.220 | |
plot_RES | 1.130 | 0.056 | 1.196 | |
preprocessInputData | 0.499 | 0.089 | 0.598 | |
rankTFs | 5.144 | 0.614 | 5.776 | |
set_user_data | 0.678 | 0.018 | 0.696 | |
txt2GR | 0.011 | 0.004 | 0.015 | |