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14 changes: 14 additions & 0 deletions docs/changelog/index.html
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<h1>Changelog</h1>

<h3 id="2024">2024</h3>
<p>2024-05-12 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: Document 24.04 support
</code></pre>
<p>2024-05-11 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/package.R (.get_source_file): Always download source file if
'force' and 'compile' are set
* R/controlFiles.R (.addDepends): Refine one regular expression
</code></pre>
<p>2024-05-10 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: Support Ubuntu 24.04
* R/package.R: Idem
* inst/scripts/add_cranapt_noble.sh: Idem
* docker/noble/*: Build and run-time support for 24.04
</code></pre>
<p>2024-04-12 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 (.loadRuntimedepends): Support run-time dependency
declarations via config file
Expand Down
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<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 (currently) ~ 22913 CRAN packages (and 406 from BioConductor) using
<strong>current versions</strong>: We use R 4.3.3, and BioConductor 3.18.</p>
<p><strong>Complete coverage</strong> with (currently, using 22.04) ~ 23199 CRAN packages (and 411 from
BioConductor) using <strong>current versions</strong>: We use R 4.4.0, and BioConductor 3.19 (on 24.04, and
soon too on 22.04) and 3.18 (on 20.04).</p>
</li>
<li>
<p>Complete support for both <strong>Ubuntu 20.04</strong> ("focal") <strong>and Ubuntu 22.04</strong> ("jammy").</p>
<p>Complete support for both <strong>Ubuntu 20.04</strong> ("focal") <strong>and Ubuntu 22.04</strong> ("jammy") <strong>and Ubuntu
24.04</strong> ("noble").</p>
</li>
<li>
<p>Optional (but recommended) <a href="https://cloud.r-project.org/package=bspm">bspm</a> use
Expand All @@ -1037,10 +1039,10 @@ <h3 id="key-features">Key features</h3>
</li>
<li>
<p><strong>Docker containers</strong> <code>rocker/r2u</code> from the <a href="https://rocker-project.org/">Rocker Project</a> for both
'focal' and 'jammy'.</p>
'focal', 'jammy' and 'noble'.</p>
</li>
<li>
<p><strong>GitHub Actions support</strong> to set up on Ubuntu 22.04 "jammy" or via container</p>
<p><strong>GitHub Actions support</strong> to set up on Ubuntu 22.04 "jammy" or via container.</p>
</li>
</ul>
<h3 id="brief-demo">Brief Demo</h3>
Expand All @@ -1054,16 +1056,16 @@ <h3 id="what-is-covered">What is Covered ?</h3>
<p>We generally support amd64 (<em>i.e.</em> standard 64-bit Intel/AMD cpus, sometimes also called x86_64) for
the current Ubuntu LTS release and its predecessor release (more on this
<a href="https://eddelbuettel.github.io/r2u/vignettes/FAQ/#what-about-other-architectures-besides-x86_64">here</a>).
We use 'r-release' just like CRAN. So currently the 'focal' 20.04 LTS and 'jammy' 22.04 LTS releases
are fully supported.</p>
We use 'r-release' just like CRAN. So currently the 'focal' 20.04 LTS, 'jammy' 22.04 LTS and 'noble'
24.04 releases are fully supported.</p>
<p>Support for other cpu architectures is certainly possible but somewhat unlikely due to a lack of
(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 based on R 4.3.3, and BioConductor release 3.18 packages are provided when
required by CRAN packages. Binaries are generally R 4.3.<em> based. Some older packages released when
we used R 4.2.</em> may have been built with R 4.2.<em>, they will still work the same with R 4.3.</em> as R is
generally forward-compatible.</p>
<p>Current versions are based on R 4.4.0, and BioConductor release 3.19 (for 'noble' and 'jammy')
packages are provided when required by CRAN packages. Binaries are generally R 4.4.<em> based. 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.</em> as R is generally forward-compatible.</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>
Expand All @@ -1078,17 +1080,19 @@ <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 23002 and 22913 binary packages from CRAN in "focal" and "jammy",
respectively, and 406 and 406 BioConductor packages, respectively, from the 3.18 release. (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.)</p>
<p>This currently results in 23286, 23199, 20744 binary packages from CRAN in "focal", "jammy", and
"noble", respectively, and 412, 411, and 428 BioConductor packages, respectively, from the 3.19 and
3.18 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 two packages we cannot build (as we do not have the required commercial
software it accessess) plus less than a handful of 'odd builds' that fail and
are skipped.</p>
<h3 id="what-is-it-based-on">What is it Based On?</h3>
<p>For the CRAN binaries we either repackage
<a href="https://packagemanager.rstudio.com/client/#/repos/2/packages/">RSPM/PPM</a> builds (where available)
or build natively. All selected BioConductor 3.18 packages are built natively. For all of these,
full dependency resolution and integration with the system is a key feature.</p>
<a href="https://packagemanager.rstudio.com/client/#/repos/2/packages/">P3M/RSPM/PPM</a> builds (where
available) or build natively. All selected BioConductor packages are built natively. For all of
these, full dependency resolution and integration with the system is a key feature.</p>
<p>Everything is provided as <code>.deb</code> binary files with proper dependency
resolution by using a proper <code>apt</code> repo which also has a signed Release file.</p>
<h3 id="usage-and-setup">Usage and Setup</h3>
Expand Down Expand Up @@ -1169,14 +1173,14 @@ <h3 id="about-pinning">About Pinning</h3>
give the r2u / cranapt repo a weight of 700 which is higher than the package default value of
500.</p>
<h3 id="docker">Docker</h3>
<p>There are also two Docker containers for Ubuntu 20.04 'focal' and 22.04 'jammy', respectively.
