Merge pull request #49 from ropensci/cran-resubmission

Cran resubmission

Author: atsyplenkov

CONTRIBUTING.md

@@ -6,19 +6,19 @@ We love collaboration.
 
 ### Bugs?
 
-* Submit an issue on the Issues page [here](https://github.com/marcosci/landscapetools/issues)
+* Submit an issue on the Issues page [here](https://github.com/ropensci/landscapetools/issues)
 
 ### Code contributions
 
 * Fork this repo to your Github account
 * Clone your version on your account down to your machine from your account, e.g,. `git clone https://github.com/<yourgithubusername>/landscapetools.git`
-* Make sure to track progress upstream (i.e., on our version of `landscapetools` at `marcosci/landscapetools`) by doing `git remote add upstream https://github.com/marcosci/landscapetools.git`. Before making changes make sure to pull changes in from upstream by doing either `git fetch upstream` then merge later or `git pull upstream` to fetch and merge in one step
+* Make sure to track progress upstream (i.e., on our version of `landscapetools` at `ropensci/landscapetools`) by doing `git remote add upstream https://github.com/ropensci/landscapetools.git`. Before making changes make sure to pull changes in from upstream by doing either `git fetch upstream` then merge later or `git pull upstream` to fetch and merge in one step
 * Make your changes (bonus points for making changes on a new branch)
 * If you alter package functionality at all (e.g., the code itself, not just documentation)
 please do write some tests to cover the new functionality.
 * Push up to your account
-* Submit a pull request to home base at `marcosci/landscapetools`
+* Submit a pull request to home base at `ropensci/landscapetools`
 
-### Questions? Get in touch: [sciaini.marco@gmail.com](mailto:sciaini.marco@gmail.com)
+### Questions? Get in touch: [s2@sent.com](mailto:s2@sent.com)
 
 ### Thanks for contributing!

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: landscapetools
 Type: Package
 Title: Landscape Utility Toolbox
-Version: 0.6.2.9001
+Version: 0.6.3
 Description: Provides utility functions for some of the less-glamorous tasks involved
     in landscape analysis. It includes functions to coerce raster data to the
     common tibble format and vice versa, it helps with flexible reclassification
@@ -11,18 +11,22 @@ Description: Provides utility functions for some of the less-glamorous tasks inv
     landscapes, rasterstacks, -bricks and lists of raster.
 Authors@R: c(
     person("Marco", "Sciaini", email = "sciaini.marco@gmail.com",
-       role = c("aut", "cre"), comment = c(ORCID = '0000-0002-3042-5435')), 
+       role = "aut", comment = c(ORCID = '0000-0002-3042-5435')), 
     person("Matthias", "Fritsch",
                 email = "matthias.fritsch@forst.uni-goettingen.de",
-                role =  c("aut")),
+                role =  "aut"),
     person("Maximilian H.K.", "Hesselbarth",
-             role = c("aut"),
+             role = "aut",
              email = "mhk.hesselbarth@gmail.com",
              comment = c(ORCID = "0000-0003-1125-9918")),
     person("Jakub", "Nowosad", 
              role = "aut",
              email = "nowosad.jakub@gmail.com", 
              comment = c(ORCID = "0000-0002-1057-3721")),
+    person("Anatoly", "Tsyplenkov",
+             role = c("aut", "cre"),
+             email = "s2@sent.com",
+             comment = c(ORCID = "0000-0003-4144-8402")),
     person("Laura", "Graham", role = "rev",
        comment = "Laura reviewed the package for rOpenSci, see 
                   https://github.com/ropensci/onboarding/issues/188"),
@@ -38,7 +42,6 @@ Depends:
 URL: https://docs.ropensci.org/landscapetools/
 BugReports: https://github.com/ropensci/landscapetools/issues
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 Imports: 
     ggplot2,
     raster,
@@ -53,3 +56,4 @@ Suggests:
 VignetteBuilder: knitr
 LinkingTo: 
     Rcpp
+Config/roxygen2/version: 8.0.0

NEWS.md

@@ -1,3 +1,12 @@
+# landscapetools 0.6.3 (2026-06-23)
+
+## BUG FIXES
+- Fix compilation with `STRICT_R_HEADERS` by replacing R memory allocation macros with standard C functions in `src/get_jenkbreaks.c`.
+- Fix broken or redirected URLs in the package vignettes.
+
+## MAINTENANCE
+- New package maintainer -- Anatoly Tsyplenkov (#48).
+
 # landscapetools 0.6.2
 - Bugfix in `util_classify`
 

codemeta.json

@@ -7,13 +7,13 @@
   "codeRepository": "https://docs.ropensci.org/landscapetools/",
   "issueTracker": "https://github.com/ropensci/landscapetools/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.6.2.9001",
+  "version": "0.6.3",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.5.2 (2025-10-31)",
+  "runtimePlatform": "R version 4.6.0 (2026-04-24)",
   "author": [
     {
       "@type": "Person",
@@ -41,15 +41,22 @@
       "familyName": "Nowosad",
       "email": "nowosad.jakub@gmail.com",
       "@id": "https://orcid.org/0000-0002-1057-3721"
+    },
+    {
+      "@type": "Person",
+      "givenName": "Anatoly",
+      "familyName": "Tsyplenkov",
+      "email": "s2@sent.com",
+      "@id": "https://orcid.org/0000-0003-4144-8402"
     }
   ],
   "maintainer": [
     {
       "@type": "Person",
-      "givenName": "Marco",
-      "familyName": "Sciaini",
-      "email": "sciaini.marco@gmail.com",
-      "@id": "https://orcid.org/0000-0002-3042-5435"
+      "givenName": "Anatoly",
+      "familyName": "Tsyplenkov",
+      "email": "s2@sent.com",
+      "@id": "https://orcid.org/0000-0003-4144-8402"
     }
   ],
   "softwareSuggestions": [
@@ -171,7 +178,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "1376.685KB",
+  "fileSize": "1377.102KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
@@ -194,20 +201,22 @@
         },
         {
           "@type": "Person",
-          "givenName": ["Craig", "E."],
+          "givenName": "Craig E.",
           "familyName": "Simpkins"
         }
       ],
-      "name": "NLMR and landscapetools: An integrated environment for simulating and modifying neutral landscape models in R",
-      "url": "https://doi.org/10.1111/2041-210X.13076",
-      "pagination": "1--9",
+      "name": "NLMR and landscapetools: An integrated environment for simulating and modifying neutral landscape models in R",
+      "identifier": "10.1111/2041-210X.13076",
+      "pagination": "2240--2248",
+      "@id": "https://doi.org/10.1111/2041-210X.13076",
+      "sameAs": "https://doi.org/10.1111/2041-210X.13076",
       "isPartOf": {
         "@type": "PublicationIssue",
         "datePublished": "2018",
         "isPartOf": {
           "@type": ["PublicationVolume", "Periodical"],
-          "volumeNumber": "00",
-          "name": "Methods in Ecololgy and Evolution"
+          "volumeNumber": "9",
+          "name": "Methods in Ecology and Evolution"
         }
       }
     }

cran-comments.md

@@ -1,23 +1,28 @@
 ## Submission
 
-New version includes massive dependency trimming and new functionality.
+This is a resubmission of an archived package. The previous version was archived because the maintainer email was undeliverable. The maintainer has been updated to Anatoly Tsyplenkov <s2@sent.com> (see ropensci/landscapetools#48).
+
+This release also fixes the compilation failure under `STRICT_R_HEADERS` reported on CRAN by replacing R's `Calloc`/`Free` macros with standard C `calloc`/`free` in `src/get_jenkbreaks.c`.
 
