| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-11-03 11:33 -0500 (Mon, 03 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" | 4775 |
| 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 412/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cogeqc 1.15.0 (landing page) Fabrício Almeida-Silva
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
|
To the developers/maintainers of the cogeqc package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cogeqc.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: cogeqc |
| Version: 1.15.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cogeqc |
| StartedAt: 2025-11-02 16:57:21 -0500 (Sun, 02 Nov 2025) |
| EndedAt: 2025-11-02 16:58:48 -0500 (Sun, 02 Nov 2025) |
| EllapsedTime: 87.1 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 cogeqc
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* checking for file ‘cogeqc/DESCRIPTION’ ... OK
* preparing ‘cogeqc’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘vignette_01_assessing_genome_assembly.Rmd’ using rmarkdown
Quitting from vignette_01_assessing_genome_assembly.Rmd:74-85 [get_maize_genomes]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/taxon/4577/dataset_report?page_size=1000'
---
Backtrace:
▆
1. └─cogeqc::get_genome_stats(taxon = 4577)
2. └─jsonlite::read_json(base_url, simplifyVector = TRUE)
3. └─jsonlite::parse_json(...)
4. └─jsonlite:::parse_and_simplify(...)
5. └─jsonlite:::parseJSON(txt, bigint_as_char)
6. └─jsonlite:::parse_con(txt, bigint_as_char)
7. ├─base::open(con, "rb")
8. └─base::open.connection(con, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'vignette_01_assessing_genome_assembly.Rmd' failed with diagnostics:
cannot open the connection to 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/taxon/4577/dataset_report?page_size=1000'
--- failed re-building ‘vignette_01_assessing_genome_assembly.Rmd’
--- re-building ‘vignette_02_assessing_orthogroup_inference.Rmd’ using rmarkdown
--- finished re-building ‘vignette_02_assessing_orthogroup_inference.Rmd’
--- re-building ‘vignette_03_assessing_synteny.Rmd’ using rmarkdown
--- finished re-building ‘vignette_03_assessing_synteny.Rmd’
SUMMARY: processing the following file failed:
‘vignette_01_assessing_genome_assembly.Rmd’
Error: Vignette re-building failed.
Execution halted