Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-13 11:41 -0400 (Mon, 13 Oct 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" | 4833 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 914/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
granulator 1.16.0 (landing page) Sabina Pfister
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the granulator package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/granulator.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: granulator |
Version: 1.16.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:granulator.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings granulator_1.16.0.tar.gz |
StartedAt: 2025-10-10 09:40:06 -0000 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 09:50:26 -0000 (Fri, 10 Oct 2025) |
EllapsedTime: 619.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: granulator.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:granulator.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings granulator_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/granulator.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘granulator/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘granulator’ version ‘1.16.0’ * 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 ‘granulator’ 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 ... 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 deconvolute 78.097 0.252 80.676 plot_deconvolute 47.190 0.214 51.741 plot_regress 46.501 0.148 46.774 plot_benchmark 45.762 0.091 49.209 plot_correlate 44.751 0.088 48.143 benchmark 44.187 0.451 44.739 plot_proportions 44.216 0.230 44.561 correlate 43.346 0.147 43.596 plot_similarity 9.586 0.020 9.621 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: y[1]: "gg" ── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ──────────────── class(plot_benchmark(bench))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ──────────────── class(plot_correlate(correl))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" [ FAIL 40 | WARN 24 | SKIP 0 | PASS 97 ] Error: Test failures Execution halted * 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 ERROR See ‘/home/biocbuild/bbs-3.21-bioc/meat/granulator.Rcheck/00check.log’ for details.
granulator.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL granulator ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘granulator’ ... ** this is package ‘granulator’ version ‘1.16.0’ ** using staged installation ** R ** data ** 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 (granulator)
granulator.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 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("granulator") > > test_check("granulator") [ FAIL 40 | WARN 24 | SKIP 0 | PASS 97 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-data.R:10:5'): Load data ───────────────────────────────────── class(plot_similarity(sigMatrix_ABIS_S0))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-data.R:14:5'): Load data ───────────────────────────────────── class(plot_similarity(sigMatrix_ABIS_S1))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-data.R:18:5'): Load data ───────────────────────────────────── class(plot_similarity(sigMatrix_ABIS_S2))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-data.R:22:5'): Load data ───────────────────────────────────── class(plot_similarity(sigMatrix_ABIS_S3))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-data.R:30:5'): Load data ───────────────────────────────────── class(plot_similarity(sigList))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ──────────────── class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ──────────────── class(plot_deconvolute(decon))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ──────────────── class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ──────────────── class(plot_benchmark(bench))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ──────────────── class(plot_correlate(correl))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ──────────────── class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ──────────────── class(plot_deconvolute(decon))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ──────────────── class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ──────────────── class(plot_benchmark(bench))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ──────────────── class(plot_correlate(correl))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ──────────────── class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ──────────────── class(plot_deconvolute(decon))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ──────────────── class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ──────────────── class(plot_benchmark(bench))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ──────────────── class(plot_correlate(correl))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ──────────────── class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ──────────────── class(plot_deconvolute(decon))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ──────────────── class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ──────────────── class(plot_benchmark(bench))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ──────────────── class(plot_correlate(correl))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ──────────────── class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ──────────────── class(plot_deconvolute(decon))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ──────────────── class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ──────────────── class(plot_benchmark(bench))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ──────────────── class(plot_correlate(correl))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ──────────────── class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ──────────────── class(plot_deconvolute(decon))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ──────────────── class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ──────────────── class(plot_benchmark(bench))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ──────────────── class(plot_correlate(correl))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ──────────────── class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ──────────────── class(plot_deconvolute(decon))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ──────────────── class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ──────────────── class(plot_benchmark(bench))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" ── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ──────────────── class(plot_correlate(correl))[1] not equal to "gg". 1/1 mismatches x[1]: "ggplot2::ggplot" y[1]: "gg" [ FAIL 40 | WARN 24 | SKIP 0 | PASS 97 ] Error: Test failures Execution halted
granulator.Rcheck/granulator-Ex.timings
name | user | system | elapsed | |
benchmark | 44.187 | 0.451 | 44.739 | |
correlate | 43.346 | 0.147 | 43.596 | |
deconvolute | 78.097 | 0.252 | 80.676 | |
get_TPM | 0.001 | 0.000 | 0.001 | |
get_decon_methods | 0 | 0 | 0 | |
load_ABIS | 0.014 | 0.000 | 0.014 | |
plot_benchmark | 45.762 | 0.091 | 49.209 | |
plot_correlate | 44.751 | 0.088 | 48.143 | |
plot_deconvolute | 47.190 | 0.214 | 51.741 | |
plot_proportions | 44.216 | 0.230 | 44.561 | |
plot_regress | 46.501 | 0.148 | 46.774 | |
plot_similarity | 9.586 | 0.020 | 9.621 | |