Merge branch 'master' into testing

Author: cmjt

.github/workflows/R-CMD-check.yaml

@@ -21,14 +21,13 @@ jobs:
           - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/test-coverage.yaml

@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -49,7 +49,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: stelfi
 Type: Package
 Title: Hawkes and Log-Gaussian Cox Point Processes Using Template Model Builder
-Version: 1.0.1
-Date: 2023-09-29
+Version: 1.0.2
+Date: 2025-08-12
 Authors@R: 
   c(person(given = "Charlotte M.",
            family = "Jones-Todd",
@@ -29,7 +29,7 @@ Authors@R:
            family = "FA2386-21-1-4028",
            role = "fnd"))
 Depends:
-    R (>= 4.3.0)
+    R (>= 4.5.0)
 Imports:
     TMB (>= 1.9.6),
     sf (>= 1.0.14),
@@ -49,7 +49,7 @@ BugReports: https://github.com/cmjt/stelfi/issues
 LazyData: TRUE
 LazyDataCompression: xz
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Suggests:
     testthat (>= 3.1.10),
     rmarkdown,

NEWS.md

@@ -1,5 +1,20 @@
 # stelfi (development version)
 
+# stelfi 1.0.2
+
+## Breaking changes
+
+ + None
+
+## New features
+
+ + None
+
+## Minor improvements and fixes
+
+ + fixing CRAN NOTE for CRAN (re)release 
+
+
 # stelfi 0.0.3
 
 ## Breaking changes

R/data.r

@@ -92,7 +92,7 @@ NULL
 #' \item{luminosity}{scaled: luminosity}
 #' \item{tt}{scaled: time to nearest city in minutes}
 #' }
-#' @source \url{https://www.start.umd.edu/gtd/}
+#' @source \url{https://www.start.umd.edu/data-tools/GTD}
 #' @name iraq_terrorism
 NULL
 #' Example marked point pattern data set

R/stelfi.r

@@ -45,7 +45,6 @@
 #' @references Kristensen, K., Nielsen, A., Berg, C. W., Skaug, H., and
 #'  Bell B. M. (2016). {TMB}: Automatic Differentiation and Laplace
 #' Approximation. \emph{Journal of Statistical Software}, \strong{70}: 1--21.
-#' @docType package
-#' @aliases stelfi-package
-#' @name stelfi
+#' @keywords internal
+"_PACKAGE"
 NULL

cran-comments.md

@@ -1,28 +1,42 @@
-## Resubmission
+## New submission
 
-This is a resubmission. In this version I have:
-
-* Removed, now, broken link from `man/uk_serial.Rd`
-* Fixed the M1mac issue as requested by Prof Brian Ripley
+Package was archived on CRAN on 2025-04-02
 
+Apologies for not fixing issue in time to maintain continued hosting on CRAN.
+The issue related to the INFO note below, which
+was previously piaked up as a NOTE. As noted the sub-directory in questions
+is created when the C++ template, required for its functionality, is compiled.
 
 ## Test environments
 
 * ubuntu-latest (release & devel)
-* local ubuntu 18.04 & 20.04
+* local ubuntu 20.04
 * windows-latest (release)
 * macos-latest (release)
 
 ## R CMD check results
 
 * No ERRORs or WARNINGs
+ 
+The following NOTE was received
+
+* Maintainer: ‘Charlotte M. Jones-Todd <[email protected]>’
+
+New submission
+
+Package was archived on CRAN
+
+CRAN repository db overrides:
+  X-CRAN-Comment: Archived on 2025-04-02 as issues were not corrected
+    in time
+
 
-On all tests the following NOTE was received
+The following INFO was received
 
-* checking installed package size ... NOTE
- installed size is 62.7Mb 
- sub-directories of 1Mb or more:
- libs  61.5Mb
+* checking installed package size ... INFO
+ installed size is 84.5Mb
+  sub-directories of 1Mb or more:
+    libs  83.2Mb
 
  * This sub-directory is created when the C++ template, required for its functionality, is compiled.
 

docs/data.html

@@ -287,7 +287,7 @@ <h3 class="unnumbered anchored" data-anchor-id="retweets_niwa"><code>retweets_ni
 <p>In 2019 a <a href="https://niwa.co.nz/">NIWA</a> scientist <a href="https://www.nzherald.co.nz/nz/news/article.cfm?c_id=1&amp;objectid=12201147">found a working USB in the scat of a leopard seal</a>, they then <a href="https://twitter.com/niwa_nz/status/1092610541401587712">tweeted about it</a> in the hopes of finding its owner. In <a href="#hawkes">this chapter</a> a Hawkes process is fitted to these data.</p>
 <div class="cell">
 <div class="cell-output-display">
-<blockquote class="twitter-tweet blockquote" data-width="550" data-lang="en" data-dnt="true" data-theme="light"><p lang="en" dir="ltr">NIWA is searching for the owner of a USB stick found in the poo of a leopard seal… <br>Recognise this video? Scientists analysing the scat of leopard seals have come across an unexpected discovery – a USB stick full of photos &amp; still in working order!  <a href="https://t.co/2SZVkm5az4">https://t.co/2SZVkm5az4</a> <a href="https://t.co/JLEC8vuHH0">pic.twitter.com/JLEC8vuHH0</a></p>— NIWA (@niwa_nz) <a href="https://twitter.com/niwa_nz/status/1092610541401587712?ref_src=twsrc%5Etfw">February 5, 2019</a></blockquote>
+<blockquote class="twitter-tweet blockquote" data-width="550" data-lang="en" data-dnt="true" data-theme="light"><p lang="en" dir="ltr">NIWA is searching for the owner of a USB stick found in the poo of a leopard seal… <br>Recognise this video? Scientists analysing the scat of leopard seals have come across an unexpected discovery – a USB stick full of photos &amp; still in working order!  <a href="https://t.co/2SZVkm5az4">https://t.co/2SZVkm5az4</a> <a href="https://t.co/JLEC8vuHH0">pic.twitter.com/JLEC8vuHH0</a></p>— Earth Sciences New Zealand (@earthsciencesnz) <a href="https://twitter.com/earthsciencesnz/status/1092610541401587712?ref_src=twsrc%5Etfw">February 5, 2019</a></blockquote>
 
 </div>
 </div>