• using R version 4.5.2 (2025-10-31)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.3.0-10) 14.3.0     GNU Fortran (Debian 14.3.0-10) 14.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘dependentsimr/DESCRIPTION’ ... OK
• this is package ‘dependentsimr’ version ‘1.0.0.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘DESeq2’
• 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 ‘dependentsimr’ 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 ... [0s/0s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/0s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
• checking loading without being on the library search path ... [0s/0s] 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 ... [5s/6s] 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... 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 ... [2s/2s] ERROR   Running ‘testthat.R’ [1s/2s] 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/testing-design.html#sec-tests-files-overview   > # * https://testthat.r-lib.org/articles/special-files.html   >   > library(testthat)   > library(dependentsimr)   >   > test_check("dependentsimr")   Saving _problems/test-dependentsim-77.R   [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-dependentsim.R:77:1'): (code run outside of `test_that()`) ─────   <rlib_error_package_not_found/rlang_error/error/condition>   Error in `fit_deseq(data)`: The package "DESeq2" is required Using type='DESeq2' requires DESeq2   Backtrace:       ▆    1. └─dependentsimr::get_random_structure(...) at test-dependentsim.R:77:1    2. └─dependentsimr:::marginals_and_transform(datasets, types)    3. └─dependentsimr:::fit_deseq(data)    4. └─rlang::check_installed("DESeq2", reason = "Using type='DESeq2' requires DESeq2")      [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [3s/5s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘simulate_data.Rmd’ using rmarkdown Quitting from simulate_data.Rmd:85-87 [unnamed-chunk-7] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'simulate_data.Rmd' failed with diagnostics: The package "DESeq2" is required Using type='DESeq2' requires DESeq2 --- failed re-building ‘simulate_data.Rmd’ SUMMARY: processing the following file failed:   ‘simulate_data.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [0s/0s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs