Last updated on 2025-03-19 08:52:41 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.7.6 | 24.80 | 233.47 | 258.27 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.7.6 | 15.17 | 147.99 | 163.16 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.7.6 | 425.05 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.7.6 | 431.64 | OK | |||
| r-devel-macos-arm64 | 0.7.6 | 91.00 | OK | |||
| r-devel-macos-x86_64 | 0.7.6 | 224.00 | OK | |||
| r-devel-windows-x86_64 | 0.7.6 | 30.00 | 253.00 | 283.00 | OK | |
| r-patched-linux-x86_64 | 0.7.6 | 23.88 | 220.71 | 244.59 | OK | |
| r-release-linux-x86_64 | 0.7.6 | 23.13 | 189.78 | 212.91 | OK | |
| r-release-macos-arm64 | 0.7.6 | 121.00 | NOTE | |||
| r-release-macos-x86_64 | 0.7.6 | 228.00 | OK | |||
| r-release-windows-x86_64 | 0.7.6 | 30.00 | 241.00 | 271.00 | OK | |
| r-oldrel-macos-arm64 | 0.7.6 | 95.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.7.6 | 209.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.7.6 | 36.00 | 334.00 | 370.00 | OK |
Version: 0.7.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘introduction_to_dnapath.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dnapath.Rcheck/vign_test/dnapath/vignettes/introduction_to_dnapath_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 83472 bytes
Input file size = 83670 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 76968
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 76968
Output IDAT size = 76968 bytes (6504 bytes decrease)
Output file size = 77046 bytes (6624 bytes = 7.92% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dnapath.Rcheck/vign_test/dnapath/vignettes/introduction_to_dnapath_files/figure-html/unnamed-chunk-7-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25119 bytes
Input file size = 25233 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19956
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19956
Output IDAT size = 19956 bytes (5163 bytes decrease)
Output file size = 20034 bytes (5199 bytes = 20.60% decrease)
Quitting from introduction_to_dnapath.Rmd:220-224 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.processResults()`:
! Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_113: DBI connect('database=ensembl_mart_113;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_113/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
---
Backtrace:
▆
1. ├─dnapath::rename_genes(...)
2. │ └─dnapath::entrez_to_symbol(genes, species = species, ...)
3. │ ├─... %>% ...
4. │ └─dnapath::get_biomart_mapping(...)
5. │ └─biomaRt::getBM(...)
6. │ └─biomaRt:::.processResults(...)
7. ├─dplyr::summarise(., dplyr::across(dplyr::everything(), dplyr::first))
8. └─dplyr::group_by(., entrezgene_id)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'introduction_to_dnapath.Rmd' failed with diagnostics:
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_113: DBI connect('database=ensembl_mart_113;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_113/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
--- failed re-building ‘introduction_to_dnapath.Rmd’
--- re-building ‘package_data.Rmd’ using rmarkdown
--- finished re-building ‘package_data.Rmd’
SUMMARY: processing the following file failed:
‘introduction_to_dnapath.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.7.6
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘reactome.db’
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64