* using log directory ‘/home/hornik/tmp/CRAN_special_donttest/rmzqc.Rcheck’
* using R Under development (unstable) (2025-05-21 r88220)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-19) 14.2.0
    GNU Fortran (Debian 14.2.0-19) 14.2.0
* running under: Debian GNU/Linux 13 (trixie)
* using session charset: UTF-8
* using option ‘--run-donttest’
* checking for file ‘rmzqc/DESCRIPTION’ ... OK
* this is package ‘rmzqc’ version ‘0.5.6’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/7s] 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 serialization versions ... OK
* checking whether package ‘rmzqc’ 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/4s] ERROR
Running examples in ‘rmzqc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: toQCMetric
> ### Title: Create an 'MzQCqualityMetric' object from two inputs (id and
> ###   value).
> ### Aliases: toQCMetric
> 
> ### ** Examples
> 
>    ## single value
>    toQCMetric(id = "MS:4000059", value = 13405) # number of MS1 spectra
Reference class object of class "MzQCqualityMetric"
Field "accession":
[1] "MS:4000059"
Field "name":
[1] "number of MS1 spectra"
Field "description":
[1] "\"The number of MS1 events in the run.\" [PSI:MS]"
Field "value":
[1] 13405
Field "unit":
list()
> 
>    ## n-tuple
>    toQCMetric(id = "MS:4000051", value = c(31.3, 35.99, 38.44)) # XIC-FWHM quantiles
Reference class object of class "MzQCqualityMetric"
Field "accession":
[1] "MS:4000051"
Field "name":
[1] "XIC-FWHM quantiles"
Field "description":
[1] "\"The first to n-th quantile of peak widths for XICs. A metric's value triplet represents the related QuaMeter metrics of XIC-FWHM-Q1,Q2,Q3.\" [PSI:MS]"
Field "value":
[1] 31.30 35.99 38.44
Field "unit":
list()
> 
>    ## table
>    toQCMetric(id = "MS:4000063",  # MS2 known precursor charges fractions
+               value = list("MS:1000041" = 1:3,
+                            "UO:0000191" = c(0.7, 0.6, 0.8)))
Reference class object of class "MzQCqualityMetric"
Field "accession":
[1] "MS:4000063"
Field "name":
[1] "MS2 known precursor charges fractions"
Field "description":
[1] "\"The fraction of MS/MS precursors of the corresponding charge. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. The highest charge state is to be interpreted as that charge state or higher.\" [PSI:MS]"
Field "value":
$`MS:1000041`
[1] 1 2 3

$`UO:0000191`
[1] 0.7 0.6 0.8

Field "unit":
list()
> 
>    ## test an invalid CV accession/id
>    toQCMetric(id = "MS:0000", value = "ID_is_not_valid", allow_unknown_id = TRUE)
Warning in CV$byID(id) :
  Could not find id 'MS:0000' in CV list (length: 6806)
Reference class object of class "MzQCqualityMetric"
Field "accession":
[1] "MS:0000"
Field "name":
character(0)
Field "description":
character(0)
Field "value":
[1] "ID_is_not_valid"
Field "unit":
list()
> 
>    ## No test: 
>    ## matrix (there is no example in the CV yet, so this cannot be tested)
>    toQCMetric(id = "MS:400000?", value = matrix(1:12, nrow = 3, ncol = 4)) # ???
Warning in CV$byID(id) :
  Could not find id 'MS:400000?' in CV list (length: 6806)
Error in toQCMetric(id = "MS:400000?", value = matrix(1:12, nrow = 3,  : 
  The ID 'MS:400000?' is unknown in the current CV. Either fix the ID or use a more recent CV (see getCVSingleton()).
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [8s/9s] OK
  Running ‘testthat.R’ [8s/9s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [11s/13s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR