* using log directory ‘/home/hornik/tmp/CRAN_pretest/AMR.Rcheck’
* using R Under development (unstable) (2026-10-15 r90676)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 23.1.0 (2)
    Debian flang version 23.1.0 (2)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-10-16 10:02:10 UTC
* checking for file ‘AMR/DESCRIPTION’ ... OK
* this is package ‘AMR’ version ‘3.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/14s] 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 ‘AMR’ can be installed ... [14s/14s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... WARNING
Output(s) listed in 'build/vignette.rds' but not in package:
  ‘inst/doc/AMR_for_Python.html’
  ‘inst/doc/welcome_to_AMR.html’
* 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 whether startup messages can be suppressed ... [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 ... [29s/29s] OK
* checking Rd files ... [1s/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 ... INFO
Exported functions without usage information:
  scale_color_mic scale_color_sir scale_sir_colors
* 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 ... [2s/2s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking relative paths in package URLs ... NOTE
Checking relative paths failed with message:
  error in inferior call:
  Failed to locate ‘weave’ output file ‘AMR_for_Python.pdf’ or ‘AMR_for_Python.html’ for vignette with name ‘AMR_for_Python’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/home/hornik/tmp/CRAN_pretest/AMR.Rcheck/AMR/doc’: ‘AMR_for_Python.R’ (199 bytes), ‘AMR_for_Python.Rmd’ (11535 bytes), ‘index.html’ (1837 bytes), ‘welcome_to_AMR.R’ (199 bytes), ‘welcome_to_AMR.Rmd’ (7677 bytes)
* checking examples ... [35s/35s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [5s/5s] OK
  Running ‘testthat.R’ [5s/5s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... WARNING
Failed to locate ‘weave’ output file ‘AMR_for_Python.pdf’ or ‘AMR_for_Python.html’ for vignette with name ‘AMR_for_Python’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/home/hornik/tmp/CRAN_pretest/AMR.Rcheck/00_pkg_src/AMR/inst/doc’: ‘AMR_for_Python.R’ (199 bytes), ‘AMR_for_Python.Rmd’ (11535 bytes), ‘welcome_to_AMR.R’ (199 bytes), ‘welcome_to_AMR.Rmd’ (7677 bytes)Failed to locate ‘weave’ output file ‘welcome_to_AMR.pdf’ or ‘welcome_to_AMR.html’ for vignette with name ‘welcome_to_AMR’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/home/hornik/tmp/CRAN_pretest/AMR.Rcheck/00_pkg_src/AMR/inst/doc’: ‘AMR_for_Python.R’ (199 bytes), ‘AMR_for_Python.Rmd’ (11535 bytes), ‘welcome_to_AMR.R’ (199 bytes), ‘welcome_to_AMR.Rmd’ (7677 bytes)
Package vignettes without corresponding single PDF/HTML:
  ‘AMR_for_Python.Rmd’
  ‘welcome_to_AMR.Rmd’
* checking re-building of vignette outputs ... [2s/2s] OK
* checking PDF version of manual ... [6s/6s] OK
* checking HTML version of manual ... [5s/5s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE