Last updated on 2026-03-21 21:53:09 CET.
| Package | ERROR | OK |
|---|---|---|
| annotaR | 4 | 10 |
| BioMoR | 14 | |
| resLIK | 14 |
Current CRAN status: ERROR: 4, OK: 10
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘annotaR-workflow.Rmd’ using rmarkdown
Quitting from annotaR-workflow.Rmd:45-56 [annotation]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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. ├─... %>% add_drug_links()
2. ├─annotaR::add_drug_links(.)
3. │ └─"gene" %in% names(annotaR_object)
4. └─annotaR::add_disease_links(.)
5. └─biomaRt::getBM(...)
6. └─biomaRt:::.processResults(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'annotaR-workflow.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 ‘annotaR-workflow.Rmd’
SUMMARY: processing the following file failed:
‘annotaR-workflow.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘annotaR-workflow.Rmd’ using rmarkdown
Quitting from annotaR-workflow.Rmd:45-56 [annotation]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/httr2_failure>
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [useast.ensembl.org]:
Operation timed out after 10002 milliseconds with 0 bytes received
---
Backtrace:
▆
1. ├─... %>% add_drug_links()
2. ├─annotaR::add_drug_links(.)
3. │ └─"gene" %in% names(annotaR_object)
4. └─annotaR::add_disease_links(.)
5. ├─biomaRt::getBM(...)
6. │ └─biomaRt:::martCheck(mart)
7. └─biomaRt::useEnsembl("genes", "hsapiens_gene_ensembl")
8. └─biomaRt:::.listEnsembl(version = version, GRCh = GRCh, mirror = mirror)
9. └─biomaRt:::.currentEnsemblVersion()
10. └─biomaRt::listEnsemblArchives()
11. └─biomaRt:::.listEnsemblArchives(http_config = list())
12. └─biomaRt:::.checkArchiveList(http_config)
13. └─biomaRt:::.getArchiveList(http_config = http_config)
14. └─httr2::req_perform(html_request)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'annotaR-workflow.Rmd' failed with diagnostics:
Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [useast.ensembl.org]:
Operation timed out after 10002 milliseconds with 0 bytes received
--- failed re-building ‘annotaR-workflow.Rmd’
SUMMARY: processing the following file failed:
‘annotaR-workflow.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Current CRAN status: OK: 14
Current CRAN status: OK: 14