Mauro Castro
| Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/RTN |
| git_branch: RELEASE_3_22 |
| git_last_commit: 355296b |
| git_last_commit_date: 2025-10-29 10:15:52 -0500 (Wed, 29 Oct 2025) |
| Back toMultiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-15 12:05 -0500 (Mon, 15 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 | ||||
| Package1861/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RTN 2.34.0 (landing page) Mauro Castro
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
| To the developers/maintainers of the RTN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTN.git to reflect on this report. SeeTroubleshooting Build Report for more information. - Use the followingRenviron 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. SeeRenviron.bioc for more information. |
| Package: RTN |
| Version: 2.34.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RTN.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RTN_2.34.0.tar.gz |
| StartedAt: 2025-12-12 04:19:38 -0500 (Fri, 12 Dec 2025) |
| EndedAt: 2025-12-12 04:25:44 -0500 (Fri, 12 Dec 2025) |
| EllapsedTime: 365.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RTN.Rcheck |
| Warnings: 0 |
################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RTN.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RTN_2.34.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RTN.Rcheck’* using R version 4.5.2 (2025-10-31)* 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 ‘RTN/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘RTN’ version ‘2.34.0’* 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 ‘RTN’ can be installed ... OK* checking installed package size ... INFO installed size is 9.8Mb sub-directories of 1Mb or more: R 1.0Mb data 8.6Mb* 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 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 ... NOTEcheckRd: (-1) TNI.data.Rd:14-15: Lost braces 14 | \code{stni}{A TNI-class with a subset of samples and genes from | ^* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors: tni.area3.Rd: aREAPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* 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* 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 re-building of vignette outputs ... OK* checking PDF version of manual ... OK* DONEStatus: 2 NOTEsSee ‘/home/biocbuild/bbs-3.22-bioc/meat/RTN.Rcheck/00check.log’for details.RTN.Rcheck/00install.out
################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL RTN###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘RTN’ ...** this is package ‘RTN’ version ‘2.34.0’** 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 (RTN)
RTN.Rcheck/tests/runTests.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnuR 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("RTN")-Preprocessing for input data...--Mapping 'expData' to 'rowAnnotation'...--Checking 'regulatoryElements' in 'rowAnnotation'...--Checking 'expData'...-Preprocessing complete!-Performing permutation analysis...--For 5 regulons... | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%-Permutation analysis complete! -Performing bootstrap analysis...--For 5 regulons... | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%-Bootstrap analysis complete! -Applying dpi filter...-DPI filter complete! -Preprocessing for input data...--Mapping 'phenotype' to 'phenoIDs'...--Removing genes without names or values in 'phenotype'...--Removing duplicated genes...--Mapping 'hits' to 'phenoIDs'...--Removing duplicated hits...--Mapping 'transcriptionalNetwork' annotation to 'phenotype'...--Checking agreement between 'transcriptionalNetwork' and 'phenotype'... 99.8% ! --Removing 'hits' not listed in 'transcriptionalNetwork' universe...--Extracting regulons...-Preprocessing complete!-Performing master regulatory analysis...--For 5 regulons... | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100%-Master regulatory analysis complete-Performing gene set enrichment analysis...--For 5 regulons... | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100%-Gene set enrichment analysis complete -Performing two-tailed GSEA analysis...--For 5 regulons... | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100%-GSEA2 analysis complete -Preprocessing for input data...--Mapping 'expData' to 'rowAnnotation'...--Checking 'regulatoryElements' in 'rowAnnotation'...--Checking 'expData'...-Preprocessing complete!-Performing permutation analysis...--For 2 regulons... | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%-Permutation analysis complete! -Performing bootstrap analysis...--For 2 regulons... | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%-Bootstrap analysis complete! -Applying dpi filter...-DPI filter complete! -Preprocessing for input data...--Checking modulators in the dataset...--Extracting TF-targets...--Applying modulator independence constraint...--Applying modulator range constraint...--Selecting subsamples...-Estimating mutual information threshold... | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%-Performing conditional mutual information analysis...--For 2 tfs and 2 candidate modulator(s) | | | 0% | |=================================== | 50% | |======================================================================| 100%-Conditional analysis complete! RUNIT TEST PROTOCOL -- Fri Dec 12 04:23:46 2025 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : RTN RUnit Tests - 2 test functions, 0 errors, 0 failuresNumber of test functions: 2 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 35.602 0.822 36.415RTN.Rcheck/RTN-Ex.timings
| name | user | system | elapsed | |
| AVS-class | 0 | 0 | 0 | |
| RTN.data | 0.350 | 0.007 | 0.358 | |
| TNA-class | 0 | 0 | 0 | |
| TNI-class | 0 | 0 | 0 | |
| TNI.data | 0.335 | 0.017 | 0.351 | |
| avs.evse | 0 | 0 | 0 | |
| avs.get | 0.001 | 0.000 | 0.000 | |
| avs.pevse | 0.000 | 0.000 | 0.001 | |
| avs.plot1 | 0 | 0 | 0 | |
| avs.plot2 | 0 | 0 | 0 | |
| avs.rvse | 0 | 0 | 0 | |
| avs.vse | 0 | 0 | 0 | |
| tna.get | 0.24 | 0.01 | 0.25 | |
| tna.gsea1 | 0.257 | 0.016 | 0.273 | |
| tna.gsea2 | 0.238 | 0.014 | 0.252 | |
| tna.mra | 0.275 | 0.018 | 0.294 | |
| tna.plot.gsea1 | 0.236 | 0.003 | 0.239 | |
| tna.plot.gsea2 | 0.835 | 0.102 | 0.936 | |
| tni.alpha.adjust | 0.115 | 0.001 | 0.116 | |
| tni.annotate.regulons | 0.054 | 0.002 | 0.056 | |
| tni.annotate.samples | 0.055 | 0.001 | 0.056 | |
| tni.area3 | 0.053 | 0.004 | 0.057 | |
| tni.bootstrap | 0.051 | 0.005 | 0.056 | |
| tni.conditional | 0.053 | 0.004 | 0.056 | |
| tni.constructor | 0.152 | 0.007 | 0.159 | |
| tni.dpi.filter | 0.073 | 0.001 | 0.073 | |
| tni.get | 0.054 | 0.002 | 0.056 | |
| tni.graph | 0 | 0 | 0 | |
| tni.gsea2 | 0.053 | 0.002 | 0.056 | |
| tni.overlap.genesets | 0.054 | 0.002 | 0.056 | |
| tni.permutation | 0.056 | 0.003 | 0.059 | |
| tni.plot.checks | 0.057 | 0.003 | 0.060 | |
| tni.plot.sre | 0.048 | 0.009 | 0.056 | |
| tni.preprocess | 0 | 0 | 0 | |
| tni.prune | 0.060 | 0.006 | 0.066 | |
| tni.regulon.summary | 0.054 | 0.001 | 0.054 | |
| tni.replace.samples | 0 | 0 | 0 | |
| tni.sre | 0.054 | 0.003 | 0.057 | |
| tni2tna.preprocess | 0.244 | 0.004 | 0.247 | |
| upgradeTNA | 0 | 0 | 0 | |
| upgradeTNI | 0 | 0 | 0 | |