 ## Test environments
 
-* local Ubuntu Linux 16.04 LTS install, R 3.4.1
-* Ubuntu 14.04 (on travis-ci), R 3.4.1
-* Windows Server 2012 R2 x64 (build 9600) (on appveyor), R 3.4.2
-* Rhub
-* Windows Server 2008 R2 SP1, R-devel, 32/64 bit
-* Debian Linux, R-devel, GCC ASAN/UBSAN
-* Fedora Linux, R-devel, clang, gfortran
-* macOS 10.11 El Capitan, R-release
-* macOS 10.9 Mavericks, R-oldrel
-* win-builder (devel and release)
+* local Arch Linux, R 4.6.0
+* win-builder, R-devel (r90185 ucrt)
 
 ## R CMD check results
 
-0 errors | 0 warnings | 0 note
+win-builder R-devel:
+
+```
+0 errors | 0 warnings | 1 note
+```
+
+The single NOTE is the expected CRAN incoming feasibility message for a new submission of a previously archived package. It also flags two possibly misspelled words in `DESCRIPTION`:
+
+* `tibble` — the name of the tidyverse data-frame package.
+* `rasterstacks` — refers to `RasterStack` objects from the `raster` package.
+
+Both are intentional technical terms.
 
 ## Reverse dependencies
 

inst/CITATION

@@ -1,16 +1,17 @@
-citHeader("To cite NLMR in publications use:")
-
-citEntry(entry = "Article",
-         title        = "NLMR and landscapetools: An integrated environment for simulating and modifying neutral landscape models in R",
-         author       = personList(as.person("Marco Sciaini"),
-                                   as.person("Matthias Fritsch"),
-                                   as.person("Cedric Scherer"),
-                                   as.person("Craig E. Simpkins")),
-         journal = "Methods in Ecololgy and Evolution",
-         volume = "00",
-         pages = "1--9",
-         year         = "2018",
-         url          = "https://doi.org/10.1111/2041-210X.13076",
-
-         textVersion  =
-             paste("Sciaini M, Fritsch M, Scherer C, Simpkins CE. NLMR and landscapetools: An integrated environment for simulating and modifying neutral landscape models in R. Methods Ecol Evol. 2018;9:2240–2248."))
+bibentry(
+  header = "To cite NLMR in publications use:",
+  bibtype = "Article",
+  title = "NLMR and landscapetools: An integrated environment for simulating and modifying neutral landscape models in R",
+  author = c(
+    person("Marco", "Sciaini"),
+    person("Matthias", "Fritsch"),
+    person("Cedric", "Scherer"),
+    person("Craig E.", "Simpkins")
+  ),
+  journal = "Methods in Ecology and Evolution",
+  volume = "9",
+  pages = "2240--2248",
+  year = "2018",
+  doi = "10.1111/2041-210X.13076",
+  textVersion = "Sciaini M, Fritsch M, Scherer C, Simpkins CE. NLMR and landscapetools: An integrated environment for simulating and modifying neutral landscape models in R. Methods Ecol Evol. 2018;9:2240-2248."
+)

man/landscapetools-package.Rd

@@ -28,7 +28,7 @@ It is basically designed to accompany all the packages in [r-spatialecology](htt
 
 # Visualize 
 
-There are a plethora of R packages to visualize spatial data, all of them covering unique aspects and ways to do that (find a short introduction [here](https://docs.ropensci.org/NLMR/articles/articles/visualize_nlms.html)). With [NLMR](https://docs.ropensci.org/NLMR), we needed a way to visualize landscapes without much fuss and also have a way to visualize many of them in a way we found sufficient.
+There are a plethora of R packages to visualize spatial data, all of them covering unique aspects and ways to do that (find a short introduction [here](https://docs.ropensci.org/NLMR/articles/getstarted.html)). With [NLMR](https://docs.ropensci.org/NLMR/), we needed a way to visualize landscapes without much fuss and also have a way to visualize many of them in a way we found sufficient.
 
 ## General raster plotting
 ```{r fig.retina=2, message=FALSE, warning=FALSE}
@@ -122,7 +122,7 @@ summary(scaled_landscape)
 ```
 
 ## Merge
-`util_merge` most likely makes sense in the context of [NLMR](https://docs.ropensci.org/NLMR). If you merge multiple 
+`util_merge` most likely makes sense in the context of [NLMR](https://docs.ropensci.org/NLMR/). If you merge multiple 
 neutral landscapes models, you can create more feasible landscape
 patterns for certain questions, or come up with ecotones if you
 merge fractal patterns with gradients.