* using log directory ‘/srv/hornik/tmp/CRAN_pretest/mvgam.Rcheck’
* using R Under development (unstable) (2024-09-02 r87090)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘mvgam/DESCRIPTION’ ... OK
* this is package ‘mvgam’ version ‘1.1.3’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [8s/70s] NOTE
Maintainer: ‘Nicholas J Clark <nicholas.j.clark1214@gmail.com>’

Suggests or Enhances not in mainstream repositories:
  cmdstanr
Availability using Additional_repositories specification:
  cmdstanr   yes   https://mc-stan.org/r-packages/

Found the following (possibly) invalid URLs:
  URL: https://www.jeffdoser.com/files/spabundance-web/articles/nmixturemodels (moved to https://doserlab.com/files/spabundance-web/articles/nmixturemodels)
    From: inst/doc/nmixtures.html
    Status: 301
    Message: Moved Permanently
  URL: https://www.sciencedirect.com/book/9780128237687/applied-hierarchical-modeling-in-ecology-analysis-of-distribution-abundance-and-species-richness-in-r-and-bugs
    From: inst/doc/nmixtures.html
    Status: 403
    Message: Forbidden
  URL: https://www.sciencedirect.com/science/article/pii/S0167947322002390
    From: inst/doc/trend_formulas.html
    Status: 403
    Message: Forbidden
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 ... NOTE
Package suggested but not available for checking: ‘cmdstanr’
* 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 ‘mvgam’ can be installed ... [34s/34s] OK
* used C++ compiler: ‘Debian clang version 18.1.8 (9)’
* 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/2s] OK
* checking whether the package can be unloaded cleanly ... [3s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [5s/5s] OK
* checking whether startup messages can be suppressed ... [3s/3s] 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 ... [41s/39s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘cmdstanr’
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory newer than same file in 'inst/doc':
  ‘data_in_mvgam.Rmd’ ‘mvgam_overview.Rmd’ ‘nmixtures.Rmd’
  ‘shared_states.Rmd’
* checking examples ... [16s/16s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [16s/16s] OK
  Running ‘testthat.R’ [16s/16s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [11s/11s] OK
* checking PDF version of manual ... [5s/5s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 3 NOTEs