• using R Under development (unstable) (2026-04-15 r89888)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.8 (3+b1)     Debian flang version 21.1.8 (3+b1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-04-17 05:39:55 UTC
• checking for file ‘promor/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘promor’ version ‘0.2.2’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] OK
• 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 See the install log for details.
• 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 ... [8s/12s] OK
• checking whether the package can be loaded with stated dependencies ... [8s/10s] OK
• checking whether the package can be unloaded cleanly ... [7s/8s] OK
• checking whether the namespace can be loaded with stated dependencies ... [8s/10s] OK
• checking whether the namespace can be unloaded cleanly ... [8s/10s] OK
• checking loading without being on the library search path ... [9s/11s] 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 ... [39s/48s] OK
• checking Rd files ... [1s/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 ... [1s/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 ... [49s/63s] OK Examples with CPU (user + system) or elapsed time > 5s                user system elapsed impute_na 11.941 0.323 14.005 feature_plot 6.370 0.059 7.858 impute_plot 5.827 0.052 7.363 heatmap_na 4.698 0.186 7.173
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [17s/19s] ERROR   Running ‘testthat.R’ [17s/19s] 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 ... [2s/2s] OK
• checking PDF version of manual ... [7s/9s] OK
• checking HTML version of manual ... [4s/6s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR