Update for R 4.6.0, 26.04, BioC 3.23

Author: eddelbuettel

ChangeLog

@@ -1,3 +1,7 @@
+2026-05-03  Dirk Eddelbuettel  <edd@debian.org>
+
+	* R/init.R: Update defaults to R 4.6.0 and BioConductor 3.23
+
 2026-04-05  Dirk Eddelbuettel  <edd@debian.org>
 
 	* README.md: Announce 'resolute' aka 26.04

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: r2u
 Type: Package
 Title: Turn CRAN Source Packages into Binary Ubuntu Packages
-Version: 0.0.9.3
-Date: 2025-03-16
+Version: 0.0.9.4
+Date: 2026-05-03
 Authors@R: person("Dirk", "Eddelbuettel", role = c("aut", "cre"), email = "edd@debian.org",
                   comment = c(ORCID = "0000-0001-6419-907X"))
 Description: CRAN source packages are turned into Ubuntu packages containing

R/init.R

@@ -29,10 +29,10 @@
     }
     cat("in_docker:", .in.docker(), "\n",   file = fname, append = TRUE)
     cat("debhelper_compat: 13\n",           file = fname, append = TRUE)
-    cat("minimum_r_version: 4.4.0\n",       file = fname, append = TRUE)
+    cat("minimum_r_version: 4.6.0\n",       file = fname, append = TRUE)
     cat("r_api_version: 4.0\n",             file = fname, append = TRUE)
-    cat("bioc_version: 3.22\n",             file = fname, append = TRUE)
-    cat("debian_policy_version: 4.7.0\n",   file = fname, append = TRUE)
+    cat("bioc_version: 3.23\n",             file = fname, append = TRUE)
+    cat("debian_policy_version: 4.7.4\n",   file = fname, append = TRUE)
     cat("cache_age_hours_cran_db: 3\n",     file = fname, append = TRUE)
     cat("package_repo_preference: cran\n",   file = fname, append = TRUE)
     cat("r2u_directory: /var/local/r2u/\n", file = fname, append = TRUE)

README.md

@@ -19,10 +19,11 @@
 - **Fast and well-connected mirror** at
   [r2u.stat.illinois.edu](https://r2u.stat.illinois.edu) on the [Internet2](https://internet2.edu/) 
 
-- **Complete coverage** with (using 24.04 for amd64 and arm64) about 31039 CRAN packages (and 623
-  from BioConductor) using **current versions**: We support R 4.4.* and 4.5.*, and BioConductor 3.22
-  (on resolute, noble and jammy; focal is in archived mode and remains at 3.21); for 24.04 (aka
-  'noble') and 26.04 (aka 'resolute') BioConductor is available for both amd64 and arm64.
+- **Complete coverage** with (using 24.04 for both amd64 and arm64) about 31485 CRAN
+  packages (and 633 from BioConductor) using **current versions**: We support R 4.6.0, and
+  BioConductor 3.23 (on resolute, noble and jammy; focal is in archived mode and remains at 3.21);
+  for 24.04 (aka 'noble') and 26.04 (aka 'resolute') BioConductor is available for both amd64 and
+  arm64.
 
 - Complete support for **Ubuntu 20.04 ("focal")**, **22.04 ("jammy")**, **24.04 ("noble")** and
   **26.04 ("resolute")** on amd64, as well as **24.04 ("noble")** and **26.04 ("resolute")** support
@@ -61,7 +62,7 @@ the five easy setup steps detailed here.
 
 ### What is Covered ?
 
-We generally support amd64 (_i.e._ standard 64-bit Intel/AMD cpus, sometimes also called x86_64) for
+We generally support amd64 (_i.e._ standard 64-bit Intel/AMD cpus, sometimes also called x86\_64) for
 the current Ubuntu LTS release and its predecessor release, and support arm64 on the current release
 (more on this
 [here](https://eddelbuettel.github.io/r2u/vignettes/FAQ/#what-about-other-architectures-besides-x86_64)).
@@ -75,11 +76,12 @@ Support for additional cpu architectures is certainly possible but somewhat unli
 right now (due to a lack of resources and time). P3M/PPM/RSPM now appears to also support Debian which
 could be added at some later point.
 
-Current versions are built under R 4.4.x and R 4.5.* and are usable under 4.4.x and
-4.5.x. BioConductor release 3.22 packages are provided when required by CRAN packages for resolute,
-noble and jammy; focal is at 3.21.  Binaries were initially R 4.4.* based and are now built under R
-4.5.0. Some older packages released when we used R 4.2.* or 4.3.* may have been built with R 4.2.*
-or R 4.3.*, they will still work the same with R 4.4.* as R is generally forward-compatible.
+Current versions are built under R 4.6.0 and are usable under the current R 4.6.0. BioConductor
+release 3.23 packages are provided when required by CRAN packages for resolute, noble and jammy;
+focal is at 3.21.  Binaries were initially R 4.4.x based and are now built under R 4.6.0. Some older
+packages released when we used R 4.2.x or 4.3.x may have been built with R 4.2.x or R 4.3.x, they
+will still work the same with R 4.4.x as R is generally forward-compatible. There are exceptions
+(due to how R Core changes this) so if you notice an older package not loading please file an issue.
 
 
 
@@ -100,9 +102,10 @@ So we now cover
   [scoring](https://bioconductor.org/packages/stats/bioc/bioc_pkg_scores.tab) BioConductor packages
   (also covering _e.g._ all BioConductor packages in the Debian and Ubuntu distributions)
 
-This currently results in 25706, 28053, 31326, 28920 binary packages from CRAN in "focal", "jammy",
-"noble", and "resolute", respectively. It also contains 431, 527, 623, and 609 BioConductor
-packages, respectively, from their 3.22 (noble, jammy) and 3.21 (focal) releases. (See this
+This currently results in 25706, 28188, 31485, 29106 binary packages from CRAN in "focal", "jammy",
+"noble", and "resolute", respectively. It also contains 431, 534, 633, and 620 BioConductor
+packages, respectively, from their 3.23 (resolute, noble, jammy) and 3.21 (focal) releases. (See
+this
 [FAQ](https://eddelbuettel.github.io/r2u/vignettes/FAQ/#why-does-it-have-more-packages-than-cran)
 about why this number is higher than CRAN, and variable between releases.)
 

docs/changelog/index.html

@@ -704,6 +704,9 @@
   <h1>Changelog</h1>
 
 <h3 id="2026">2026</h3>
+<p>2026-05-03  Dirk Eddelbuettel  <a href="&#109;&#97;&#105;&#108;&#116;&#111;&#58;&#101;&#100;&#100;&#64;&#100;&#101;&#98;&#105;&#97;&#110;&#46;&#111;&#114;&#103;">&#101;&#100;&#100;&#64;&#100;&#101;&#98;&#105;&#97;&#110;&#46;&#111;&#114;&#103;</a> </p>
+<pre><code>    * R/init.R: Update defaults to R 4.6.0 and BioConductor 3.23
+</code></pre>
 <p>2026-04-05  Dirk Eddelbuettel  <a href="&#109;&#97;&#105;&#108;&#116;&#111;&#58;&#101;&#100;&#100;&#64;&#100;&#101;&#98;&#105;&#97;&#110;&#46;&#111;&#114;&#103;">&#101;&#100;&#100;&#64;&#100;&#101;&#98;&#105;&#97;&#110;&#46;&#111;&#114;&#103;</a> </p>
 <pre><code>    * README.md: Announce 'resolute' aka 26.04
 </code></pre>

