Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-02 11:38 -0400 (Thu, 02 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" | 4831 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4612 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4584 |
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 1507/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
orthos 1.6.1 (landing page) Panagiotis Papasaikas
| 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 | ERROR | skipped | ||||||||||
To the developers/maintainers of the orthos package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/orthos.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: orthos |
Version: 1.6.1 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data orthos |
StartedAt: 2025-10-01 19:02:57 -0400 (Wed, 01 Oct 2025) |
EndedAt: 2025-10-01 19:04:46 -0400 (Wed, 01 Oct 2025) |
EllapsedTime: 109.1 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data orthos ### ############################################################################## ############################################################################## * checking for file ‘orthos/DESCRIPTION’ ... OK * preparing ‘orthos’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘orthosIntro.Rmd’ using rmarkdown Channels: - conda-forge Platform: linux-64 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/noarch/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/linux-64/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/linux-64/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/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/linux-64/repodata.json.zst failed CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/conda-forge/linux-64/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/linux-64' Quitting from orthosIntro.Rmd:280-285 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! Error creating conda environment '/home/biocbuild/.cache/R/basilisk/1.20.0/orthos/1.6.1/orthos' [exit code 1] --- Backtrace: ▆ 1. └─orthos::decomposeVar(...) 2. └─basilisk::basiliskStart(orthosenv, testload = "tensorflow") 3. └─basilisk::obtainEnvironmentPath(env) 4. └─basilisk::setupBasiliskEnv(...) 5. └─reticulate::conda_install(...) 6. └─reticulate::conda_create(...) 7. └─reticulate:::stopf(fmt, envname, result, call. = FALSE) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'orthosIntro.Rmd' failed with diagnostics: Error creating conda environment '/home/biocbuild/.cache/R/basilisk/1.20.0/orthos/1.6.1/orthos' [exit code 1] --- failed re-building ‘orthosIntro.Rmd’ SUMMARY: processing the following file failed: ‘orthosIntro.Rmd’ Error: Vignette re-building failed. Execution halted