* using log directory 'd:/Rcompile/CRANpkg/local/4.4/promor.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'promor/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'promor' version '0.2.1'
* 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 hidden files and directories ... OK
* checking for portable file names ... 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 ... [9s] OK
* checking whether the package can be loaded with stated dependencies ... [8s] OK
* checking whether the package can be unloaded cleanly ... [8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s] OK
* checking loading without being on the library search path ... [8s] 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 ... [19s] OK
* checking Rd files ... [1s] NOTE
checkRd: (-1) impute_plot.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{global}{Logical. If \code{TRUE} ({default}), a global density plot is
       |                                        ^
* 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 ... [1s] 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 ... [61s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [18s] ERROR
  Running 'testthat.R' [18s]
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.
    missForest iteration 1 in progress...done!
      estimated error(s): 1.04084 
      difference(s): 0.0005251996 
      time: 0.06 seconds
  
    missForest iteration 2 in progress...done!
      estimated error(s): 1.067432 
      difference(s): 0.002956259 
      time: 0.03 seconds
  
   b  c  b  c 
  20 22 39 82 
   a  c  a  c 
  11 22 83 82 
   a  b  a  b 
  11 20 83 39 
  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 
  1 siginificantly differentially expressed proteins found.
  
  Testing glm...
  
  
  Testing rf...
  
  
  Testing svmRadial...
  
  
  Done!
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-protein_analysis.R:336:3'): impute_na works for rf ───────────
  impute_na(df, method = "RF", seed = 327) (`actual`) not equal to `df_rf` (`expected`).
  
  actual vs expected
                         a        b      c
  - actual[1, ]   12.00000 29.33333 82.000
  + expected[1, ] 12.00000 26.60000 82.000
  - actual[2, ]   34.00000 29.33333 40.000
  + expected[2, ] 34.00000 32.15000 40.000
    actual[3, ]   11.00000 39.00000 22.000
  - actual[4, ]   83.00000 29.00000 50.350
  + expected[4, ] 83.00000 29.00000 53.125
  - actual[5, ]   42.09000 20.00000 50.350
  + expected[5, ] 62.16333 20.00000 66.025
  - actual[6, ]   67.00000 29.33333 70.000
  + expected[6, ] 67.00000 22.30000 70.000
  
    `actual$a[2:6]`: 34.0 11.0 83.0 42.1 67.0
  `expected$a[2:6]`: 34.0 11.0 83.0 62.2 67.0
  
    `actual$b`: 29.3 29.3 39.0 29.0 20.0 29.3
  `expected$b`: 26.6 32.1 39.0 29.0 20.0 22.3
  
    `actual$c`: 82.0 40.0 22.0 50.4 50.4 70.0
  `expected$c`: 82.0 40.0 22.0 53.1 66.0 70.0
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-protein_analysis.R:336:3
   2. │ └─base::withCallingHandlers(...)
   3. └─testthat::expect_equal(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [3s] OK
* checking PDF version of manual ... [24s] OK
* checking HTML version of manual ... [6s] OK
* DONE
Status: 1 ERROR, 1 NOTE