docs/index.html

@@ -930,10 +930,11 @@ <h3 id="key-features">Key features</h3>
   <a href="https://r2u.stat.illinois.edu">r2u.stat.illinois.edu</a> on the <a href="https://internet2.edu/">Internet2</a> </p>
 </li>
 <li>
-<p><strong>Complete coverage</strong> with (using 24.04 for amd64 and arm64) about 31039 CRAN packages (and 623
-  from BioConductor) using <strong>current versions</strong>: We support R 4.4.<em> and 4.5.</em>, and BioConductor 3.22
-  (on resolute, noble and jammy; focal is in archived mode and remains at 3.21); for 24.04 (aka
-  'noble') and 26.04 (aka 'resolute') BioConductor is available for both amd64 and arm64.</p>
+<p><strong>Complete coverage</strong> with (using 24.04 for both amd64 and arm64) about 31485 CRAN
+  packages (and 633 from BioConductor) using <strong>current versions</strong>: We support R 4.6.0, and
+  BioConductor 3.23 (on resolute, noble and jammy; focal is in archived mode and remains at 3.21);
+  for 24.04 (aka 'noble') and 26.04 (aka 'resolute') BioConductor is available for both amd64 and
+  arm64.</p>
 </li>
 <li>
 <p>Complete support for <strong>Ubuntu 20.04 ("focal")</strong>, <strong>22.04 ("jammy")</strong>, <strong>24.04 ("noble")</strong> and
@@ -985,11 +986,12 @@ <h3 id="what-is-covered">What is Covered ?</h3>
 (additional hardware) resources and time. Support for other distributions is possible but unlikely
 right now (due to a lack of resources and time). P3M/PPM/RSPM now appears to also support Debian which
 could be added at some later point.</p>
-<p>Current versions are built under R 4.4.x and R 4.5.<em> and are usable under 4.4.x and
-4.5.x. BioConductor release 3.22 packages are provided when required by CRAN packages for resolute,
-noble and jammy; focal is at 3.21.  Binaries were initially R 4.4.</em> based and are now built under R
-4.5.0. Some older packages released when we used R 4.2.<em> or 4.3.</em> may have been built with R 4.2.<em>
-or R 4.3.</em>, they will still work the same with R 4.4.* as R is generally forward-compatible.</p>
+<p>Current versions are built under R 4.6.0 and are usable under the current R 4.6.0. BioConductor
+release 3.23 packages are provided when required by CRAN packages for resolute, noble and jammy;
+focal is at 3.21.  Binaries were initially R 4.4.x based and are now built under R 4.6.0. Some older
+packages released when we used R 4.2.x or 4.3.x may have been built with R 4.2.x or R 4.3.x, they
+will still work the same with R 4.4.x as R is generally forward-compatible. There are exceptions
+(due to how R Core changes this) so if you notice an older package not loading please file an issue.</p>
 <h3 id="what-is-selected">What is Selected ?</h3>
 <p>Everything :)</p>
 <p>Initially, we started from <a href="https://cran-logs.rstudio.com/">cran-logs</a> by picking the <em>N</em>
@@ -1004,9 +1006,10 @@ <h3 id="what-is-selected">What is Selected ?</h3>
   <a href="https://bioconductor.org/packages/stats/bioc/bioc_pkg_scores.tab">scoring</a> BioConductor packages
   (also covering <em>e.g.</em> all BioConductor packages in the Debian and Ubuntu distributions)</li>
 </ul>
-<p>This currently results in 25706, 28053, 31326, 28920 binary packages from CRAN in "focal", "jammy",
-"noble", and "resolute", respectively. It also contains 431, 527, 623, and 609 BioConductor
-packages, respectively, from their 3.22 (noble, jammy) and 3.21 (focal) releases. (See this
+<p>This currently results in 25706, 28188, 31485, 29106 binary packages from CRAN in "focal", "jammy",
+"noble", and "resolute", respectively. It also contains 431, 534, 633, and 620 BioConductor
+packages, respectively, from their 3.23 (resolute, noble, jammy) and 3.21 (focal) releases. (See
+this
 <a href="https://eddelbuettel.github.io/r2u/vignettes/FAQ/#why-does-it-have-more-packages-than-cran">FAQ</a>
 about why this number is higher than CRAN, and variable between releases.)</p>
 <p>The sole exception are packages we cannot build (as we do not have the required commercial software

docs/mkdmt-src/docs/changelog/index.html

@@ -704,6 +704,9 @@
   <h1>Changelog</h1>
 
 <h3 id="2026">2026</h3>
+<p>2026-05-03  Dirk Eddelbuettel  <a href="&#109;&#97;&#105;&#108;&#116;&#111;&#58;&#101;&#100;&#100;&#64;&#100;&#101;&#98;&#105;&#97;&#110;&#46;&#111;&#114;&#103;">&#101;&#100;&#100;&#64;&#100;&#101;&#98;&#105;&#97;&#110;&#46;&#111;&#114;&#103;</a> </p>
+<pre><code>    * R/init.R: Update defaults to R 4.6.0 and BioConductor 3.23
+</code></pre>
 <p>2026-04-05  Dirk Eddelbuettel  <a href="&#109;&#97;&#105;&#108;&#116;&#111;&#58;&#101;&#100;&#100;&#64;&#100;&#101;&#98;&#105;&#97;&#110;&#46;&#111;&#114;&#103;">&#101;&#100;&#100;&#64;&#100;&#101;&#98;&#105;&#97;&#110;&#46;&#111;&#114;&#103;</a> </p>
 <pre><code>    * README.md: Announce 'resolute' aka 26.04
 </code></pre>

