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This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1467/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.12.1  (landing page)
Denes Turei
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_19
git_last_commit: a310819
git_last_commit_date: 2024-05-29 08:39:10 -0400 (Wed, 29 May 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for OmnipathR on lconway

To the developers/maintainers of the OmnipathR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.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.

raw results


Summary

Package: OmnipathR
Version: 3.12.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
StartedAt: 2024-06-09 17:34:52 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 17:36:25 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 93.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
###
##############################################################################
##############################################################################


* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* preparing ‘OmnipathR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 17:35:11] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 17:35:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/Rtmp2cyc6D/Rinst180f818a3314c/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/Rtmp2cyc6D/Rinst180f818a3314c/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/Rtmp2cyc6D/Rinst180f818a3314c/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/Rtmp2cyc6D/Rinst180f818a3314c/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 17:35:11] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-06-09 17:35:11] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 17:35:12] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 17:35:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 17:35:12] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 17:35:12] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 17:35:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 17:35:12] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-06-09 17:35:12] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-06-09 17:35:12] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:35:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:35:13] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:35:13] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 17:35:18] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:35:18] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:35:18] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 17:35:23] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:35:23] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:35:23] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403

Quitting from lines 225-227 [network] (bioc_workshop.Rmd)
Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error:
! HTTP 403
--- failed re-building ‘bioc_workshop.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2024-06-09 17:35:24] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `(function (to, from = "accession", reviewed = TRUE, organism = 9606) `.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `{`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    .slow_doctest()`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    From <- To <- NULL`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    strip_semicol <- function(v) {`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `        sub(";$", "", v)`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    }`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    ids <- c(.nse_ensure_str(!!enquo(to)), .nse_ensure_str(!!enquo(from)))`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    reviewed <- if ("trembl" %in% ids) `.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `        FALSE`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    else if ("swissprot" %in% ids) `.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `        TRUE`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    else reviewed`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    to <- .nse_ensure_str(!!enquo(to)) %>% uniprot_id_type`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    from <- .nse_ensure_str(!!enquo(from)) %>% uniprot_id_type`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    reens <- "ENS[A-Z]+\\d+"`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    to_ens <- to == "xref_ensembl"`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    from_ens <- from == "xref_ensembl"`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    log_trace(paste0("Creating ID mapping table from `%s` to `%s`, ", `.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `        "for organism %d (only reviewed: %s)"), from, to, organism, `.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `        reviewed)`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    c(from, to) %>% all_uniprots(reviewed = reviewed, organism = organism) %>% `.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `        rename(From = 1, To = 2) %>% mutate(From = strip_semicol(From), `.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `        To = strip_semicol(To)) %>% separate_rows(From, sep = "[; ]") %>% `.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `        separate_rows(To, sep = "[; ]") %>% filter(!is.na(From) & `.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `        !is.na(To)) %>% {`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `        if (from_ens) `.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `            mutate(., From = str_extract(From, reens))`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `        else .`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    } %>% {`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `        if (to_ens) `.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `            mutate(., To = str_extract(To, reens))`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `        else .`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `    } %>% trim_and_distinct`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] Bypassing call: `})(to = "genesymbol", organism = 9606L)`.
[2024-06-09 17:35:24] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-06-09 17:35:24] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2024-06-09 17:35:36] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 17:35:36] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 17:35:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 17:35:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 17:35:36] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2024-06-09 17:35:36] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2024-06-09 17:35:36] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:35:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:35:37] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:35:37] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 17:35:42] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:35:42] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:35:42] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 17:35:47] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:35:47] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:35:47] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403

Quitting from lines 46-51 [unnamed-chunk-2] (drug_targets.Rmd)
Error: processing vignette 'drug_targets.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error:
! HTTP 403
--- failed re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2024-06-09 17:35:47] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 17:35:47] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 17:35:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 17:35:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 17:35:47] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3.
[2024-06-09 17:35:47] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html
[2024-06-09 17:35:47] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:35:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:35:48] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:35:48] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 17:35:53] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:35:53] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:35:53] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 17:35:58] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:35:58] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:35:58] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403

Quitting from lines 56-58 [load-interactions] (extra_attrs.Rmd)
Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error:
! HTTP 403
--- failed re-building ‘extra_attrs.Rmd’

--- re-building ‘nichenet.Rmd’ using rmarkdown
--- finished re-building ‘nichenet.Rmd’

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2024-06-09 17:36:03] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-09 17:36:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 17:36:03] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 17:36:03] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 17:36:03] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 17:36:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 17:36:03] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 4.
[2024-06-09 17:36:03] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-4.html
[2024-06-09 17:36:03] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:36:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:36:03] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:36:03] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 17:36:09] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:36:09] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:36:09] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 17:36:14] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:36:14] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:36:14] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403

Quitting from lines 167-178 [interactions] (omnipath_intro.Rmd)
Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error:
! HTTP 403
--- failed re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2024-06-09 17:36:14] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 17:36:14] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 17:36:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 17:36:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 17:36:14] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 5.
[2024-06-09 17:36:14] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-5.html
[2024-06-09 17:36:14] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:36:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:36:14] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:36:14] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 17:36:19] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:36:19] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:36:19] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 17:36:24] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 17:36:25] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 17:36:25] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403

Quitting from lines 56-67 [tfcensus-op] (paths.Rmd)
Error: processing vignette 'paths.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error:
! HTTP 403
--- failed re-building ‘paths.Rmd’

SUMMARY: processing the following files failed:
  ‘bioc_workshop.Rmd’ ‘drug_targets.Rmd’ ‘extra_attrs.Rmd’ ‘omnipath_intro.Rmd’ ‘paths.Rmd’

Error: Vignette re-building failed.
Execution halted