Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-07-29 12:10 -0400 (Tue, 29 Jul 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" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4535 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4516 |
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 140/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
basilisk.utils 1.21.2 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the basilisk.utils package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/basilisk.utils.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: basilisk.utils |
Version: 1.21.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.utils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk.utils_1.21.2.tar.gz |
StartedAt: 2025-07-28 18:12:55 -0400 (Mon, 28 Jul 2025) |
EndedAt: 2025-07-28 18:15:02 -0400 (Mon, 28 Jul 2025) |
EllapsedTime: 127.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: basilisk.utils.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.utils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk.utils_1.21.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/basilisk.utils.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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘basilisk.utils/DESCRIPTION’ ... OK * this is package ‘basilisk.utils’ version ‘1.21.2’ * 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 ‘basilisk.utils’ 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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: 1. └─basilisk.utils::configureEnvironments(ext) at test-configureEnvironments.R:45:5 2. ├─base::do.call(.create_environment, cur.args) 3. └─basilisk.utils (local) `<fn>`(...) ── Error ('test-createEnvironment.R:4:1'): (code run outside of `test_that()`) ── Error in `.create_environment(env.loc, conda = conda, packages = packages, channels = channels, override.channels = override.channels, extra = extra)`: failed to create conda environment at '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpSUgb7S/fileadc312f86e11/test_env/1.0.0' (returned 1) Backtrace: ▆ 1. └─basilisk.utils::createEnvironment(...) at test-createEnvironment.R:4:1 2. └─basilisk.utils:::.create_environment(...) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 13 ] 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 ‘/Users/biocbuild/bbs-3.22-bioc/meat/basilisk.utils.Rcheck/00check.log’ for details.
basilisk.utils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL basilisk.utils ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘basilisk.utils’ ... ** this is package ‘basilisk.utils’ version ‘1.21.2’ ** 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 (basilisk.utils)
basilisk.utils.Rcheck/tests/testthat.Rout.fail
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(basilisk.utils) Attaching package: 'basilisk.utils' The following object is masked from 'package:utils': find > test_check("basilisk.utils") Retrieving notices: ...working... Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=5)")': /conda-forge/notices.json Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=5)")': /conda-forge/notices.json Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=5)")': /conda-forge/notices.json ERROR conda.notices.fetch:get_channel_notice_response(72): Request error <HTTPSConnectionPool(host='conda.anaconda.org', port=443): Max retries exceeded with url: /conda-forge/notices.json (Caused by ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=5)"))> for channel: conda-forge url: https://conda.anaconda.org/conda-forge/notices.json done Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-arm64/repodata.json.zst Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-arm64/repodata.json.zst Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-arm64/repodata.json.zst Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst failed CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/conda-forge/osx-arm64/repodata.json> Elapsed: - An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple retry will get you on your way. 'https//conda.anaconda.org/conda-forge/osx-arm64' Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-arm64/repodata.json.zst Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-arm64/repodata.json.zst Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-arm64/repodata.json.zst failed CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/conda-forge/osx-arm64/repodata.json> Elapsed: - An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple retry will get you on your way. 'https//conda.anaconda.org/conda-forge/osx-arm64' [ FAIL 2 | WARN 0 | SKIP 0 | PASS 13 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-configureEnvironments.R:45:5'): configureEnvironments works as expected ── Error in `(function (env.loc, conda, packages, channels, override.channels, extra) { success <- FALSE on.exit(if (!success) unlink2(env.loc), add = TRUE, after = FALSE) if (is.null(conda)) { conda <- find() } more.args <- character(0) for (ch in channels) { more.args <- c(more.args, "-c", ch) } if (override.channels) { more.args <- c(more.args, "--override-channels") } status <- system2(conda, c("create", "--prefix", env.loc, "--yes", packages, more.args, extra)) if (status != 0L) { stop(sprintf("failed to create conda environment at '%s' (returned %i)", env.loc, status)) } success <- TRUE })(env.loc = "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpSUgb7S/fileadc33926cfdb/foo/biocconda/more-test-env", packages = "pandas", conda = NULL, channels = "conda-forge", override.channels = TRUE, extra = "--quiet")`: failed to create conda environment at '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpSUgb7S/fileadc33926cfdb/foo/biocconda/more-test-env' (returned 1) Backtrace: ▆ 1. └─basilisk.utils::configureEnvironments(ext) at test-configureEnvironments.R:45:5 2. ├─base::do.call(.create_environment, cur.args) 3. └─basilisk.utils (local) `<fn>`(...) ── Error ('test-createEnvironment.R:4:1'): (code run outside of `test_that()`) ── Error in `.create_environment(env.loc, conda = conda, packages = packages, channels = channels, override.channels = override.channels, extra = extra)`: failed to create conda environment at '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpSUgb7S/fileadc312f86e11/test_env/1.0.0' (returned 1) Backtrace: ▆ 1. └─basilisk.utils::createEnvironment(...) at test-createEnvironment.R:4:1 2. └─basilisk.utils:::.create_environment(...) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 13 ] Error: Test failures Execution halted
basilisk.utils.Rcheck/basilisk.utils-Ex.timings
name | user | system | elapsed | |
binaryPath | 0 | 0 | 0 | |
configureEnvironments | 0 | 0 | 0 | |
createEnvironment | 0.001 | 0.001 | 0.004 | |
defaults | 0 | 0 | 0 | |
download | 0.001 | 0.001 | 0.007 | |
find | 0.241 | 0.156 | 1.213 | |