* using log directory 'd:/RCompile/CRANincoming/R-devel/romic.Rcheck'
* using R Under development (unstable) (2026-01-29 r89354 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'romic/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'romic' version '1.3.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Sean Hackett <seanrhackett@gmail.com>'

New submission

Package was archived on CRAN

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2025-12-03 as email to the maintainer is
    undeliverable.
* 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 serialization versions ... OK
* checking whether package 'romic' can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [10s] OK
* checking Rd files ... 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 ... 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 ... [13s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
  Running 'testthat.R'
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
  > 
  > suppressPackageStartupMessages(library(testthat))
  > library(romic)
  > 
  > test_check("romic")
  Saving _problems/test-data_classes-266.R
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 118 ]
  
  ══ Skipped tests (19) ══════════════════════════════════════════════════════════
  • On CRAN (16): 'test-data_classes.R:14:1', 'test-data_classes.R:81:1',
    'test-data_classes.R:270:1', 'test-data_classes.R:283:1',
    'test-data_classes.R:308:1', 'test-design.R:1:1', 'test-design.R:15:1',
    'test-dim_reduction.R:45:1', 'test-filters.R:1:1', 'test-filters.R:1:1',
    'test-filters.R:1:1', 'test-filters.R:1:1', 'test-mutates.R:14:1',
    'test-mutates.R:37:1', 'test-mutates.R:78:1', 'test-mutates.R:141:1'
  • empty test (3): 'test-export.R:1:1', 'test-export.R:50:1',
    'test-export.R:82:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-data_classes.R:261:3'): Catch corner cases when reading wide data ──
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: `mutate_()` was deprecated in dplyr 0.7.0 and is now defunct.
  i Please use `mutate()` instead.
  i See vignette('programming') for more help
  Backtrace:
      ▆
   1. ├─romic::convert_wide_to_tidy_omic(...)
   2. │ └─... %>% dplyr::select(-n_entries)
   3. ├─dplyr::select(., -n_entries)
   4. └─dplyr::mutate_(...)
   5.   └─dplyr:::lazy_defunct("mutate")
   6.     └─lifecycle::deprecate_stop(...)
   7.       └─lifecycle:::deprecate_stop0(msg)
   8.         └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 118 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... [12s] OK
* DONE
Status: 1 ERROR, 1 NOTE