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waldronlab / bugsigdbr

R-side access to published microbial signatures from BugSigDB
https://bioconductor.org/packages/bugsigdbr
GNU General Public License v3.0
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Can't download uberon #45

Closed sdgamboa closed 11 months ago

sdgamboa commented 11 months ago

I'm not able to download Uberon. I think this might have something to do with the ontology source rather than with bugsgidbr, but still, I'm reporting it in case it's related to bugsigdbr.

BiocManager::version()
#> [1] '3.17'
BiocManager::install('bugsigdbr', force = TRUE)
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest
#> Bioconductor version 3.17 (BiocManager 1.30.21.1), R 4.3.1 (2023-06-16)
#> Installing package(s) 'bugsigdbr'
BiocManager::install('ontologyIndex', force = TRUE)
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest
#> Bioconductor version 3.17 (BiocManager 1.30.21.1), R 4.3.1 (2023-06-16)
#> Installing package(s) 'ontologyIndex'
library(bugsigdbr)
ef <- getOntology('efo')
#> Loading required namespace: ontologyIndex
#> Using cached version from 2023-08-09 14:54:57
ef
#> Ontology with 44661 terms
#> 
#> format-version: 1.2
#> data-version: http://www.ebi.ac.uk/efo/releases/v3.56.0/efo.owl
#> ontology: http://www.ebi.ac.uk/efo/efo.owl
#> 
#> Properties:
#>  id: character
#>  name: character
#>  parents: list
#>  children: list
#>  ancestors: list
#>  obsolete: logical
#>  equivalent_to: list
#> Roots:
#>  EFO:0000001 - experimental factor
#>  EFO:0000824 - relationship
#>  has_characteristic - bearer_of
#>  RO:0000057 - has_participant
#>  has_part - has part
#>  RO:0000056 - participates_in
#>  RO:0002502 - depends on
#>  disease_has_feature - disease has feature
#>  located_in - located_in
#>  location_of - location_of
#>  ... 49 more
ub <- getOntology('uberon')
#> Error: download failed; see warnings()
ub
#> Error in eval(expr, envir, enclos): object 'ub' not found
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.1 (2023-06-16)
#>  os       Pop!_OS 22.04 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2023-08-09
#>  pandoc   3.1.1 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package       * version   date (UTC) lib source
#>  BiocFileCache   2.8.0     2023-04-25 [1] Bioconductor
#>  BiocManager     1.30.21.1 2023-07-18 [1] RSPM (R 4.3.1)
#>  bit             4.0.5     2022-11-15 [1] CRAN (R 4.3.1)
#>  bit64           4.0.5     2020-08-30 [1] CRAN (R 4.3.1)
#>  blob            1.2.4     2023-03-17 [1] CRAN (R 4.3.1)
#>  bugsigdbr     * 1.6.4     2023-07-30 [1] Bioconductor
#>  cachem          1.0.8     2023-05-01 [1] CRAN (R 4.3.1)
#>  cli             3.6.1     2023-03-23 [1] CRAN (R 4.3.1)
#>  curl            5.0.1     2023-06-07 [1] CRAN (R 4.3.1)
#>  DBI             1.1.3     2022-06-18 [1] CRAN (R 4.3.1)
#>  dbplyr          2.3.3     2023-07-07 [1] CRAN (R 4.3.1)
#>  digest          0.6.33    2023-07-07 [1] CRAN (R 4.3.1)
#>  dplyr           1.1.2     2023-04-20 [1] CRAN (R 4.3.1)
#>  evaluate        0.21      2023-05-05 [1] CRAN (R 4.3.1)
#>  fansi           1.0.4     2023-01-22 [1] CRAN (R 4.3.1)
#>  fastmap         1.1.1     2023-02-24 [1] CRAN (R 4.3.1)
