* using log directory ‘/srv/hornik/tmp/CRAN/PointedSDMs.Rcheck’
* using R Under development (unstable) (2024-07-07 r86880)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (1+b1)
    Debian flang-new version 18.1.8 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘PointedSDMs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PointedSDMs’ version ‘2.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/65s] NOTE
Maintainer: ‘Philip Mostert <philip.s.mostert@ntnu.no>’

Suggests or Enhances not in mainstream repositories:
  INLA
Availability using Additional_repositories specification:
  INLA   yes   https://inla.r-inla-download.org/R/testing

Found the following (possibly) invalid URLs:
  URL: http://www.pabirdatlas.psu.edu
    From: man/BBA.Rd
    Status: Error
    Message: Could not resolve host: www.pabirdatlas.psu.edu
  URL: http://www.pabirdatlas.psu.edu/
    From: inst/doc/Setophaga.html
    Status: Error
    Message: Could not resolve host: www.pabirdatlas.psu.edu
  URL: https://zenodo.org/badge/latestdoi/368823136
    From: README.md
    Status: 504
    Message: Gateway Timeout
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘INLA’
* 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 ‘PointedSDMs’ can be installed ... [20s/20s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘DI_Data.Rdata’
* 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 ... [5s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [5s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/5s] OK
* checking loading without being on the library search path ... [5s/5s] 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 ... [25s/25s] 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: ‘INLA’

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  specifyISDM.Rd: bru
  specifyMarks.Rd: bru
  specifySpecies.Rd: bru
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... WARNING
Files not of a type allowed in a ‘data’ directory:
  ‘mee313110-sup-0001-supplementa.zip’
Please use e.g. ‘inst/extdata’ for non-R data files

* checking data for non-ASCII characters ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] 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 ... OK
* checking re-building of vignette outputs ... [10s/10s] OK
* checking PDF version of manual ... [4s/4s] 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 WARNING, 4 NOTEs