Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-03 11:49 -0400 (Thu, 03 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
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 1442/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OmnipathR 3.13.26 (landing page) Denes Turei
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: OmnipathR |
Version: 3.13.26 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.13.26.tar.gz |
StartedAt: 2024-10-03 07:42:04 -0000 (Thu, 03 Oct 2024) |
EndedAt: 2024-10-03 08:02:33 -0000 (Thu, 03 Oct 2024) |
EllapsedTime: 1228.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: OmnipathR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.13.26.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.13.26’ * 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 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 ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * 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 [2024-10-03 07:42:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-03 07:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:42:36] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-10-03 07:42:36] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-03 07:42:36] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-10-03 07:42:36] [TRACE] [OmnipathR] Contains 1 files. [2024-10-03 07:42:36] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-03 07:42:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-03 07:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:42:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-10-03 07:42:36] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-10-03 07:42:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-03 07:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:42:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-03 07:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:42:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-03 07:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:42:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-03 07:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:42:36] [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 [2024-10-03 07:42:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-03 07:42:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:42:53] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-10-03 07:42:53] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-03 07:42:53] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-10-03 07:42:53] [TRACE] [OmnipathR] Contains 1 files. [2024-10-03 07:42:53] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-03 07:42:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-03 07:42:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:42:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-10-03 07:42:53] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-10-03 07:42:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-03 07:42:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:42:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-03 07:42:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:42:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-03 07:42:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:42:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-03 07:42:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:42:53] [TRACE] [OmnipathR] Cache locked: FALSE oma_organisms: no visible binding for global variable ‘ncbi_tax_id’ Undefined global functions or variables: ncbi_tax_id * checking Rd files ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: all_uniprots > ### Title: A table with all UniProt records > ### Aliases: all_uniprots > > ### ** Examples > > human_swissprot_entries <- all_uniprots(fields = 'id') [2024-10-03 07:43:33] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-10-03 07:43:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-03 07:43:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:43:33] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-10-03 07:43:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-03 07:43:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:43:33] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-10-03 07:43:33] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-10-03 07:43:33] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-10-03 07:43:33] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-10-03 07:46:37] [WARN] [OmnipathR] HTTP 404 [2024-10-03 07:46:37] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404 [2024-10-03 07:46:42] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-10-03 07:49:44] [WARN] [OmnipathR] HTTP 404 [2024-10-03 07:49:44] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404 [2024-10-03 07:49:49] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-10-03 07:52:51] [WARN] [OmnipathR] HTTP 404 [2024-10-03 07:52:51] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404 Error in `map_int()`: ℹ In index: 1. Caused by error: ! HTTP 404 Backtrace: ▆ 1. ├─OmnipathR::all_uniprots(fields = "id") 2. │ └─organism %<>% ncbi_taxid 3. ├─OmnipathR::ncbi_taxid(.) 4. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 5. ├─purrr::map_int(., taxon_name, "ncbi") 6. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 7. │ ├─purrr:::with_indexed_errors(...) 8. │ │ └─base::withCallingHandlers(...) 9. │ ├─purrr:::call_with_cleanup(...) 10. │ └─OmnipathR (local) .f(.x[[i]], ...) 11. │ ├─... %>% if_null_len0(NA) 12. │ └─OmnipathR::get_db("organisms") 13. │ └─OmnipathR::load_db(key, param = param) 14. │ ├─rlang::exec(loader, !!!param) 15. │ └─OmnipathR (local) `<fn>`() 16. │ ├─... %>% ... 17. │ └─OmnipathR::ensembl_organisms() 18. │ ├─... %>% ... 19. │ └─OmnipathR::ensembl_organisms_raw() 20. │ └─... %>% html_table() 21. ├─OmnipathR:::if_null_len0(., NA) 22. │ └─value1 %>% is_empty_2 %>% if (value2) value1 23. ├─OmnipathR:::is_empty_2(.) 24. │ └─value %>% ... 25. ├─dplyr::first(.) 26. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm) 27. │ └─vctrs::vec_size(x) 28. ├─dplyr::pull(., name_type) 29. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name)) 30. ├─dplyr::select(., -latin_name.x, -latin_name.y) 31. ├─dplyr::mutate(...) 32. ├─dplyr::full_join(...) 33. ├─dplyr::mutate(...) 34. ├─dplyr::select(...) 