Marcel Ramos
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/XeniumIO |
| git_branch: RELEASE_3_21 |
| git_last_commit: b7166d4 |
| git_last_commit_date: 2025-04-15 13:47:31 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 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 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 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 2325/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| XeniumIO 1.0.0 (landing page) Marcel Ramos
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the XeniumIO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/XeniumIO.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: XeniumIO |
| Version: 1.0.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data XeniumIO |
| StartedAt: 2025-10-14 05:45:44 -0000 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 05:46:34 -0000 (Tue, 14 Oct 2025) |
| EllapsedTime: 50.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data XeniumIO
###
##############################################################################
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* checking for file ‘XeniumIO/DESCRIPTION’ ... OK
* preparing ‘XeniumIO’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘XeniumIO.Rmd’ using rmarkdown
Quitting from XeniumIO.Rmd:178-184 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! NotImplemented: Support for codec 'zstd' not built
In order to read this file, you will need to reinstall arrow with additional features enabled.
Set one of these environment variables before installing:
* Sys.setenv(LIBARROW_MINIMAL = "false") (for all optional features, including 'zstd')
* Sys.setenv(ARROW_WITH_ZSTD = "ON") (for just 'zstd')
See https://arrow.apache.org/docs/r/articles/install.html for details
---
Backtrace:
▆
1. ├─BiocIO::import(TENxXenium(xeniumOut = outfold), ref = "Gene Expression")
2. └─XeniumIO::import(TENxXenium(xeniumOut = outfold), ref = "Gene Expression")
3. ├─BiocIO::import(con@colData)
4. └─VisiumIO::import(con@colData)
5. └─arrow::read_parquet(path(con))
6. └─base::tryCatch(reader$ReadTable(), error = read_compressed_error)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'XeniumIO.Rmd' failed with diagnostics:
NotImplemented: Support for codec 'zstd' not built
In order to read this file, you will need to reinstall arrow with additional features enabled.
Set one of these environment variables before installing:
* Sys.setenv(LIBARROW_MINIMAL = "false") (for all optional features, including 'zstd')
* Sys.setenv(ARROW_WITH_ZSTD = "ON") (for just 'zstd')
See https://arrow.apache.org/docs/r/articles/install.html for details
--- failed re-building ‘XeniumIO.Rmd’
SUMMARY: processing the following file failed:
‘XeniumIO.Rmd’
Error: Vignette re-building failed.
Execution halted