update urls

Author: olivroy

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

@@ -8,7 +8,9 @@ on:
   schedule:
     - cron: "0 4 * * *"
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -54,3 +56,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -23,23 +25,32 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results

CONDUCT.md

@@ -22,4 +22,4 @@ opening an issue or contacting one or more of the project maintainers.
 
 This Code of Conduct is adapted from the Contributor Covenant 
 (http:contributor-covenant.org), version 1.0.0, available at 
-http://contributor-covenant.org/version/1/0/0/
+https://www.contributor-covenant.org/version/1/0/0/code-of-conduct/

NEWS.md

@@ -907,7 +907,7 @@
 
 # version 0.5-1
 
-* add spatial indexes to most binary geometry operations; #394 and http://r-spatial.org/r/2017/06/22/spatial-index.html
+* add spatial indexes to most binary geometry operations; #394 and https://r-spatial.org/r/2017/06/22/spatial-index.html
 
 * drastically reduce memory footprint of `st_intersection` and similar; #394
 

PROPOSAL.md

@@ -4,7 +4,7 @@ Applicant: [Edzer Pebesma](https://github.com/edzer/), [Institute for Geoinforma
 
 Supporting authors: Edzer Pebesma, Roger Bivand, Michael Sumner, Robert Hijmans, Virgilio Gómez-Rubio
 
-[Simple features](https://en.wikipedia.org/wiki/Simple_Features) is an open ([OGC](https://www.ogc.org/standard/sfa/) and [ISO](https://www.iso.org/standard/40114.html)) interface standard for access and manipulation of spatial vector data (points, lines, polygons). It includes a standard [SQL schema](http://www.opengeospatial.org/standards/sfs) that supports storage, retrieval, query and update of feature collections via a SQL interface. All commonly used databases provide this interface. [GeoJSON](https://geojson.org/) is a standard for encoding simple features in JSON, and is used in JavaScript and MongoDB. Well-known-text ([WKT](https://en.wikipedia.org/wiki/Well-known_text)) is a text representation of simple features used often in linked data; well-known-binary ([WKB] (https://en.wikipedia.org/wiki/Well-known_text)) a standard binary representation used in databases. _Simple Feature Access_ defines coordinate reference systems, and makes it easy to move data from longitude-latitude to projections back and forth in a standardized way. 
+[Simple features](https://en.wikipedia.org/wiki/Simple_Features) is an open ([OGC](https://www.ogc.org/standard/sfa/) and [ISO](https://www.iso.org/standard/40114.html)) interface standard for access and manipulation of spatial vector data (points, lines, polygons). It includes a standard [SQL schema](https://www.ogc.org/standard/sfs/) that supports storage, retrieval, query and update of feature collections via a SQL interface. All commonly used databases provide this interface. [GeoJSON](https://geojson.org/) is a standard for encoding simple features in JSON, and is used in JavaScript and MongoDB. Well-known-text ([WKT](https://en.wikipedia.org/wiki/Well-known_text)) is a text representation of simple features used often in linked data; well-known-binary ([WKB] (https://en.wikipedia.org/wiki/Well-known_text)) a standard binary representation used in databases. _Simple Feature Access_ defines coordinate reference systems, and makes it easy to move data from longitude-latitude to projections back and forth in a standardized way. 
 
 
 [GDAL](https://gdal.org/) is an open source C++ library for reading and writing both raster and vector data with more than 225 drivers (supported file formats, data base connectors, web service interfaces). GDAL is used by practically all open source geospatial projects and by many industry products (including ESRI's ArcGIS, ERDAS, and FME). It provides coordinate transformations (built on top of PROJ.4) and geometric operations (e.g. polygon intersections, unions, buffers and distance). Standards for coordinate transformations change over time; such changes are typically adopted directly in GDAL/PROJ.4 but do not easily find their way into R-only packages such as `mapproj`.
@@ -16,7 +16,7 @@ Today, 221 CRAN packages depend on, import or link to `sp`, 259 when including _
 Off-CRAN package [rgdal2](https://github.com/thk686/rgdal2) is an interface to GDAL 2.0, which uses raw pointers to interface features, but does not import any data in R, using GDAL to handle everything. CRAN Package [wkb](https://cran.r-project.org/package=wkb), contributed by Tibco Software, converts between WKB representations of several simple feature classes and corresponding classes in `sp`, and seems to be needed for Tibco software purposes.
 
 <!---
-[second edition](http://www.springer.com/statistics/life+sciences%2C+medicine+%26+health/book/978-1-4614-7617-7))
+[second edition](https://link.springer.com/book/10.1007/978-1-4614-7618-4))
 -->
 
 ## The problem

R/plot.R

@@ -824,7 +824,7 @@ get_asp = function(bb) {
 
 bb2merc = function(x, cls = "ggmap") { # return bbox in the appropriate "web mercator" CRS
 	wgs84 = st_crs(4326)
-	merc =  st_crs(3857) # http://wiki.openstreetmap.org/wiki/EPSG:3857
+	merc =  st_crs(3857) # https://wiki.openstreetmap.org/wiki/Web_Mercator
 	pts = if (cls == "ggmap") {
 		b = vapply(attr(x, "bb"), c, 0.0)
 		st_sfc(st_point(c(b[2:1])), st_point(c(b[4:3])), crs = wgs84)

README.md

@@ -1,11 +1,11 @@
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/r-spatial/sf/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/r-spatial/sf/actions/workflows/R-CMD-check.yaml)
 [![tic-db](https://github.com/r-spatial/sf/actions/workflows/tic-db.yml/badge.svg)](https://github.com/r-spatial/sf/actions/workflows/tic-db.yml)
-[![Coverage Status](https://img.shields.io/codecov/c/github/r-spatial/sf/main.svg)](https://app.codecov.io/gh/r-spatial/sf)
-[![License](http://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html)
-[![CRAN](http://www.r-pkg.org/badges/version/sf)](https://cran.r-project.org/package=sf)
+[![Codecov test coverage](https://codecov.io/gh/r-spatial/sf/graph/badge.svg)](https://app.codecov.io/gh/r-spatial/sf)
+[![License](https://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html)
+[![CRAN](https://www.r-pkg.org/badges/version/sf)](https://cran.r-project.org/package=sf)
 [![cran checks](https://badges.cranchecks.info/worst/sf.svg)](https://cran.r-project.org/web/checks/check_results_sf.html)
-[![Downloads](http://cranlogs.r-pkg.org/badges/sf?color=brightgreen)](https://www.r-pkg.org:443/pkg/sf)
+[![Downloads](https://cranlogs.r-pkg.org/badges/sf?color=brightgreen)](https://www.r-pkg.org:443/pkg/sf)
 [![status](https://tinyverse.netlify.com/badge/sf)](https://CRAN.R-project.org/package=sf)
 <!-- badges: end -->
 
@@ -24,9 +24,9 @@ Package sf:
 * represents natively in R all 17 simple feature types for all dimensions (XY, XYZ, XYM, XYZM)
 * interfaces to [GEOS](https://libgeos.org) for geometrical operations on projected coordinates, and (through R package [s2](https://cran.r-project.org/package=s2)) to [s2geometry](http://s2geometry.io/) for geometrical operations on ellipsoidal coordinates
 * interfaces to [GDAL](https://gdal.org/), supporting all driver options, `Date` and `POSIXct` and list-columns
-* interfaces to [PRØJ](http://proj.org/) for coordinate reference system conversion and transformation
+* interfaces to [PRØJ](https://proj.org/) for coordinate reference system conversion and transformation
 * uses [well-known-binary](https://en.wikipedia.org/wiki/Well-known_text#Well-known_binary) serialisations written in C++/Rcpp for fast I/O with GDAL and GEOS 
-* reads from and writes to spatial databases such as [PostGIS](http://postgis.net/) using [DBI](https://cran.r-project.org/package=DBI)
+* reads from and writes to spatial databases such as [PostGIS](https://postgis.net/) using [DBI](https://cran.r-project.org/package=DBI)
 * is extended by 
     * [lwgeom](https://github.com/r-spatial/lwgeom/) for selected liblwgeom/PostGIS functions
     * [stars](https://github.com/r-spatial/stars/) for raster data, and raster or vector data cubes (spatial time series)

configure

@@ -2397,7 +2397,7 @@ printf "%s\n" "no" >&6; }
 	echo "Error: gdal-config not found"
 	echo "The gdal-config script distributed with GDAL could not be found."
 	echo "If you have not installed the GDAL libraries, you can"
-	echo "download the source from  http://www.gdal.org/"
+	echo "download the source from  https://www.gdal.org/"
 	echo "If you have installed the GDAL libraries, then make sure that"
 	echo "gdal-config is in your path. Try typing gdal-config at a"
 	echo "shell prompt and see if it runs. If not, use:"
@@ -4113,7 +4113,7 @@ if test "$WARN" = "warn" ; then
     echo "Note: proj/conus not found"
     echo "No support available in PROJ4 for NAD grid datum transformations"
     echo "If required, consider re-installing from source with the contents"
-    echo "of proj-datumgrid-1.<latest>.zip from http://download.osgeo.org/proj/ in nad/."
+    echo "of proj-datumgrid-1.<latest>.zip from https://download.osgeo.org/proj/ in nad/."
 fi
 
 fi # PROJH = no

configure.ac

@@ -93,7 +93,7 @@ else
 	echo "Error: gdal-config not found"
 	echo "The gdal-config script distributed with GDAL could not be found."
 	echo "If you have not installed the GDAL libraries, you can"
-	echo "download the source from  http://www.gdal.org/"
+	echo "download the source from  https://www.gdal.org/"
 	echo "If you have installed the GDAL libraries, then make sure that"
 	echo "gdal-config is in your path. Try typing gdal-config at a"
 	echo "shell prompt and see if it runs. If not, use:"
@@ -628,7 +628,7 @@ if test "$WARN" = "warn" ; then
     echo "Note: proj/conus not found"
     echo "No support available in PROJ4 for NAD grid datum transformations"
     echo "If required, consider re-installing from source with the contents"
-    echo "of proj-datumgrid-1.<latest>.zip from http://download.osgeo.org/proj/ in nad/."
+    echo "of proj-datumgrid-1.<latest>.zip from https://download.osgeo.org/proj/ in nad/."
 fi
 
 fi # PROJH = no

inst/docker/arrow/Dockerfile

@@ -89,7 +89,7 @@ ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 # GEOS:
 ENV GEOS_VERSION 3.11.0
 
-RUN wget -q http://download.osgeo.org/geos/geos-${GEOS_VERSION}.tar.bz2 \
+RUN wget -q https://download.osgeo.org/geos/geos-${GEOS_VERSION}.tar.bz2 \
   && bzip2 -d geos-*bz2 \
   && tar xf geos*tar \
   && cd geos* \
@@ -104,7 +104,7 @@ RUN wget -q http://download.osgeo.org/geos/geos-${GEOS_VERSION}.tar.bz2 \
 #RUN git clone --depth 1 https://github.com/OSGeo/PROJ.git
 # https://download.osgeo.org/proj/proj-9.0.0RC1.tar.gz
 ENV PROJ_VERSION 9.0.1
-RUN wget -q http://download.osgeo.org/proj/proj-${PROJ_VERSION}.tar.gz
+RUN wget -q https://download.osgeo.org/proj/proj-${PROJ_VERSION}.tar.gz
 RUN tar zxvf proj-${PROJ_VERSION}.tar.gz
 RUN cd proj* \
   && ls -l \
@@ -120,7 +120,7 @@ RUN cd proj* \
 ENV GDAL_VERSION 3.5.1
 ENV GDAL_VERSION_NAME 3.5.1
 
-RUN wget -q http://download.osgeo.org/gdal/${GDAL_VERSION}/gdal-${GDAL_VERSION_NAME}.tar.gz \
+RUN wget -q https://download.osgeo.org/gdal/${GDAL_VERSION}/gdal-${GDAL_VERSION_NAME}.tar.gz \
   && tar -xf gdal-${GDAL_VERSION_NAME}.tar.gz \
   && cd gdal* \
   && mkdir build \