* using log directory ‘/srv/hornik/tmp/CRAN_pretest/RAMClustR.Rcheck’
* using R Under development (unstable) (2026-02-12 r89409)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (1+b1)
    Debian flang version 21.1.8 (1+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-02-13 22:23:07 UTC
* checking for file ‘RAMClustR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RAMClustR’ version ‘1.3.4’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/5s] NOTE
Maintainer: ‘Corey D. Broeckling <Corey.Broeckling@ColoState.EDU>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  Broeckling (26:267)
  Metabolomics (3:26)
  Spectrometry (3:13)
  et (26:278)
  indiscriminant (26:198)
  metabolomics (26:81)
  spectrometric (26:67)
  spectrometry (26:174, 26:225)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2025-04-05 as issues were not corrected
    despite reminders.

Uses the non-portable packages: ‘MSnbase’, ‘xcms’
* 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 ‘RAMClustR’ can be installed ... [4s/4s] 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 ... [8s/8s] 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 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 ... [38s/38s] ERROR
  Running ‘testthat.R’ [37s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RAMClustR)
  > 
  > test_check("RAMClustR")
  plotting findmain annotation results 
  finished 
  plotting findmain annotation results 
  finished 
  organizing dataset 
    normalizing dataset 
  writing msp formatted spectra 
  msp file complete 
  organizing dataset 
    normalizing dataset 
  writing msp formatted spectra 
  msp file complete 
  organizing dataset 
    normalizing dataset 
  writing msp formatted spectra 
  msp file complete 
  Saving _problems/test-31.R
  [ FAIL 1 | WARN 22 | SKIP 0 | PASS 27 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test.R:31:3'): RAMClustR with csv works ─────────────────────────────
  Error in `gzfile(file, "rb")`: cannot open the connection
  Backtrace:
      ▆
   1. └─base::readRDS(file = file.path("testdata", "test_csv.Rds")) at test.R:31:3
   2.   └─base::gzfile(file, "rb")
  
  [ FAIL 1 | WARN 22 | SKIP 0 | PASS 27 ]
  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 ... [3s/3s] OK
* checking HTML version of manual ... [2s/2s] 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