* using log directory ‘/Users/ripley/R/packages/tests-devel/promor.Rcheck’
* using R Under development (unstable) (2026-04-12 r89873)
* using platform: aarch64-apple-darwin25.4.0
* R was compiled by
    Apple clang version 21.0.0 (clang-2100.0.123.102)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.4.1
* using session charset: UTF-8
* current time: 2026-04-13 17:20:38 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘promor/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘promor’ version ‘0.2.2’
* 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 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 ‘promor’ can be installed ... OK
* 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 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 ... OK
* checking Rd files ... 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 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 ... [14s/19s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(promor)
  > 
  > test_check("promor")
  0 empty row(s) removed.
  2 empty column(s) removed.
  1 protein(s) (rows) only identified by site removed.
  4 protein(s) identified by 2 or fewer unique peptides removed.
  Zeros have been replaced with NAs.
  Data have been log-transformed.
  4 proteins with higher than 33% NAs in at least one group removed.
  0 empty row(s) removed.
  4 empty column(s) removed.
  10 protein contaminant(s) (rows) removed.
  0 protein(s) identified by 2 or fewer unique peptides removed.
  Zeros have been replaced with NAs.
  Data have been log-transformed.
  change in estimate:  0.02415548 
  change in estimate:  0.02101209 
  change in estimate:  0.01821531 
  change in estimate:  0.0157772 
  change in estimate:  0.01367284 
  change in estimate:  0.01186459 
  change in estimate:  0.01031291 
  change in estimate:  0.008980791 
  Saving _problems/test-protein_analysis-424.R
  1 siginificantly differentially expressed proteins found.
  
  Testing glm...
  
  
  Testing rf...
  
  
  Testing svmRadial...
  
  
  Done!
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-protein_analysis.R:419:3'): normalization works for cyclicloess ──
  Expected `normalize_data(df_mp, method = "cyclicloess")` to equal `df_norm_c`.
  Differences:
  actual vs expected
                       [,1]     [,2]      [,3]
  - actual[1, ]   10.086035 20.13598 70.205445
  + expected[1, ]  8.875947 21.90757 81.928810
  - actual[2, ]   34.229368 34.59707 29.475138
  + expected[2, ] 35.918001 38.54878 35.918001
  - actual[3, ]   20.748909 34.27025 17.497403
  + expected[3, ] 24.161291 24.16129 24.161291
  - actual[4, ]   65.531947 57.33665 -6.608449
  + expected[4, ] 43.541565 43.54156 43.541565
  - actual[5, ]   18.860601 11.89760 20.730052
  + expected[5, ] 17.339630 17.33963 17.339630
  - actual[6, ]   42.446533 35.35054 45.603037
  + expected[6, ] 44.825964 44.82596 44.825964
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ]
  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 ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/promor.Rcheck/00check.log’
for details.

      101.40 real        83.46 user        11.19 sys