[ Started: 2024-09-29 15:57:06 CEST ]
[ OmnipathR v3.12.3 for BioC-3.19 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_19 (7085ced 2024-08-16 13:11:39) ]

* checking for file ‘./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
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 15:57:17] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Contains 1 files.
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 15:57:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpGdG6Yu/Rinst286c8844d0b77/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpGdG6Yu/Rinst286c8844d0b77/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpGdG6Yu/Rinst286c8844d0b77/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpGdG6Yu/Rinst286c8844d0b77/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-09-29 15:57:17] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 15:57:17] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 15:57:17] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 15:57:17] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] HTTP 200
[2024-09-29 15:57:17] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 15:57:17] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 15:57:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 15:57:17] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 15:57:17] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-29 15:57:17] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-29 15:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 15:57:17] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.

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 in `full_join()`:
! Can't join `x$ncbi_tax_id` with `y$ncbi_tax_id` due to incompatible types.
ℹ `x$ncbi_tax_id` is a <integer>.
ℹ `y$ncbi_tax_id` is a <character>.
--- failed re-building ‘bioc_workshop.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2024-09-29 15:57:18] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `(function (to, from = "accession", reviewed = TRUE, organism = 9606) `.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `{`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    .slow_doctest()`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    From <- To <- NULL`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    strip_semicol <- function(v) {`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `        sub(";$", "", v)`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    }`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    ids <- c(.nse_ensure_str(!!enquo(to)), .nse_ensure_str(!!enquo(from)))`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    reviewed <- if ("trembl" %in% ids) `.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `        FALSE`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    else if ("swissprot" %in% ids) `.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `        TRUE`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    else reviewed`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    to <- .nse_ensure_str(!!enquo(to)) %>% uniprot_id_type`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    from <- .nse_ensure_str(!!enquo(from)) %>% uniprot_id_type`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    reens <- "ENS[A-Z]+\\d+"`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    to_ens <- to == "xref_ensembl"`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    from_ens <- from == "xref_ensembl"`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    log_trace(paste0("Creating ID mapping table from `%s` to `%s`, ", `.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `        "for organism %d (only reviewed: %s)"), from, to, organism, `.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `        reviewed)`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    c(from, to) %>% all_uniprots(reviewed = reviewed, organism = organism) %>% `.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `        rename(From = 1, To = 2) %>% mutate(From = strip_semicol(From), `.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `        To = strip_semicol(To)) %>% separate_rows(From, sep = "[; ]") %>% `.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `        separate_rows(To, sep = "[; ]") %>% filter(!is.na(From) & `.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `        !is.na(To)) %>% {`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `        if (from_ens) `.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `            mutate(., From = str_extract(From, reens))`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `        else .`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    } %>% {`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `        if (to_ens) `.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `            mutate(., To = str_extract(To, reens))`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `        else .`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `    } %>% trim_and_distinct`.
[2024-09-29 15:57:18] [TRACE]   [OmnipathR] Bypassing call: `})(to = "genesymbol", organism = 9606L)`.
[2024-09-29 15:57:18] [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.
[2024-09-29 15:57:18] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2024-09-29 15:57:29] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 15:57:29] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 15:57:29] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 15:57:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 15:57:29] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.

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 in `full_join()`:
! Can't join `x$ncbi_tax_id` with `y$ncbi_tax_id` due to incompatible types.
ℹ `x$ncbi_tax_id` is a <integer>.
ℹ `y$ncbi_tax_id` is a <character>.
--- failed re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2024-09-29 15:57:29] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 15:57:29] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 15:57:29] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 15:57:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 15:57:29] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.

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 in `full_join()`:
! Can't join `x$ncbi_tax_id` with `y$ncbi_tax_id` due to incompatible types.
ℹ `x$ncbi_tax_id` is a <integer>.
ℹ `y$ncbi_tax_id` is a <character>.
--- failed re-building ‘extra_attrs.Rmd’

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

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2024-09-29 15:57:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-29 15:57:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-29 15:57:30] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 15:57:30] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 15:57:30] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 15:57:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 15:57:31] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.

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 in `full_join()`:
! Can't join `x$ncbi_tax_id` with `y$ncbi_tax_id` due to incompatible types.
ℹ `x$ncbi_tax_id` is a <integer>.
ℹ `y$ncbi_tax_id` is a <character>.
--- failed re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2024-09-29 15:57:31] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-29 15:57:31] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-29 15:57:31] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-29 15:57:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-29 15:57:31] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.

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 in `full_join()`:
! Can't join `x$ncbi_tax_id` with `y$ncbi_tax_id` due to incompatible types.
ℹ `x$ncbi_tax_id` is a <integer>.
ℹ `y$ncbi_tax_id` is a <character>.
--- 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
[ Finished: 2024-09-29 15:57:31 CEST ]