| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-04-22 11:58 -0400 (Wed, 22 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4796 |
| 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 2103/2351 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SPONGE 1.33.0 (landing page) Markus List
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for SPONGE in R Universe. | ||||||||||||||
|
To the developers/maintainers of the SPONGE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SPONGE.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: SPONGE |
| Version: 1.33.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 SPONGE |
| StartedAt: 2026-04-21 21:07:06 -0400 (Tue, 21 Apr 2026) |
| EndedAt: 2026-04-21 21:10:31 -0400 (Tue, 21 Apr 2026) |
| EllapsedTime: 204.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 SPONGE
###
##############################################################################
##############################################################################
* checking for file ‘SPONGE/DESCRIPTION’ ... OK
* preparing ‘SPONGE’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘SPONGE.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "SPONGE vignette", and the latter is "Sparse Partial correlation ON Gene Expression with SPONGE". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘SPONGE.Rmd’
--- re-building ‘spongEffects.Rmd’ using rmarkdown
Quitting from spongEffects.Rmd:264-272 [unnamed-chunk-25]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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. └─SPONGE::plot_involved_miRNAs_to_modules(...)
2. └─biomaRt::getBM(...)
3. └─biomaRt:::.processResults(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'spongEffects.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 ‘spongEffects.Rmd’
SUMMARY: processing the following file failed:
‘spongEffects.Rmd’
Error: Vignette re-building failed.
Execution halted