Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-27 12:07 -0400 (Sat, 27 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4832 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4620 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4565 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
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 243/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BreastSubtypeR 1.1.3 (landing page) Qiao Yang
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the BreastSubtypeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BreastSubtypeR.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. |
Package: BreastSubtypeR |
Version: 1.1.3 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BreastSubtypeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BreastSubtypeR_1.1.3.tar.gz |
StartedAt: 2025-09-26 05:53:06 -0000 (Fri, 26 Sep 2025) |
EndedAt: 2025-09-26 05:57:45 -0000 (Fri, 26 Sep 2025) |
EllapsedTime: 279.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: BreastSubtypeR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:BreastSubtypeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BreastSubtypeR_1.1.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BreastSubtypeR.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BreastSubtypeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BreastSubtypeR’ version ‘1.1.3’ * 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 ‘BreastSubtypeR’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘BreastSubtypeR’ See ‘/home/biocbuild/bbs-3.22-bioc/meat/BreastSubtypeR.Rcheck/00install.out’ for details. * checking installed package size ... INFO installed size is 10.5Mb sub-directories of 1Mb or more: RshinnyTest 1.2Mb RshinyTest 4.8Mb data 4.0Mb * 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 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’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Vis_heatmap 5.558 0.092 5.664 * 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 ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ≤ (U+2264) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ≥ (U+2265) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ≤ (U+2264) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ≥ (U+2265) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ≤ (U+2264) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ≥ (U+2265) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ≤ (U+2264) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ≥ (U+2265) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ≡ (U+2261) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ≤ (U+2264) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ≥ (U+2265) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ≤ (U+2264) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ≥ (U+2265) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ! Package inputenc Error: Unicode character ₂ (U+2082) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. * checking PDF version of manual without index ... ERROR * DONE Status: 1 ERROR, 2 WARNINGs See ‘/home/biocbuild/bbs-3.22-bioc/meat/BreastSubtypeR.Rcheck/00check.log’ for details.
BreastSubtypeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BreastSubtypeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘BreastSubtypeR’ ... ** this is package ‘BreastSubtypeR’ version ‘1.1.3’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘BreastSubtypeR’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘BreastSubtypeR’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘BreastSubtypeR’ ** testing if installed package keeps a record of temporary installation path * DONE (BreastSubtypeR)
BreastSubtypeR.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" 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. > library(testthat) > library(BreastSubtypeR) Warning message: replacing previous import 'e1071::element' by 'ggplot2::element' when loading 'BreastSubtypeR' > > test_that("BS_Multi performs subtyping correctly", { + # Load required dataset + data("OSLO2EMIT0obj") + + # Define methods to use for subtyping + methods <- c("genefu.robust", "PCAPAM50", "ssBC", "AIMS") + + # Perform subtyping + res.test <- BS_Multi( + data_input = OSLO2EMIT0obj$data_input, + methods = methods, + Subtype = FALSE, + hasClinical = FALSE + ) + + # Validate results + expect_true(identical(res.test$res_subtypes[, methods], OSLO2EMIT0obj$res$res_subtypes[, methods])) # Validate results + }) Test passed 🎊 > > proc.time() user system elapsed 13.340 0.620 13.992
BreastSubtypeR.Rcheck/BreastSubtypeR-Ex.timings
name | user | system | elapsed | |
AIMSmodel | 0.000 | 0.003 | 0.003 | |
BS_AIMS | 0.367 | 0.040 | 0.409 | |
BS_Multi | 1.496 | 0.051 | 1.553 | |
BS_PCAPAM50 | 0.567 | 0.084 | 0.653 | |
BS_cIHC | 0.263 | 0.024 | 0.288 | |
BS_cIHC.itr | 2.492 | 0.064 | 2.563 | |
BS_parker | 0.272 | 0.000 | 0.273 | |
BS_ssBC | 0.524 | 0.024 | 0.550 | |
BS_sspbc | 0.619 | 0.000 | 0.620 | |
BreastSubtypeRobj | 0.000 | 0.003 | 0.004 | |
Gene.ID.ann | 0.151 | 0.008 | 0.159 | |
Mapping | 0 | 0 | 0 | |
OSLO2EMIT0obj | 0.02 | 0.00 | 0.02 | |
TCGABRCAobj | 0.053 | 0.000 | 0.054 | |
Vis_Multi | 1.255 | 0.051 | 1.310 | |
Vis_PCA | 1.303 | 0.019 | 1.332 | |
Vis_boxplot | 0.491 | 0.008 | 0.500 | |
Vis_heatmap | 5.558 | 0.092 | 5.664 | |
Vis_pie | 0.775 | 0.012 | 0.789 | |
iBreastSubtypeR | 0 | 0 | 0 | |
sspbc.models | 0.015 | 0.000 | 0.015 | |
sspbc.models.fullname | 0.015 | 0.000 | 0.014 | |