* using log directory ‘/srv/hornik/tmp/CRAN_pretest/metabodecon.Rcheck’
* using R Under development (unstable) (2025-01-16 r87584)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.6 (1+b1)
    Debian flang-new version 19.1.6 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘metabodecon/DESCRIPTION’ ... OK
* this is package ‘metabodecon’ version ‘1.2.5’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/6s] NOTE
Maintainer: ‘Tobias Schmidt <tobias.schmidt331@gmail.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  Beirnaert (27:8)
  Deconvolution (2:8)
  Haeckl (30:5)
  Koh (25:28)
  NMR (2:42, 23:55)
  Vu (27:71)
  al (25:35, 27:21, 27:77, 30:15)
  deconvolution (22:30, 24:52)
  et (25:32, 27:18, 27:74, 30:12)
  postprocessing (22:59)
* 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 ‘metabodecon’ can be installed ... [5s/5s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [11s/11s] 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 examples ... [0s/0s] ERROR
Running examples in ‘metabodecon-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MetaboDecon1D
> ### Title: Deconvolute 1D NMR spectrum
> ### Aliases: MetaboDecon1D
> 
> ### ** Examples
> 
> 
> ## ATTENTION: using MetaboDecon1D() for deconvolution is deprecated. Please use
> ## generate_lorentz_curves() instead.
> 
> ## The following example shows how a subset of the Sim dataset, consisting
> ## of two spectrum objects, can be deconvoluted using `MetaboDecon1D()`. The
> ## whole example code is wrapped into `evalwith()` to simulate user input.
> ## When using the function interactively, you should type in the answers to
> ## the questions manually.
> expected_answers <- c(
+      "10",   # Subfolder of your filepath, i.e. the experiment number?
+      "10",   # Subsubsubfolder of filepath, i.e. the processing number?
+      "y",    # Use same parameters for all spectra?
+      "1",    # File to adjust all parameters.
+      "n",    # Signal free region borders correct selected?
+      "3.55", # Left border.
+      "3.35", # Right border.
+      "y",    # Signal free region borders correct selected?
+      "n",    # Water artefact fully inside red vertical lines?
+      "0",    # Half width range (in ppm) for the water artefact.
+      "y",    # Water artefact fully inside red vertical lines?
+      "n"     # Save results as text documents?
+ )
> sim <- metabodecon_file("bruker/sim_subset")
> evalwith(answers = expected_answers, {
+      sim_decon <- MetaboDecon1D(sim)
+ })
Timing stopped at: 0 0 0
Error in setwd(file.path(getwd(), filepath)) : 
  cannot change working directory
Calls: evalwith ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [7s/4s] OK
  Running ‘testthat.R’ [7s/4s]
* 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, 1 NOTE