• using R Under development (unstable) (2025-10-25 r88970)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.4     flang version 21.1.4
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• 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 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 ... [41s/55s] OK See the install log for details.
• 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 ... [12s/18s] OK
• checking whether the package can be loaded with stated dependencies ... [11s/20s] OK
• checking whether the package can be unloaded cleanly ... [11s/16s] OK
• checking whether the namespace can be loaded with stated dependencies ... [11s/17s] OK
• checking whether the namespace can be unloaded cleanly ... [12s/18s] OK
• checking loading without being on the library search path ... [11s/16s] 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 ... [53s/92s] OK
• checking Rd files ... 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 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 ... [60s/82s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [24s/31s] ERROR   Running ‘testthat.R’ [24s/30s] 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): 1.104733       difference(s): 0.000166978       time: 0.084 seconds        missForest iteration 2 in progress...done!       estimated error(s): 1.021219       difference(s): 0.002309109       time: 0.048 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 28.70 82.000   + expected[1, ] 12.00000 26.60 82.000   - actual[2, ] 34.00000 28.70 40.000   + expected[2, ] 34.00000 32.15 40.000     actual[3, ] 11.00000 39.00 22.000   - actual[4, ] 83.00000 29.00 52.150   + expected[4, ] 83.00000 29.00 53.125   - actual[5, ] 42.69000 20.00 52.150   + expected[5, ] 62.16333 20.00 66.025   - actual[6, ] 67.00000 28.70 70.000   + expected[6, ] 67.00000 22.30 70.000        `actual$a[2:6]`: 34.0 11.0 83.0 42.7 67.0   `expected$a[2:6]`: 34.0 11.0 83.0 62.2 67.0        `actual$b`: 28.7 28.7 39.0 29.0 20.0 28.7   `expected$b`: 26.6 32.1 39.0 29.0 20.0 22.3        `actual$c`: 82.00 40.00 22.00 52.15 52.15 70.00   `expected$c`: 82.00 40.00 22.00 53.12 66.03 70.00   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 ... OK
• checking PDF version of manual ... [11s/14s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE