Diana Low
| Snapshot Date: 2025-03-21 13:40 -0400 (Fri, 21 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/SPLINTER |
| git_branch: devel |
| git_last_commit: 15c4210 |
| git_last_commit_date: 2024-10-29 10:14:24 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-22 11:41 -0400 (Sat, 22 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4547 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
| 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 2060/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SPLINTER 1.33.0 (landing page) Diana Low
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the SPLINTER package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SPLINTER.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: SPLINTER |
| Version: 1.33.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SPLINTER |
| StartedAt: 2025-03-21 19:24:33 -0400 (Fri, 21 Mar 2025) |
| EndedAt: 2025-03-21 19:26:58 -0400 (Fri, 21 Mar 2025) |
| EllapsedTime: 145.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SPLINTER
###
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* checking for file ‘SPLINTER/DESCRIPTION’ ... OK
* preparing ‘SPLINTER’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from vignette.Rmd:43-57 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! cannot open URL 'https://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/chromInfo.txt.gz'
---
Backtrace:
x
1. +-txdbmaker::makeTxDbFromGFF(file = gtf_file, chrominfo = Seqinfo(genome = "mm9"))
2. | \-txdbmaker:::.tidy_seqinfo(gr, circ_seqs, chrominfo)
3. \-GenomeInfoDb::Seqinfo(genome = "mm9")
4. \-GenomeInfoDb:::.make_Seqinfo_from_genome(genome)
5. \-GenomeInfoDb::getChromInfoFromUCSC(genome, as.Seqinfo = TRUE)
6. \-GenomeInfoDb:::.get_chrom_info_for_registered_UCSC_genome(...)
7. \-GenomeInfoDb:::.get_raw_chrom_info_for_registered_UCSC_genome(...)
8. \-GenomeInfoDb:::.fetch_raw_chrom_info_from_UCSC(...)
9. \-GenomeInfoDb (local) FETCH_ORDERED_CHROM_SIZES(goldenPath.url = goldenPath.url)
10. \-GenomeInfoDb:::fetch_chrom_sizes_from_UCSC(GENOME, goldenPath.url = goldenPath.url)
11. \-GenomeInfoDb:::.fetch_chrom_sizes_from_UCSC_database(...)
12. \-GenomeInfoDb:::fetch_table_dump_from_UCSC(...)
13. \-GenomeInfoDb:::fetch_table_from_url(...)
14. +-base::suppressWarnings(download.file(url, destfile, quiet = TRUE))
15. | \-base::withCallingHandlers(...)
16. \-utils::download.file(url, destfile, quiet = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
cannot open URL 'https://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/chromInfo.txt.gz'
--- failed re-building ‘vignette.Rmd’
SUMMARY: processing the following file failed:
‘vignette.Rmd’
Error: Vignette re-building failed.
Execution halted