Ege Rubak and Adrian Baddeley

This repository contains the result of running a script to update reverse dependencies of spatstat to the new spatstat 2.0 structure (see https://github.com/rubak/spatstat.revdep.helpers for details).

The rest of this README is intended to give a continuous update of the current recommendations and state of affairs for spatstat 2.0, with planned submission to CRAN on Monday 22 Feb. 2021.

To adapt your package to spatstat please follow the advice sent by email to authors of reverse dependencies and further detailed below. Once you have followed the steps below to update your package to spatstat 2.0 you may experience problems checking your package if it depends on other packages that have not yet been adapted to statstat 2.0. In particular you may need updated versions of sf and maptools as explained in this issue, where you can also help us by announcing a developement version of your own package for others to install. If you need an updated dependency you can search for it in the issue, and if it is missing you may try to reach out to Ege via the issue or by direct email.

We have registred the following packages as updated and ready for CRAN submission once spatstat 2.0 is accepted on CRAN:

csvfile <- file.path(tempdir(), "spatstat.csv")
download.file("https://docs.google.com/spreadsheets/d/1RTmP2iwZGlxSUToYaht-H1SlS4CyFgbQ0Umv5i3x-1Q/export?format=csv", 
              destfile = csvfile)
done <- trimws(unlist(strsplit(read.csv(csvfile)[,2], ",")))
unlink(csvfile)
sort(done)

##  [1] "AROC"           "CalSim"         "dixon"          "ecespa"        
##  [5] "envi"           "ETAS"           "gateR"          "GmAMisc"       
##  [9] "graph4lg"       "idar"           "inlabru"        "maptools"      
## [13] "overlapptest"   "rcarbon"        "replicatedpp2w" "RImageJROI"    
## [17] "ROCnReg"        "selectspm"      "sf"             "shar"          
## [21] "spagmix"        "sparr"          "sparrpowR"      "stars"         
## [25] "tabularaster"   "trajectories"   "trip"

If your package should be included on this list of packages please submit its name using this webform.

1. Install all the sub-packages from CRAN by just typing

   install.packages('spatstat.linnet', dependencies=TRUE)

2. Install spatstat 2.0-0 from https://spatstat.r-universe.dev

   install.packages("spatstat", repos = "https://spatstat.r-universe.dev")

3. Modify your package so that it works with spatstat 2.0-0 and the relevant spatstat subpackages (please see details further below). You can find scripts to help you with this at https://github.com/rubak/spatstat.revdep.helpers and a result of running these scripts for your package at the repository you are currently in: https://github.com/rubak/spatstat.revdep

4. Run the CRAN package checker on your modified package (possibly with development versions of other packages installed as detailed above)

5. Let us know that your package is updated and ready for submission by typing its name in the webform mention previously. This is to help us tell CRAN that maintainers are ready with updated packages once spatstat 2.0-0 is on CRAN and makes old packages break.

We strongly recommend that you

DO NOT submit your updated package to CRAN yet

DO help us by adding spatstat (>= 2.0-0) to Imports/Depends/Suggests as detailed below even if it isn’t strictly necessary.

(Explanation: many other packages depend on spatstat. There are still many copies of the old spatstat lying around. When your package depends on spatstat.geom (for example) then the old and new code may coexist on some systems. and this will cause problems, so we really want to get spatstat 2.0-0 to any system that installs spatstat.xxxx. See ‘Collision Avoidance’ below)

How to use spatstat 2.0-0 in your package depends on how you currently use spatstat:

If your package currently ‘Depends’ on spatstat, the general advice is to have the following in DESCRIPTION (in addition to other packages you use):

Depends: spatstat (>= 2.0-0)
Imports: spatstat.geom, spatstat.core, spatstat.linnet

It may seem excessive to have all the sub-packages here, but they are strictly needed if you currently use the double-colon idiom spatstat:: in your code. If not you could omit those that you don’t use.

In NAMESPACE you need something like:

import(spatstat.geom, spatstat.core, spatstat.linnet, spatstat)

If your package currently ‘Suggests’ spatstat, the general advice which should work out of the box for most cases (together with the automated code changes by the script):

Suggests: spatstat.geom, spatstat.core, spatstat.linnet, spatstat (>= 2.0-0)

You can omit any spatstat.xxxx that you don’t use, and in the long run you can omit spatstat (>= 2.0-0), but we would really appreciate it if you can keep it in for now.

See ‘Collision Avoidance’ below, for some code which you can use to automatically check for possible conflicts.

For DESCRIPTION:

Imports: spatstat.geom, spatstat.core, spatstat.linnet, spatstat (>= 2.0-0)

Where you must delete any sub-packages you don’t actually use. For NAMESPACE you have to add mandatory imports(spatstat.xxxx) or preferably importFrom(spatstat.xxxx, yyyy) for all the subpackages/functions you use, and if you kindly put spatstat (>= 2.0-0) in DESCRIPTION then you should add a line in NAMESPACE:

import("spatstat")

This line can be deleted in a few months together with the dependence on umbrella spatstat when the dust has settled, and then you should only depend on relevant sub-packages.

Much of this code update may be achieved by using the script here, but many will also need manual changes to DESCRIPTION and NAMESPACE as detailed above as well as development versions of other packages. Please reach out if you are in doubt or need help. In particular if your package is on GitHub Ege is happy to run the script for you and make a pull request with the relevant changes if you send him an email with the repository information.

Maintainers of packages with spatstat in Suggests will typically change their package so that it Suggests the relevant sub-packages spatstat.xxxx as well. Any code which requires spatstat would typically have been wrapped in

if(require(spatstat)) {
    # Run spatstat code
}

This should now change to require(spatstat.geom), etc. We offer the following replacement which can be used to check that the relevant subpackage is available (and that an old spatstat is no longer installed). Note that this will only pass the R package checker if spatstat is in the list of Suggested packages.

Example:

if(check_spatstat("spatstat.geom")){
      # Run spatstat code
}

Function definition:

check_spatstat <- function(pkg){
  if(!requireNamespace(pkg, quietly = TRUE)){
    stop(paste("Package", pkg, "required; please install it (or the full spatstat package) first."))
  } else{
    spst_ver <- try(packageVersion("spatstat"), silent = TRUE)
    if(!inherits(spst_ver, "try-error") && spst_ver < 2.0-0){
      stop(paste0("You have an old version of spatstat installed which is incompatible with ", 
                 pkg, 
                 ". Please update spatstat (or uninstall it)."))
    }
  }
}