35. ├─rvest::html_table(.) 36. ├─rvest::html_element(., "table") 37. ├─xml2::read_html(.) 38. ├─OmnipathR:::download_to_cache(., req_headers = user_agent()) 39. │ └─OmnipathR:::download_base(...) 40. │ └─base::stop(result) 41. └─purrr (local) `<fn>`(`<smplErrr>`) 42. └─cli::cli_abort(...) 43. └─rlang::abort(...) 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: Caused by error in `map_int()`: ℹ In index: 1. Caused by error: ! HTTP 404 Class: purrr_error_indexed/rlang_error/error/condition ── Error ('test_import.R:182:13'): (code run outside of `test_that()`) ───────── Error in `eval(code, test_env)`: object 'response' not found Backtrace: ▆ 1. ├─response %<>% separate_rows(sources, sep = ";") at test_import.R:182:13 2. └─tidyr::separate_rows(., sources, sep = ";") [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! Package textcomp Error: Symbol \textrightarrow not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead. See the textcomp package documentation for explanation. * checking PDF version of manual without index ... ERROR * DONE Status: 3 ERRORs, 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘OmnipathR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-10-02 19:54:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-02 19:54:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-02 19:54:23] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-10-02 19:54:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-02 19:54:23] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-10-02 19:54:23] [TRACE] [OmnipathR] Contains 6 files. [2024-10-02 19:54:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-02 19:54:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-02 19:54:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-02 19:54:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-10-02 19:54:23] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-10-02 19:54:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-02 19:54:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-02 19:54:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-02 19:54:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-02 19:54:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-02 19:54:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-02 19:54:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-02 19:54:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-02 19:54:23] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-10-02 19:54:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-02 19:54:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-02 19:54:26] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-10-02 19:54:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-02 19:54:26] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-10-02 19:54:26] [TRACE] [OmnipathR] Contains 1 files. [2024-10-02 19:54:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-02 19:54:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-02 19:54:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-02 19:54:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-10-02 19:54:26] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-10-02 19:54:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-02 19:54:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-02 19:54:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-02 19:54:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-02 19:54:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-02 19:54:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-02 19:54:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-02 19:54:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-02 19:54:26] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > #!/usr/bin/env Rscript > > # > # This file is part of the `OmnipathR` R package > # > # Copyright > # 2018-2024 > # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University > # > # File author(s): Alberto Valdeolivas > # Dénes Türei (turei.denes@gmail.com) > # Attila Gábor > # > # Distributed under the MIT (Expat) License. > # See accompanying file `LICENSE` or find a copy at > # https://directory.fsf.org/wiki/License:Expat > # > # Website: https://r.omnipathdb.org/ > # Git repo: https://github.com/saezlab/OmnipathR > # > > > library(testthat) > library(OmnipathR) [2024-10-03 07:52:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-03 07:52:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:52:56] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-10-03 07:52:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-03 07:52:56] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-10-03 07:52:56] [TRACE] [OmnipathR] Contains 2 files. [2024-10-03 07:52:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-03 07:52:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-03 07:52:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:52:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-10-03 07:52:56] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-10-03 07:52:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-03 07:52:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:52:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-03 07:52:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:52:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-03 07:52:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:52:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-03 07:52:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-03 07:52:56] [TRACE] [OmnipathR] Cache locked: FALSE > > test_check('OmnipathR') [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_import.R:169:9'): Testing `complexes` ──────────────────────── `assign("response", method(resources = resources), envir = top_env)` threw an error. Message: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error: ! HTTP 404 Class: purrr_error_indexed/rlang_error/error/condition ── Error ('test_import.R:182:13'): (code run outside of `test_that()`) ───────── Error in `eval(code, test_env)`: object 'response' not found Backtrace: ▆ 1. ├─response %<>% separate_rows(sources, sep = ";") at test_import.R:182:13 2. └─tidyr::separate_rows(., sources, sep = ";") [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0 | 0 | 0 | |
all_uniprot_acs | 0.031 | 0.000 | 0.031 | |