[ Started: 2024-03-22 17:58:46 CET ] [ OmnipathR v3.11.8 for BioC-3.19 from https://github.com/saezlab/OmnipathR@master (99a4f09 2024-03-22 11:55:42) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-03-22_1751/OmnipathR/OmnipathR.Rcheck’ * using R Under development (unstable) (2024-03-21 r86166) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.11.8’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... WARNING Found the following significant warnings: Warning: OmnipathR.Rd:3: docType ‘_PACKAGE’ is unrecognized See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-03-22_1751/OmnipathR/OmnipathR.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: doc 4.8Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2024-03-22 17:59:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-22 17:59:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-22 17:59:07] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-22 17:59:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-22 17:59:07] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-22 17:59:07] [TRACE] [OmnipathR] Contains 1 files. [2024-03-22 17:59:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-22 17:59:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-22 17:59:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-22 17:59:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-22 17:59:07] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-22 17:59:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-03-22_1751/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-22 17:59:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-22 17:59:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-03-22_1751/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-22 17:59:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-22 17:59:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-03-22_1751/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-22 17:59:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-22 17:59:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-03-22_1751/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-22 17:59:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-22 17:59:07] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2024-03-22 17:59:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-22 17:59:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-22 17:59:14] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-22 17:59:14] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-22 17:59:14] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-22 17:59:14] [TRACE] [OmnipathR] Contains 1 files. [2024-03-22 17:59:14] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-22 17:59:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-22 17:59:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-22 17:59:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-22 17:59:14] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-22 17:59:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-03-22_1751/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-22 17:59:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-22 17:59:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-03-22_1751/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-22 17:59:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-22 17:59:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-03-22_1751/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-22 17:59:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-22 17:59:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-03-22_1751/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-22 17:59:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-22 17:59:14] [TRACE] [OmnipathR] Cache locked: FALSE * checking Rd files ... WARNING prepare_Rd: OmnipathR.Rd:3: docType ‘_PACKAGE’ is unrecognized * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > ### Name: pivot_annotations > ### Title: Converts annotation tables to a wide format > ### Aliases: pivot_annotations > > ### ** Examples > > # single resource: the result is a data frame > disgenet <- import_omnipath_annotations(resources = 'DisGeNet') > disgenet <- pivot_annotations(disgenet) > disgenet # A tibble: 128,267 × 11 uniprot genesymbol entity_type disease type score dsi dpi nof_pmids 1 P04217 A1BG protein Hepatomegaly phen… 0.3 0.7 0.538 1 2 P04217 A1BG protein Schizophren… dise… 0.3 0.7 0.538 1 3 P01023 A2M protein Alzheimer D… dise… 0.3 0.529 0.769 3 4 P01023 A2M protein Depressive … dise… 0.3 0.529 0.769 2 5 P01023 A2M protein Fibrosis, L… dise… 0.3 0.529 0.769 1 6 P01023 A2M protein alpha-2-Mac… dise… 0.31 0.529 0.769 0 7 P01023 A2M protein Nephrotic S… group 0.51 0.529 0.769 1 8 P01023 A2M protein Alzheimer D… dise… 0.37 0.529 0.769 3 9 P01023 A2M protein Lung Neopla… group 0.3 0.529 0.769 2 10 P01023 A2M protein Liver Cirrh… dise… 0.3 0.529 0.769 1 # ℹ 128,257 more rows # ℹ 2 more variables: nof_snps , source > # # A tibble: 126,588 × 11 > # uniprot genesymbol entity_type disease type score dsi dpi > # > # 1 P04217 A1BG protein Schizophren. dise. 0.3 0.7 0.538 > # 2 P04217 A1BG protein Hepatomegaly phen. 0.3 0.7 0.538 > # 3 P01023 A2M protein Fibrosis, L. dise. 0.3 0.529 0.769 > # 4 P01023 A2M protein Acute kidne. dise. 0.3 0.529 0.769 > # 5 P01023 A2M protein Mental Depr. dise. 0.3 0.529 0.769 > # # . with 126,583 more rows, and 3 more variables: nof_pmids , > # # nof_snps , source > > # multiple resources: the result is a list > annotations <- import_omnipath_annotations( + resources = c('DisGeNet', 'SignaLink_function', 'DGIdb', 'kinase.com') + ) > annotations <- pivot_annotations(annotations) Error in UseMethod("pull") : no applicable method for 'pull' applied to an object of class "list" Calls: pivot_annotations -> %>% -> unique -> pull Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 10. │ ├─vctrs:::result_get(...) 11. │ └─vctrs:::vec_as_location2_result(...) 12. │ ├─base::tryCatch(...) 13. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ └─vctrs::vec_as_location(i, n, names = names, arg = arg, call = call) 17. └─vctrs (local) ``() 18. └─vctrs:::stop_subscript_oob(...) 19. └─vctrs:::stop_subscript(...) 20. └─rlang::abort(...) [ FAIL 4 | WARN 1 | SKIP 0 | PASS 5 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 2 WARNINGs, 4 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-03-22_1751/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2024-03-22 18:11:48 CET ]