#>  filelock        1.0.2     2018-10-05 [1] RSPM (R 4.3.1)
#>  fs              1.6.3     2023-07-20 [1] CRAN (R 4.3.1)
#>  generics        0.1.3     2022-07-05 [1] CRAN (R 4.3.1)
#>  glue            1.6.2     2022-02-24 [1] CRAN (R 4.3.1)
#>  htmltools       0.5.5     2023-03-23 [1] CRAN (R 4.3.1)
#>  httr            1.4.6     2023-05-08 [1] CRAN (R 4.3.1)
#>  knitr           1.43      2023-05-25 [1] CRAN (R 4.3.1)
#>  lifecycle       1.0.3     2022-10-07 [1] CRAN (R 4.3.1)
#>  magrittr        2.0.3     2022-03-30 [1] CRAN (R 4.3.1)
#>  memoise         2.0.1     2021-11-26 [1] CRAN (R 4.3.1)
#>  ontologyIndex   2.11      2023-05-30 [1] RSPM (R 4.3.1)
#>  pillar          1.9.0     2023-03-22 [1] CRAN (R 4.3.1)
#>  pkgconfig       2.0.3     2019-09-22 [1] CRAN (R 4.3.1)
#>  purrr           1.0.1     2023-01-10 [1] CRAN (R 4.3.1)
#>  R6              2.5.1     2021-08-19 [1] CRAN (R 4.3.1)
#>  reprex          2.0.2     2022-08-17 [1] CRAN (R 4.3.1)
#>  rlang           1.1.1     2023-04-28 [1] CRAN (R 4.3.1)
#>  rmarkdown       2.23      2023-07-01 [1] CRAN (R 4.3.1)
#>  RSQLite         2.3.1     2023-04-03 [1] RSPM (R 4.3.1)
#>  rstudioapi      0.15.0    2023-07-07 [1] CRAN (R 4.3.1)
#>  sessioninfo     1.2.2     2021-12-06 [1] CRAN (R 4.3.1)
#>  tibble          3.2.1     2023-03-20 [1] CRAN (R 4.3.1)
#>  tidyselect      1.2.0     2022-10-10 [1] CRAN (R 4.3.1)
#>  utf8            1.2.3     2023-01-31 [1] CRAN (R 4.3.1)
#>  vctrs           0.6.3     2023-06-14 [1] CRAN (R 4.3.1)
#>  withr           2.5.0     2022-03-03 [1] CRAN (R 4.3.1)
#>  xfun            0.39      2023-04-20 [1] CRAN (R 4.3.1)
#>  yaml            2.3.7     2023-01-23 [1] CRAN (R 4.3.1)
#> 
#>  [1] /home/user/R/x86_64-pc-linux-gnu-library/4.3
#>  [2] /home/user/apps/R-4.3.1/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Created on 2023-08-09 with reprex v2.0.2

sdgamboa commented 11 months ago

warnings() didn't give me an output.

lgeistlinger commented 11 months ago

Thanks Samuel for reporting this. It looks like the source url http://ontologies.berkeleybop.org/uberon.obo was down yesterday, but it seems to be back up, and working for me. Can you confirm?

> ub <- getOntology("uberon", cache = FALSE)
  |======================================================================| 100%
> ub
Ontology with 14107 terms

format-version: 1.2
data-version: releases/2020-09-16
default-namespace: uberon
ontology: uberon

Properties:
    id: character
    name: character
    parents: list
    children: list
    ancestors: list
    obsolete: logical
Roots:
    part_of - part of
    has_part - has part
    functionally_related_to - functionally related to
    UBERON:0001062 - anatomical entity
    adjacent_to - adjacent_to
    UBERON:0000000 - processual entity
    anterior_to - anterior_to
    posterior_to - posterior_to
    attaches_to_part_of - attaches_to_part_of
    bearer_of - bearer of
 ... 127 more
lgeistlinger commented 11 months ago

We might want to consider changing the source url to http://purl.obolibrary.org/obo/uberon/uberon-simple.obo in the near future

sdgamboa commented 11 months ago

@lgeistlinger, thanks! It's working now. I'll close the issue.