docs/mkdmt-src/docs/index.html

@@ -930,10 +930,11 @@ <h3 id="key-features">Key features</h3>
   <a href="https://r2u.stat.illinois.edu">r2u.stat.illinois.edu</a> on the <a href="https://internet2.edu/">Internet2</a> </p>
 </li>
 <li>
-<p><strong>Complete coverage</strong> with (using 24.04 for amd64 and arm64) about 31039 CRAN packages (and 623
-  from BioConductor) using <strong>current versions</strong>: We support R 4.4.<em> and 4.5.</em>, and BioConductor 3.22
-  (on resolute, noble and jammy; focal is in archived mode and remains at 3.21); for 24.04 (aka
-  'noble') and 26.04 (aka 'resolute') BioConductor is available for both amd64 and arm64.</p>
+<p><strong>Complete coverage</strong> with (using 24.04 for both amd64 and arm64) about 31485 CRAN
+  packages (and 633 from BioConductor) using <strong>current versions</strong>: We support R 4.6.0, and
+  BioConductor 3.23 (on resolute, noble and jammy; focal is in archived mode and remains at 3.21);
+  for 24.04 (aka 'noble') and 26.04 (aka 'resolute') BioConductor is available for both amd64 and
+  arm64.</p>
 </li>
 <li>
 <p>Complete support for <strong>Ubuntu 20.04 ("focal")</strong>, <strong>22.04 ("jammy")</strong>, <strong>24.04 ("noble")</strong> and
@@ -985,11 +986,12 @@ <h3 id="what-is-covered">What is Covered ?</h3>
 (additional hardware) resources and time. Support for other distributions is possible but unlikely
 right now (due to a lack of resources and time). P3M/PPM/RSPM now appears to also support Debian which
 could be added at some later point.</p>
-<p>Current versions are built under R 4.4.x and R 4.5.<em> and are usable under 4.4.x and
-4.5.x. BioConductor release 3.22 packages are provided when required by CRAN packages for resolute,
-noble and jammy; focal is at 3.21.  Binaries were initially R 4.4.</em> based and are now built under R
-4.5.0. Some older packages released when we used R 4.2.<em> or 4.3.</em> may have been built with R 4.2.<em>
-or R 4.3.</em>, they will still work the same with R 4.4.* as R is generally forward-compatible.</p>
+<p>Current versions are built under R 4.6.0 and are usable under the current R 4.6.0. BioConductor
+release 3.23 packages are provided when required by CRAN packages for resolute, noble and jammy;
+focal is at 3.21.  Binaries were initially R 4.4.x based and are now built under R 4.6.0. Some older
+packages released when we used R 4.2.x or 4.3.x may have been built with R 4.2.x or R 4.3.x, they
+will still work the same with R 4.4.x as R is generally forward-compatible. There are exceptions
+(due to how R Core changes this) so if you notice an older package not loading please file an issue.</p>
 <h3 id="what-is-selected">What is Selected ?</h3>
 <p>Everything :)</p>
 <p>Initially, we started from <a href="https://cran-logs.rstudio.com/">cran-logs</a> by picking the <em>N</em>
@@ -1004,9 +1006,10 @@ <h3 id="what-is-selected">What is Selected ?</h3>
   <a href="https://bioconductor.org/packages/stats/bioc/bioc_pkg_scores.tab">scoring</a> BioConductor packages
   (also covering <em>e.g.</em> all BioConductor packages in the Debian and Ubuntu distributions)</li>
 </ul>
-<p>This currently results in 25706, 28053, 31326, 28920 binary packages from CRAN in "focal", "jammy",
-"noble", and "resolute", respectively. It also contains 431, 527, 623, and 609 BioConductor
-packages, respectively, from their 3.22 (noble, jammy) and 3.21 (focal) releases. (See this
+<p>This currently results in 25706, 28188, 31485, 29106 binary packages from CRAN in "focal", "jammy",
+"noble", and "resolute", respectively. It also contains 431, 534, 633, and 620 BioConductor
+packages, respectively, from their 3.23 (resolute, noble, jammy) and 3.21 (focal) releases. (See
+this
 <a href="https://eddelbuettel.github.io/r2u/vignettes/FAQ/#why-does-it-have-more-packages-than-cran">FAQ</a>
 about why this number is higher than CRAN, and variable between releases.)</p>
 <p>The sole exception are packages we cannot build (as we do not have the required commercial software

docs/mkdmt-src/docs/search/search_index.json

@@ -2,37 +2,37 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
     <url>
          <loc>https://github.com/eddelbuettel/r2u/</loc>
-         <lastmod>2026-05-01</lastmod>
+         <lastmod>2026-05-05</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://github.com/eddelbuettel/r2u/changelog/</loc>
-         <lastmod>2026-05-01</lastmod>
+         <lastmod>2026-05-05</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://github.com/eddelbuettel/r2u/news/</loc>
-         <lastmod>2026-05-01</lastmod>
+         <lastmod>2026-05-05</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://github.com/eddelbuettel/r2u/man/buildPackage/</loc>
-         <lastmod>2026-05-01</lastmod>
+         <lastmod>2026-05-05</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://github.com/eddelbuettel/r2u/man/r2u-package/</loc>
-         <lastmod>2026-05-01</lastmod>
+         <lastmod>2026-05-05</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://github.com/eddelbuettel/r2u/vignettes/Codespaces/</loc>
-         <lastmod>2026-05-01</lastmod>
+         <lastmod>2026-05-05</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://github.com/eddelbuettel/r2u/vignettes/FAQ/</loc>
-         <lastmod>2026-05-01</lastmod>
+         <lastmod>2026-05-05</lastmod>
          <changefreq>daily</changefreq>
     </url>
 </urlset>