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 12:06 -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 1829/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RTNsurvival 1.33.1 (landing page) Clarice Groeneveld
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the RTNsurvival package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTNsurvival.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: RTNsurvival |
Version: 1.33.1 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RTNsurvival.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RTNsurvival_1.33.1.tar.gz |
StartedAt: 2025-08-09 02:12:12 -0400 (Sat, 09 Aug 2025) |
EndedAt: 2025-08-09 02:16:08 -0400 (Sat, 09 Aug 2025) |
EllapsedTime: 236.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RTNsurvival.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RTNsurvival.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RTNsurvival_1.33.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RTNsurvival.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘RTNsurvival/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RTNsurvival’ version ‘1.33.1’ * 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 ‘RTNsurvival’ can be installed ... OK * checking installed package size ... OK * 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: TNS-class.Rd: TNI-class tni2tnsPreprocess-methods.Rd: TNI-class, tni.preprocess tnsAREA3-methods.Rd: tni.area3 tnsGSEA2-methods.Rd: tni.gsea2, TNI-class tnsPlotGSEA2-methods.Rd: tna.plot.gsea2 Please provide package anchors for all Rd \link{} targets not in the package 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 LazyData ... 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 * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/RTNsurvival.Rcheck/00check.log’ for details.
RTNsurvival.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL RTNsurvival ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘RTNsurvival’ ... ** this is package ‘RTNsurvival’ version ‘1.33.1’ ** 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 (RTNsurvival)
RTNsurvival.Rcheck/tests/runTests.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-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("RTNsurvival") RUNIT TEST PROTOCOL -- Sat Aug 9 02:15:48 2025 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : RTNsurvival RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 10.869 0.516 11.373
RTNsurvival.Rcheck/RTNsurvival-Ex.timings
name | user | system | elapsed | |
TNS.data | 0.000 | 0.000 | 0.002 | |
hclust_semisupervised | 0.053 | 0.004 | 0.055 | |
tni2tnsPreprocess-methods | 0.344 | 0.006 | 0.351 | |
tnsAREA3-methods | 1.179 | 0.054 | 1.235 | |
tnsCox-methods | 1.425 | 0.071 | 1.497 | |
tnsCoxInteraction-methods | 1.356 | 0.013 | 1.369 | |
tnsGSEA2-methods | 0.793 | 0.004 | 0.798 | |
tnsGet-methods | 0.844 | 0.025 | 0.867 | |
tnsInteraction-methods | 1.306 | 0.016 | 1.323 | |
tnsKM-methods | 0.836 | 0.007 | 0.844 | |
tnsKmInteraction-methods | 1.349 | 0.012 | 1.360 | |
tnsPlotCovariates-methods | 2.023 | 0.131 | 2.155 | |
tnsPlotCox-methods | 1.470 | 0.066 | 1.536 | |
tnsPlotCoxInteraction-methods | 0.789 | 0.002 | 0.792 | |
tnsPlotGSEA2-methods | 1.948 | 0.065 | 2.013 | |
tnsPlotKM-methods | 1.566 | 0.006 | 1.572 | |
tnsPlotKmInteraction-methods | 0.815 | 0.010 | 0.825 | |
tnsPlotSRE-methods | 0.893 | 0.016 | 0.910 | |
tnsSRD-methods | 1.454 | 0.011 | 1.465 | |
tnsSRE-methods | 0.865 | 0.006 | 0.871 | |
tnsStratification | 0.000 | 0.001 | 0.000 | |