annotaR
Tidy, Integrated Gene Annotation
v0.1.1
·
Jan 27, 2026
·
MIT + file LICENSE
Description
A framework for intuitive, multi-source gene and protein annotation, with a focus on integrating functional genomics with disease and drug data for translational insights. Methods used include g:Profiler (Raudvere et al. (2019) <doi:10.1093/nar/gkz369>), biomaRt (Durinck et al. (2009) <doi:10.1038/nprot.2009.97>), and the Open Targets Platform (Koscielny et al. (2017) <doi:10.1093/nar/gkw1055>).
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CRAN Check Status
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ERROR
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OK
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | ERROR |
| r-devel-linux-x86_64-debian-gcc | ERROR |
| r-devel-linux-x86_64-fedora-clang | ERROR |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | ERROR |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | ERROR |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (5 non-OK)
ERROR
r-devel-linux-x86_64-debian-clang
re-building of vignette outputs
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
ERROR
r-devel-linux-x86_64-debian-gcc
re-building of vignette outputs
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
ERROR
r-devel-linux-x86_64-fedora-clang
re-building of vignette outputs
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
ERROR
r-devel-macos-arm64
re-building of vignette outputs
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
ERROR
r-patched-linux-x86_64
re-building of vignette outputs
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
Check History
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 10, 2026
ERROR
r-devel-linux-x86_64-debian-gcc
re-building of vignette outputs
Error(s) in re-building vignettes: ... --- re-building ‘annotaR-workflow.Rmd’ using rmarkdown Quitting from annotaR-workflow.Rmd:45-56 [annotation] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error ...[truncated]... notaR-workflow.Rmd' failed with diagnostics: Unable to query any Ensembl site --- failed re-building ‘annotaR-workflow.Rmd’ SUMMARY: processing the following file failed: ‘annotaR-workflow.Rmd’ Error: Vignette re-building failed. Execution halted
Dependency Network
Version History
new
0.1.1
Mar 10, 2026