* using log directory ‘/srv/hornik/tmp/CRAN_pretest/oncmap.Rcheck’
* using R Under development (unstable) (2025-01-09 r87552)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.6 (1)
    Debian flang-new version 19.1.6 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘oncmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘oncmap’ version ‘0.1.5’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Michal Kouril <Michal.Kouril@cchmc.org>’

New submission

Possibly misspelled words in DESCRIPTION:
  EAMD (20:58, 22:60)
  EAMDs (18:89)
  OncMAP (22:36)
  actuations (22:65)
  csv (22:98)
* 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 ‘oncmap’ can be installed ... [3s/3s] 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [4s/4s] OK
* checking Rd files ... [0s/0s] 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 ... [0s/0s] 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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [3s/3s] ERROR
  Running ‘testthat.R’ [3s/3s]
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/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(oncmap)
  > 
  > test_check("oncmap")
  New names:
  * `1` -> `1...1`
  * `--` -> `--...2`
  * `` -> `...4`
  * `100018877-BR1` -> `100018877-BR1...5`
  * `100018877-BR1` -> `100018877-BR1...6`
  * `1` -> `1...8`
  * `--` -> `--...12`
  * `--` -> `--...14`
  New names:
  * `1` -> `1...1`
  * `--` -> `--...2`
  * `` -> `...4`
  * `100018877-BR1` -> `100018877-BR1...5`
  * `100018877-BR1` -> `100018877-BR1...6`
  * `1` -> `1...8`
  * `--` -> `--...12`
  * `--` -> `--...14`
  New names:
  * `1` -> `1...1`
  * `--` -> `--...2`
  * `` -> `...4`
  * `100018877-BR1` -> `100018877-BR1...5`
  * `100018877-BR1` -> `100018877-BR1...6`
  * `1` -> `1...8`
  * `--` -> `--...12`
  * `--` -> `--...14`
  New names:
  * `1` -> `1...1`
  * `--` -> `--...2`
  * `` -> `...4`
  * `100018877-BR1` -> `100018877-BR1...5`
  * `100018877-BR1` -> `100018877-BR1...6`
  * `1` -> `1...8`
  * `--` -> `--...12`
  * `--` -> `--...14`
  New names:
  * `1` -> `1...1`
  * `--` -> `--...2`
  * `` -> `...4`
  * `100018877-BR1` -> `100018877-BR1...5`
  * `100018877-BR1` -> `100018877-BR1...6`
  * `1` -> `1...8`
  * `--` -> `--...12`
  * `--` -> `--...14`
  New names:
  * `1` -> `1...1`
  * `--` -> `--...2`
  * `` -> `...4`
  * `100018877-BR1` -> `100018877-BR1...5`
  * `100018877-BR1` -> `100018877-BR1...6`
  * `1` -> `1...8`
  * `--` -> `--...12`
  * `--` -> `--...14`
  New names:
  * `1` -> `1...1`
  * `--` -> `--...2`
  * `` -> `...4`
  * `100018877-BR1` -> `100018877-BR1...5`
  * `100018877-BR1` -> `100018877-BR1...6`
  * `1` -> `1...8`
  * `--` -> `--...12`
  * `--` -> `--...14`
  New names:
  * `1` -> `1...1`
  * `--` -> `--...2`
  * `` -> `...4`
  * `100018877-BR1` -> `100018877-BR1...5`
  * `100018877-BR1` -> `100018877-BR1...6`
  * `1` -> `1...8`
  * `--` -> `--...12`
  * `--` -> `--...14`
  New names:
  * `1` -> `1...1`
  * `--` -> `--...2`
  * `` -> `...4`
  * `100018877-BR1` -> `100018877-BR1...5`
  * `100018877-BR1` -> `100018877-BR1...6`
  * `1` -> `1...8`
  * `--` -> `--...12`
  * `--` -> `--...14`
  New names:
  * `` -> `...2`
  New names:
  * `` -> `...2`
  New names:
  * `` -> `...2`
  New names:
  * `1` -> `1...1`
  * `--` -> `--...2`
  * `` -> `...4`
  * `100018877-BR1` -> `100018877-BR1...5`
  * `100018877-BR1` -> `100018877-BR1...6`
  * `1` -> `1...8`
  * `--` -> `--...12`
  * `--` -> `--...14`
  New names:
  * `1` -> `1...1`
  * `--` -> `--...2`
  * `` -> `...4`
  * `100018877-BR1` -> `100018877-BR1...5`
  * `100018877-BR1` -> `100018877-BR1...6`
  * `1` -> `1...8`
  * `--` -> `--...12`
  * `--` -> `--...14`
  New names:
  * `1` -> `1...1`
  * `--` -> `--...2`
  * `` -> `...4`
  * `100018877-BR1` -> `100018877-BR1...5`
  * `100018877-BR1` -> `100018877-BR1...6`
  * `1` -> `1...8`
  * `--` -> `--...12`
  * `--` -> `--...14`
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 15 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-adherence_preprocessing.R:34:3'): adherence_preprocess processing ──
  run_test_adherence_preprocess() (`actual`) not equal to list(68, 66, 66, 129) (`expected`).
  
    `actual[[2]]`: 65.0
  `expected[[2]]`: 66.0
  
    `actual[[4]]`: 128.0
  `expected[[4]]`: 129.0
  ── Failure ('test-adherence_preprocessing.R:35:3'): adherence_preprocess processing ──
  run_test_adherence_preprocess2() (`actual`) not equal to list(68, 66, 66, 258) (`expected`).
  
    `actual[[2]]`: 65.0
  `expected[[2]]`: 66.0
  
    `actual[[4]]`: 256.0
  `expected[[4]]`: 258.0
  ── Failure ('test-detect.R:3:3'): Detect eCAP ──────────────────────────────────
  read_input("ecap2.xls")$format (`actual`) not equal to "ecap2xls" (`expected`).
  
  `actual`:   "ecap_old"
  `expected`: "ecap2xls"
  ── Failure ('test-report_adherence.R:23:3'): report_adherence processing ───────
  run_test_report_adherence() (`actual`) not equal to list(35, 58, 0, 129) (`expected`).
  
    `actual[[1]]`: 34.0
  `expected[[1]]`: 35.0
  
    `actual[[2]]`: 57.0
  `expected[[2]]`: 58.0
  
    `actual[[4]]`: 128.0
  `expected[[4]]`: 129.0
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 15 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... [2s/2s] OK
* checking HTML version of manual ... [0s/0s] 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