Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-29 11:40 -0400 (Mon, 29 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4580 |
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 934/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GSgalgoR 1.18.0 (landing page) Carlos Catania
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the GSgalgoR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GSgalgoR.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: GSgalgoR |
Version: 1.18.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GSgalgoR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GSgalgoR_1.18.0.tar.gz |
StartedAt: 2025-09-26 23:17:01 -0400 (Fri, 26 Sep 2025) |
EndedAt: 2025-09-26 23:20:13 -0400 (Fri, 26 Sep 2025) |
EllapsedTime: 191.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GSgalgoR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GSgalgoR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GSgalgoR_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GSgalgoR.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 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GSgalgoR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GSgalgoR’ version ‘1.18.0’ * 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 ‘GSgalgoR’ 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 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: galgo.Rd: survival non_dominated_summary.Rd: survival 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_pareto 4.173 0.117 8.469 create_centroids 3.010 0.088 7.202 classify_multiple 2.924 0.111 7.336 to_dataframe 2.960 0.052 7.318 to_list 2.839 0.050 7.085 non_dominated_summary 2.643 0.075 7.463 callback_base_report 2.543 0.144 7.342 galgo 2.409 0.053 7.073 callback_default 2.272 0.066 7.431 callback_no_report 2.230 0.086 7.344 callback_base_return_pop 2.168 0.069 6.512 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/GSgalgoR.Rcheck/00check.log’ for details.
GSgalgoR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GSgalgoR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘GSgalgoR’ ... ** this is package ‘GSgalgoR’ version ‘1.18.0’ ** using staged installation ** R ** 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 (GSgalgoR)
GSgalgoR.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > library(testthat) > library(GSgalgoR) > > test_check("GSgalgoR") .......... k rnkIndex CrowD result.1 8 0.02212350 201.10126 1 Inf result.3 9 0.02402496 160.41638 1 1.37352 result.4 8 0.03651880 48.37265 1 Inf k rnkIndex CrowD result.1 8 0.02212350 201.10126 1 Inf result.3 2 0.11803624 30.01863 1 Inf result.4 4 0.04509859 173.43985 1 1.798893 ......[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ] > > proc.time() user system elapsed 22.798 1.015 66.230
GSgalgoR.Rcheck/GSgalgoR-Ex.timings
name | user | system | elapsed | |
calculate_distance | 3.710 | 0.139 | 3.902 | |
callback_base_report | 2.543 | 0.144 | 7.342 | |
callback_base_return_pop | 2.168 | 0.069 | 6.512 | |
callback_default | 2.272 | 0.066 | 7.431 | |
callback_no_report | 2.230 | 0.086 | 7.344 | |
classify_multiple | 2.924 | 0.111 | 7.336 | |
cluster_algorithm | 2.640 | 0.036 | 2.686 | |
cluster_classify | 0.752 | 0.137 | 0.894 | |
cosine_similarity | 0 | 0 | 0 | |
create_centroids | 3.010 | 0.088 | 7.202 | |
galgo | 2.409 | 0.053 | 7.073 | |
k_centroids | 2.348 | 0.062 | 2.966 | |
non_dominated_summary | 2.643 | 0.075 | 7.463 | |
plot_pareto | 4.173 | 0.117 | 8.469 | |
surv_fitness | 1.028 | 0.024 | 1.056 | |
to_dataframe | 2.960 | 0.052 | 7.318 | |
to_list | 2.839 | 0.050 | 7.085 | |