| Back to Build/check report for BioC 3.24: simplified long |
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This page was generated on 2026-04-22 11:57 -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 340/2351 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPpeakAnno 3.45.3 (landing page) Jianhong Ou
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for ChIPpeakAnno in R Universe. | ||||||||||||||
|
To the developers/maintainers of the ChIPpeakAnno package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPpeakAnno.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: ChIPpeakAnno |
| Version: 3.45.3 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 ChIPpeakAnno |
| StartedAt: 2026-04-21 17:35:22 -0400 (Tue, 21 Apr 2026) |
| EndedAt: 2026-04-21 17:42:01 -0400 (Tue, 21 Apr 2026) |
| EllapsedTime: 399.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 ChIPpeakAnno
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* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* preparing ‘ChIPpeakAnno’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘ChIPpeakAnno.Rmd’ using rmarkdown
Quitting from ChIPpeakAnno.Rmd:751-774 [unnamed-chunk-36]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Get error when calling getBM:
Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery, : 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. └─base::tryCatch(...)
2. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
3. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
4. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ChIPpeakAnno.Rmd' failed with diagnostics:
Get error when calling getBM:
Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery, : 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 ‘ChIPpeakAnno.Rmd’
SUMMARY: processing the following file failed:
‘ChIPpeakAnno.Rmd’
Error: Vignette re-building failed.
Execution halted