[ Started: 2024-10-17 12:23:31 CEST ] [ OmnipathR v3.12.4 for BioC-3.19 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_19 (edb3c69 2024-10-02 12:46:04) ] * 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 [2024-10-17 12:23:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 12:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 12:23:42] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Contains 1 files. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 12:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 12:23:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpUQajr2/Rinst1c77e6129bb2e/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-17 12:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 12:23:42] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpUQajr2/Rinst1c77e6129bb2e/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-17 12:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 12:23:42] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpUQajr2/Rinst1c77e6129bb2e/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-17 12:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 12:23:42] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpUQajr2/Rinst1c77e6129bb2e/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-17 12:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 12:23:42] [TRACE] [OmnipathR] Cache locked: FALSE [2024-10-17 12:23:42] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 12:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 12:23:42] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 12:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 12:23:42] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-10-17 12:23:42] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-10-17 12:23:42] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-10-17 12:23:42] [TRACE] [OmnipathR] HTTP 200 [2024-10-17 12:23:42] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-10-17 12:23:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 12:23:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 12:23:42] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` 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 `UseMethod()`: ! no applicable method for 'html_table' applied to an object of class "xml_missing" --- failed re-building ‘bioc_workshop.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2024-10-17 12:23:42] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: `(function (to, from = "accession", reviewed = TRUE, organism = 9606) `. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: `{`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` .slow_doctest()`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` From <- To <- NULL`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` strip_semicol <- function(v) {`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` sub(";$", "", v)`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` }`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` ids <- c(.nse_ensure_str(!!enquo(to)), .nse_ensure_str(!!enquo(from)))`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` reviewed <- if ("trembl" %in% ids) `. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` FALSE`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` else if ("swissprot" %in% ids) `. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` TRUE`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` else reviewed`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` to <- .nse_ensure_str(!!enquo(to)) %>% uniprot_id_type`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` from <- .nse_ensure_str(!!enquo(from)) %>% uniprot_id_type`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` reens <- "ENS[A-Z]+\\d+"`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` to_ens <- to == "xref_ensembl"`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` from_ens <- from == "xref_ensembl"`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` log_trace(paste0("Creating ID mapping table from `%s` to `%s`, ", `. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` "for organism %d (only reviewed: %s)"), from, to, organism, `. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` reviewed)`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` c(from, to) %>% all_uniprots(reviewed = reviewed, organism = organism) %>% `. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` rename(From = 1, To = 2) %>% mutate(From = strip_semicol(From), `. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` To = strip_semicol(To)) %>% separate_rows(From, sep = "[; ]") %>% `. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` separate_rows(To, sep = "[; ]") %>% filter(!is.na(From) & `. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` !is.na(To)) %>% {`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` if (from_ens) `. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` mutate(., From = str_extract(From, reens))`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` else .`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` } %>% {`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` if (to_ens) `. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` mutate(., To = str_extract(To, reens))`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` else .`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: ` } %>% trim_and_distinct`. [2024-10-17 12:23:42] [TRACE] [OmnipathR] Bypassing call: `})(to = "genesymbol", organism = 9606L)`. [2024-10-17 12:23:42] [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. [2024-10-17 12:23:42] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2024-10-17 12:23:53] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-10-17 12:23:53] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-10-17 12:23:53] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html 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 `UseMethod()`: ! no applicable method for 'html_table' applied to an object of class "xml_missing" --- failed re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2024-10-17 12:23:53] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-10-17 12:23:53] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-10-17 12:23:53] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html 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 `UseMethod()`: ! no applicable method for 'html_table' applied to an object of class "xml_missing" --- failed re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2024-10-17 12:23:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-10-17 12:23:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 12:23:55] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-10-17 12:23:55] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-10-17 12:23:55] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html 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 `UseMethod()`: ! no applicable method for 'html_table' applied to an object of class "xml_missing" --- failed re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2024-10-17 12:23:55] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-10-17 12:23:55] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-10-17 12:23:55] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html 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 `UseMethod()`: ! no applicable method for 'html_table' applied to an object of class "xml_missing" --- 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: 2024-10-17 12:23:55 CEST ]