Last updated on 2025-09-16 12:52:28 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| driveR | 4 | 1 | 8 |
| PANACEA | 1 | 12 | |
| pathfindR | 4 | 9 | |
| pathfindR.data | 3 | 10 |
Current CRAN status: ERROR: 4, NOTE: 1, OK: 8
Version: 0.4.1
Check: package dependencies
Result: ERROR
Packages required but not available:
'TxDb.Hsapiens.UCSC.hg19.knownGene',
'TxDb.Hsapiens.UCSC.hg38.knownGene', 'org.Hs.eg.db'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-release-macos-arm64
Version: 0.4.1
Check: package dependencies
Result: ERROR
Packages required but not available:
'TxDb.Hsapiens.UCSC.hg19.knownGene',
'TxDb.Hsapiens.UCSC.hg38.knownGene'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.4.1
Check: installed package size
Result: NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 1.6Mb
extdata 3.2Mb
Flavor: r-oldrel-windows-x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 1.0.1
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
Current CRAN status: ERROR: 4, OK: 9
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
Current CRAN status: NOTE: 3, OK: 10
Version: 2.1.0
Check: installed package size
Result: NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
R 4.0Mb
data 1.5Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64