• using R Under development (unstable) (2024-12-18 r87448)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.5 (1)     Debian flang-new version 19.1.5 (1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘cellpypes/DESCRIPTION’ ... OK
• this is package ‘cellpypes’ version ‘0.3.0’
• 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 serialization versions ... OK
• checking whether package ‘cellpypes’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [3s/4s] 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 ... [3s/4s] OK
• checking loading without being on the library search path ... [3s/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 ... [14s/18s] OK
• checking Rd files ... [0s/1s] 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 ... [2s/2s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [6s/8s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [7s/8s] ERROR   Running ‘testthat.R’ [7s/8s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(cellpypes)   >   > test_check("cellpypes")   [ FAIL 2 | WARN 5 | SKIP 0 | PASS 53 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-pseudobulk.R:10:3'): class_to_deseq2 example working ─────────   `{ ... }` threw an unexpected error.   Message: Install DESeq2 to use class_to_deseq2 function.   Class: simpleError/error/condition   Backtrace:       ▆    1. ├─testthat::expect_error(...) at test-pseudobulk.R:10:3    2. │ └─testthat:::expect_condition_matching(...)    3. │ └─testthat:::quasi_capture(...)    4. │ ├─testthat (local) .capture(...)    5. │ │ └─base::withCallingHandlers(...)    6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))    7. └─cellpypes::class_to_deseq2(obj, meta_data, "T", ~treatment) at test-pseudobulk.R:20:7   ── Error ('test-pseudobulk.R:61:3'): class_to_deseq2 stops gracefully if class has zero cells. ──   Error in `class_to_deseq2(dds, meta_data, "T", ~treatment)`: Install DESeq2 to use class_to_deseq2 function.   Backtrace:       ▆    1. ├─testthat::expect_error(...) at test-pseudobulk.R:61:3    2. │ └─testthat:::expect_condition_matching(...)    3. │ └─testthat:::quasi_capture(...)    4. │ ├─testthat (local) .capture(...)    5. │ │ └─base::withCallingHandlers(...)    6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))    7. └─cellpypes::class_to_deseq2(dds, meta_data, "T", ~treatment)      [ FAIL 2 | WARN 5 | SKIP 0 | PASS 53 ]   Error: Test failures   Execution halted
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR