* using log directory ‘/srv/hornik/tmp/CRAN_pretest/PvSTATEM.Rcheck’
* using R Under development (unstable) (2024-10-26 r87273)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.1 (1)
    Debian flang-new version 19.1.1 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘PvSTATEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PvSTATEM’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/7s] NOTE
Maintainer: ‘Tymoteusz Kwiecinski <tymoteuszkwiecinski@gmail.com>’

Package has a VignetteBuilder field but no prebuilt vignette index.

Found the following (possibly) invalid URLs:
  URL: https://mini-pw.github.io/PvSTATEM (moved to https://mini-pw.github.io/PvSTATEM/)
    From: README.md
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.
* 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 ‘PvSTATEM’ 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 ... [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 ... [6s/6s] 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 ... NOTE
Documented arguments not in \usage in Rd file 'plot_plate.Rd':
  ‘colours’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘example_script.Rmd’ ‘img/additional_notes.jpg’
  ‘img/report_analyte_details.png’ ‘img/report_layout.jpg’
  ‘img/report_summary.png’ ‘img/report_thumbnails.png’
  ‘our_datasets.Rmd’ ‘our_plots.Rmd’ ‘reports.Rmd’
* checking examples ... [51s/51s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
generate_plate_report 41.783  0.430  42.273
process_plate          5.081  0.004   5.087
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [23s/23s] OK
  Running ‘testthat.R’ [23s/23s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
  ‘example_script.Rmd’
  ‘our_datasets.Rmd’
  ‘our_plots.Rmd’
  ‘reports.Rmd’
* checking re-building of vignette outputs ... [24s/24s] OK
* checking PDF version of manual ... [4s/4s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Missing $ inserted.
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                $
l.865 ..._{max} + \text{over_max_extrapolation}}{}
                                                  ,
! Extra }, or forgotten $.
\textdef@ ...th {#1}\let \f@size #2\selectfont #3}
                                                  }
l.865 ..._{max} + \text{over_max_extrapolation}}{}
                                                  ,
! Extra }, or forgotten $.
\textdef@ ...h {#1}\let \f@size #2\selectfont #3}}
                                                  
l.865 ..._{max} + \text{over_max_extrapolation}}{}
                                                  ,
! Extra }, or forgotten $.
\text@ ...e {\textdef@ \displaystyle \f@size {#1}}
                                                  {\textdef@ \textstyle \f@s...
l.865 ..._{max} + \text{over_max_extrapolation}}{}
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                $
l.865 ..._{max} + \text{over_max_extrapolation}}{}
                                                  ,
! Extra }, or forgotten $.
\textdef@ ...th {#1}\let \f@size #2\selectfont #3}
                                                  }
l.865 ..._{max} + \text{over_max_extrapolation}}{}
                                                  ,
! Extra }, or forgotten $.
\textdef@ ...h {#1}\let \f@size #2\selectfont #3}}
                                                  
l.865 ..._{max} + \text{over_max_extrapolation}}{}
                                                  ,
! Extra }, or forgotten $.
\text@ ...xtstyle \f@size {\firstchoice@false #1}}
                                                  {\textdef@ \textstyle \sf@...
l.865 ..._{max} + \text{over_max_extrapolation}}{}
                                                  ,
! Missing $ inserted.
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l.865 ..._{max} + \text{over_max_extrapolation}}{}
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\textdef@ ...th {#1}\let \f@size #2\selectfont #3}
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l.865 ..._{max} + \text{over_max_extrapolation}}{}
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! Extra }, or forgotten $.
\textdef@ ...h {#1}\let \f@size #2\selectfont #3}}
                                                  
l.865 ..._{max} + \text{over_max_extrapolation}}{}
                                                  ,
! Extra }, or forgotten $.
\text@ ...tstyle \sf@size {\firstchoice@false #1}}
                                                  {\textdef@ \textstyle \ssf...
l.865 ..._{max} + \text{over_max_extrapolation}}{}
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\textdef@ ...th {#1}\let \f@size #2\selectfont #3}
                                                  }
l.865 ..._{max} + \text{over_max_extrapolation}}{}
                                                  ,
! Extra }, or forgotten $.
\textdef@ ...h {#1}\let \f@size #2\selectfont #3}}
                                                  
l.865 ..._{max} + \text{over_max_extrapolation}}{}
                                                  ,
! Extra }, or forgotten $.
\text@ ...style \ssf@size {\firstchoice@false #1}}
                                                  \check@mathfonts }
l.865 ..._{max} + \text{over_max_extrapolation}}{}
                                                  ,
! Extra }, or forgotten $.
\text@ ...firstchoice@false #1}}\check@mathfonts }
                                                  
l.865 ..._{max} + \text{over_max_extrapolation}}{}
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* checking PDF version of manual without index ... ERROR
* checking HTML version of manual ... [1s/1s] NOTE
Found the following math rendering problems:
Model.Rd:169: Expected 'EOF', got '_' in ...x} + \text{over_max_extrapolati...
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘PvSTATEM-manual.tex’
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 3 WARNINGs, 5 NOTEs