CRAN Package Check Results for Package pathfindR

Last updated on 2025-09-16 21:50:39 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	2.5.1	11.26	270.95	282.21	OK
r-devel-linux-x86_64-debian-gcc	2.5.1	8.27	184.76	193.03	OK
r-devel-linux-x86_64-fedora-clang	2.5.1			461.67	ERROR
r-devel-linux-x86_64-fedora-gcc	2.5.1			458.27	OK
r-devel-windows-x86_64	2.5.1	14.00	265.00	279.00	OK
r-patched-linux-x86_64	2.5.1	11.94	241.06	253.00	OK
r-release-linux-x86_64	2.5.1	10.14	259.99	270.13	OK
r-release-macos-arm64	2.5.1			6.00	ERROR
r-release-macos-x86_64	2.5.1			202.00	OK
r-release-windows-x86_64	2.5.1	14.00	274.00	288.00	OK
r-oldrel-macos-arm64	2.5.1			11.00	ERROR
r-oldrel-macos-x86_64	2.5.1			12.00	ERROR
r-oldrel-windows-x86_64	2.5.1	18.00	360.00	378.00	OK

Additional issues

ATLAS

Check Details

Version: 2.5.1
Check: tests
Result: ERROR Running ‘testthat-active_snw.R’ [48s/111s] Running ‘testthat-clustering.R’ [10s/28s] Running ‘testthat-comparison.R’ [6s/14s] Running ‘testthat-core.R’ [5s/13s] Running ‘testthat-data_generation.R’ [6s/23s] Running ‘testthat-enrichment.R’ [45s/80s] Running ‘testthat-scoring.R’ [7s/11s] Running ‘testthat-utility.R’ [28s/38s] Running ‘testthat-visualization.R’ [12s/14s] Running ‘testthat-zzz.R’ Running the tests in ‘tests/testthat-data_generation.R’ failed. Complete output: > library(testthat) > library(pathfindR) Loading required package: pathfindR.data ############################################################################## Welcome to pathfindR! Please cite the article below if you use pathfindR in published reseach: Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet. doi:10.3389/fgene.2019.00858 ############################################################################## > > test_check("pathfindR", filter = "data_generation") [ FAIL 1 | WARN 0 | SKIP 2 | PASS 18 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test-data_generation.R:94:3', 'test-data_generation.R:119:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-data_generation.R:49:3'): `get_biogrid_pin()` -- determines and downloads the latest version ── <curl_error_operation_timedout/curl_error/error/condition> Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [downloads.thebiogrid.org]: Connection timed out after 10001 milliseconds Backtrace: ▆ 1. ├─pathfindR:::get_biogrid_pin() at test-data_generation.R:49:3 2. │ └─httr::GET("https://downloads.thebiogrid.org/BioGRID/Latest-Release/") 3. │ └─httr:::request_perform(req, hu$handle$handle) 4. │ ├─httr:::request_fetch(req$output, req$url, handle) 5. │ └─httr:::request_fetch.write_memory(req$output, req$url, handle) 6. │ └─curl::curl_fetch_memory(url, handle = handle) 7. └─curl:::raise_libcurl_error(...) [ FAIL 1 | WARN 0 | SKIP 2 | PASS 18 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.5.1
Check: package dependencies
Result: ERROR Package required but not available: ‘org.Hs.eg.db’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavor: r-release-macos-arm64

Version: 2.5.1
Check: package dependencies
Result: ERROR Package required and available but unsuitable version: ‘ggkegg’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavor: r-oldrel-macos-arm64

Version: 2.5.1
Check: package dependencies
Result: ERROR Package required but not available: ‘ggkegg’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavor: r-oldrel-macos-x86_64