| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-20 11:57 -0400 (Fri, 20 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4892 |
| 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 266/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BUSpaRse 1.24.0 (landing page) Lambda Moses
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for BUSpaRse in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BUSpaRse package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BUSpaRse.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: BUSpaRse |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 BUSpaRse |
| StartedAt: 2026-03-19 16:34:35 -0400 (Thu, 19 Mar 2026) |
| EndedAt: 2026-03-19 16:39:18 -0400 (Thu, 19 Mar 2026) |
| EllapsedTime: 282.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 BUSpaRse
###
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* checking for file ‘BUSpaRse/DESCRIPTION’ ... OK
* preparing ‘BUSpaRse’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘sparse-matrix.Rmd’ using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
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--- finished re-building ‘sparse-matrix.Rmd’
--- re-building ‘tr2g.Rmd’ using rmarkdown
Quitting from tr2g.Rmd:64-69 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.processResults()`:
! Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
---
Backtrace:
▆
1. └─BUSpaRse::tr2g_ensembl(...)
2. └─biomaRt::getBM(attrs_use, mart = mart)
3. └─biomaRt:::.processResults(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'tr2g.Rmd' failed with diagnostics:
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
--- failed re-building ‘tr2g.Rmd’
SUMMARY: processing the following file failed:
‘tr2g.Rmd’
Error: Vignette re-building failed.
Execution halted