- using R version 4.3.3 (2024-02-29 ucrt)
- using platform: x86_64-w64-mingw32 (64-bit)
- R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
- checking for file 'pathfindR/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'pathfindR' version '2.3.1'
- 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 whether package 'pathfindR' can be installed ... OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking 'build' 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 R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [3s] OK
- checking whether the package can be loaded with stated dependencies ... [2s] OK
- checking whether the package can be unloaded cleanly ... [3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s] OK
- checking loading without being on the library search path ... [3s] OK
- checking startup messages can be suppressed ... [3s] OK
- checking use of S3 registration ... OK
- 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 ... [13s] OK
- checking Rd files ... [1s] 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 installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ... [46s] OK
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [121s] ERROR
Running 'testthat-active_snw.R' [32s]
Running 'testthat-clustering.R' [6s]
Running 'testthat-comparison.R' [4s]
Running 'testthat-core.R' [4s]
Running 'testthat-data_generation.R' [4s]
Running 'testthat-enrichment.R' [38s]
Running 'testthat-scoring.R' [4s]
Running 'testthat-utility.R' [19s]
Running 'testthat-visualization.R' [6s]
Running 'testthat-zzz.R' [4s]
Running the tests in 'tests/testthat-enrichment.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 = "enrichment")
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 36 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-enrichment.R:123:5'): `enrichment_analyses()` -- returns a data frame ──
enr_res1 <- ... inherits from `'NULL'` not `'character'`.
── Failure ('test-enrichment.R:127:5'): `enrichment_analyses()` -- returns a data frame ──
nrow(enr_res1) <= total is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test-enrichment.R:130:5'): `enrichment_analyses()` -- returns a data frame ──
enr_res2 <- ... inherits from `'NULL'` not `'character'`.
── Failure ('test-enrichment.R:132:5'): `enrichment_analyses()` -- returns a data frame ──
ncol(enr_res2) == ncol(enr_res1) + 1 is not TRUE
`actual`:
`expected`: TRUE
── Error ('test-enrichment.R:143:9'): `summarize_enrichment_results()` -- returns summarized enrichment results ──
Error in `summarize_enrichment_results(enrichment_res = combined_res[,
-6])`: `enrichment_res` should be a data frame
Backtrace:
▆
1. ├─testthat::expect_is(...) at test-enrichment.R:143:9
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─pathfindR::summarize_enrichment_results(...)
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 36 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in 'inst/doc' ... OK
- checking re-building of vignette outputs ... [50s] OK
- checking PDF version of manual ... [19s] OK
- checking HTML version of manual ... [10s] OK
- DONE
Status: 1 ERROR