• using R Under development (unstable) (2024-12-19 r87451)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-8) 14.2.0     GNU Fortran (Debian 14.2.0-8) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘aPEAR/DESCRIPTION’ ... OK
• this is package ‘aPEAR’ version ‘1.0.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Packages suggested but not available for checking:   'Spectrum', 'clusterProfiler', 'DOSE'
• 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 ‘aPEAR’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [2s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
• checking loading without being on the library search path ... [2s/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 ... [12s/16s] OK
• checking Rd files ... [0s/0s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 ... [3s/4s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [10s/12s] ERROR   Running ‘testthat.R’ [10s/12s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > # This file is part of the standard setup for testthat.   > # It is recommended that you do not modify it.   > #   > # Where should you do additional test configuration?   > # Learn more about the roles of various files in:   > # * https://r-pkgs.org/tests.html   > # * https://testthat.r-lib.org/reference/test_package.html#special-files   >   > library(testthat)   > library(aPEAR)   >   > test_check("aPEAR")      Attaching package: 'dplyr'      The following object is masked from 'package:testthat':          matches      The following objects are masked from 'package:stats':          filter, lag      The following objects are masked from 'package:base':          intersect, setdiff, setequal, union      [ FAIL 3 | WARN 4 | SKIP 1 | PASS 101 ]      ══ Skipped tests (1) ═══════════════════════════════════════════════════════════   • empty test (1): 'test-prepareEnrichment.R:1:1'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-cluster.R:5:3'): spectral clustering returns correct data format ──   Error in `spectral(sim, verbose = FALSE)`: Package Spectrum is required to use "spectral" clustering method.   Backtrace:       ▆    1. └─aPEAR:::spectral(sim, verbose = FALSE) at test-cluster.R:5:3   ── Error ('test-cluster.R:55:3'): pathwayClusters returns something for all implemented methods ──   Error in `spectral(sim, verbose)`: Package Spectrum is required to use "spectral" clustering method.   Backtrace:       ▆    1. └─aPEAR:::pathwayClusters(sim, method = "s") at test-cluster.R:55:3    2. └─aPEAR:::spectral(sim, verbose)   ── Error ('test-cluster.R:63:3'): pathwayClusters filters out by cluster size ──   Error in `spectral(sim, verbose)`: Package Spectrum is required to use "spectral" clustering method.   Backtrace:       ▆    1. └─aPEAR:::pathwayClusters(sim, method = "s", minClusterSize = 13) at test-cluster.R:63:3    2. └─aPEAR:::spectral(sim, verbose)      [ FAIL 3 | WARN 4 | SKIP 1 | PASS 101 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [0s/0s] NOTE Note: skipping ‘aPEAR-vignette.Rmd’ due to unavailable dependencies:   'clusterProfiler'
• checking PDF version of manual ... [3s/5s] OK
• checking HTML version of manual ... [0s/0s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE