* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rmzqc.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘rmzqc/DESCRIPTION’ ... OK
* this is package ‘rmzqc’ version ‘0.5.4’
* 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 serialization versions ... OK
* checking whether package ‘rmzqc’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/rmzqc-00install.html' 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 ... [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 ... [7s/9s] OK
* checking Rd files ... [0s/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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/7s] OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
toAnalysisSoftware 3.323  0.139   5.505
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [15s/21s] ERROR
  Running ‘testthat.R’ [15s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rmzqc)
  > 
  > test_check("rmzqc")
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest'
  Content type 'application/json; charset=utf-8' length 7346 bytes
  ==================================================
  downloaded 7346 bytes
  
  Downloading obo from 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.192/psi-ms.obo' ...
  trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.192/psi-ms.obo'
  Content type 'application/octet-stream' length 1009882 bytes (986 KB)
  ==================================================
  downloaded 986 KB
  
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest'
  Content type 'application/json; charset=utf-8' length 7346 bytes
  ==================================================
  downloaded 7346 bytes
  
  Downloading obo from 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.192/psi-ms.obo' ...
  trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.192/psi-ms.obo'
  Content type 'application/octet-stream' length 1009882 bytes (986 KB)
  ==================================================
  downloaded 986 KB
  
  Downloading obo from 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo' ...
  trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo'
  Error in download.file(custom_uri, tmp_filename) : 
    cannot open URL 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo'
  Downloading obo from 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo' ...
  trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo'
  Error in download.file(custom_uri, tmp_filename) : 
    cannot open URL 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo'
  Error in getCVDictionary(source = "custom", custom_uri = "https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo",  : 
    Download failed.
  trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest'
  Content type 'application/json; charset=utf-8' length 7346 bytes
  ==================================================
  downloaded 7346 bytes
  
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  [ FAIL 2 | WARN 14 | SKIP 0 | PASS 87 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_conversion.R:17:3'): toQCMetric = function(id, value, on_violation = c("error", "warn")) ──
  `toQCMetric(id = "MS:4000059", value = 13405)` produced messages.
  ── Failure ('test_conversion.R:18:3'): toQCMetric = function(id, value, on_violation = c("error", "warn")) ──
  `toQCMetric(id = "MS:4000059", value = "13405")` produced messages.
  
  [ FAIL 2 | WARN 14 | SKIP 0 | PASS 87 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [22s/31s] OK
* checking PDF version of manual ... [5s/6s] OK
* checking HTML version of manual ... [1s/2s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR