| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-11-01 11:33 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4774 |
| 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 1908/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scone 1.35.0 (landing page) Davide Risso
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
|
To the developers/maintainers of the scone package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scone.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: scone |
| Version: 1.35.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scone |
| StartedAt: 2025-10-31 20:02:55 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 20:04:48 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 113.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scone
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* checking for file ‘scone/DESCRIPTION’ ... OK
* preparing ‘scone’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘PsiNorm.Rmd’ using rmarkdown
--- finished re-building ‘PsiNorm.Rmd’
--- re-building ‘sconeTutorial.Rmd’ using rmarkdown
Quitting from sconeTutorial.Rmd:74-81 [datain]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h5_read_attribute()`:
! argument "bit64conversion" is missing, with no default
---
Backtrace:
▆
1. └─scRNAseq::ReprocessedFluidigmData(assays = "rsem_counts")
2. └─scRNAseq::fetchDataset("legacy", "2023-12-18", "fluidigm", realize.assays = TRUE)
3. └─alabaster.base::altReadObject(...)
4. └─scRNAseq (local) FUN(path, ...)
5. └─alabaster.base::readObject(...)
6. └─alabaster.se (local) meth(path, metadata = metadata, ...)
7. └─alabaster.base::altReadObject(...)
8. └─scRNAseq (local) FUN(path, ...)
9. └─alabaster.base::readObject(...)
10. └─alabaster.matrix (local) meth(path, metadata = metadata, ...)
11. └─(function() {...
12. └─alabaster.base::h5_read_attribute(ghandle, "type")
13. └─rhdf5::H5Aread(ahandle, bit64conversion = bit64conversion)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'sconeTutorial.Rmd' failed with diagnostics:
argument "bit64conversion" is missing, with no default
--- failed re-building ‘sconeTutorial.Rmd’
SUMMARY: processing the following file failed:
‘sconeTutorial.Rmd’
Error: Vignette re-building failed.
Execution halted