Initially published as
<p>There are also Docker containers for Ubuntu 20.04 'focal', 22.04 'jammy', and 24.04 'noble',
respectively. Initially published as
<a href="https://hub.docker.com/repository/docker/eddelbuettel/r2u">eddelbuettel/r2u</a>, these are now also
available also as <a href="https://github.com/rocker-org/r2u">rocker/r2u</a>. They all have the features
detailed above, including pinning and <a href="https://cran.r-project.org/package=bspm">bspm</a> support,
already set up. </p>
already set up.</p>
<p>Each of the Ubuntu LTS flavors, <em>i.e.</em>, 'focal' and 'jammy' is also available as an identical image
using the release version, <em>i.e.</em>, '20.04' and '22.04', respectively.</p>
using the release version, <em>i.e.</em>, '20.04', '22.04', and '24.04', respectively.</p>
<p>Note that with some builds of Docker (and possibly related to Ubuntu hosts) you may have to add
the <code>--security-opt seccomp=unconfined</code> option to your Docker invocation to take advantage of bspm
and the full system integration inside the container.
Expand Down
14 changes: 14 additions & 0 deletions docs/mkdmt-src/docs/changelog/index.html
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Expand Up @@ -676,6 +676,20 @@
<h1>Changelog</h1>

<h3 id="2024">2024</h3>
<p>2024-05-12 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: Document 24.04 support
</code></pre>
<p>2024-05-11 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/package.R (.get_source_file): Always download source file if
'force' and 'compile' are set
* R/controlFiles.R (.addDepends): Refine one regular expression
</code></pre>
<p>2024-05-10 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: Support Ubuntu 24.04
* R/package.R: Idem
* inst/scripts/add_cranapt_noble.sh: Idem
* docker/noble/*: Build and run-time support for 24.04
</code></pre>
<p>2024-04-12 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 (.loadRuntimedepends): Support run-time dependency
declarations via config file
Expand Down
46 changes: 25 additions & 21 deletions docs/mkdmt-src/docs/index.html
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Original file line number Diff line number Diff line change
Expand Up @@ -1024,11 +1024,13 @@ <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 (currently) ~ 22913 CRAN packages (and 406 from BioConductor) using
<strong>current versions</strong>: We use R 4.3.3, and BioConductor 3.18.</p>
<p><strong>Complete coverage</strong> with (currently, using 22.04) ~ 23199 CRAN packages (and 411 from
BioConductor) using <strong>current versions</strong>: We use R 4.4.0, and BioConductor 3.19 (on 24.04, and
soon too on 22.04) and 3.18 (on 20.04).</p>
</li>
<li>
<p>Complete support for both <strong>Ubuntu 20.04</strong> ("focal") <strong>and Ubuntu 22.04</strong> ("jammy").</p>
<p>Complete support for both <strong>Ubuntu 20.04</strong> ("focal") <strong>and Ubuntu 22.04</strong> ("jammy") <strong>and Ubuntu
24.04</strong> ("noble").</p>
</li>
<li>
<p>Optional (but recommended) <a href="https://cloud.r-project.org/package=bspm">bspm</a> use
Expand All @@ -1037,10 +1039,10 @@ <h3 id="key-features">Key features</h3>
</li>
<li>
<p><strong>Docker containers</strong> <code>rocker/r2u</code> from the <a href="https://rocker-project.org/">Rocker Project</a> for both
'focal' and 'jammy'.</p>
'focal', 'jammy' and 'noble'.</p>
</li>
<li>
<p><strong>GitHub Actions support</strong> to set up on Ubuntu 22.04 "jammy" or via container</p>
<p><strong>GitHub Actions support</strong> to set up on Ubuntu 22.04 "jammy" or via container.</p>
</li>
</ul>
<h3 id="brief-demo">Brief Demo</h3>
Expand All @@ -1054,16 +1056,16 @@ <h3 id="what-is-covered">What is Covered ?</h3>
<p>We generally support amd64 (<em>i.e.</em> standard 64-bit Intel/AMD cpus, sometimes also called x86_64) for
the current Ubuntu LTS release and its predecessor release (more on this
<a href="https://eddelbuettel.github.io/r2u/vignettes/FAQ/#what-about-other-architectures-besides-x86_64">here</a>).
We use 'r-release' just like CRAN. So currently the 'focal' 20.04 LTS and 'jammy' 22.04 LTS releases
are fully supported.</p>
We use 'r-release' just like CRAN. So currently the 'focal' 20.04 LTS, 'jammy' 22.04 LTS and 'noble'
24.04 releases are fully supported.</p>
<p>Support for other cpu architectures is certainly possible but somewhat unlikely due to a lack of
(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 based on R 4.3.3, and BioConductor release 3.18 packages are provided when
required by CRAN packages. Binaries are generally R 4.3.<em> based. Some older packages released when
we used R 4.2.</em> may have been built with R 4.2.<em>, they will still work the same with R 4.3.</em> as R is
generally forward-compatible.</p>
<p>Current versions are based on R 4.4.0, and BioConductor release 3.19 (for 'noble' and 'jammy')
packages are provided when required by CRAN packages. Binaries are generally R 4.4.<em> based. 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.</em> as R is generally forward-compatible.</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>
Expand All @@ -1078,17 +1080,19 @@ <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 23002 and 22913 binary packages from CRAN in "focal" and "jammy",
respectively, and 406 and 406 BioConductor packages, respectively, from the 3.18 release. (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.)</p>
<p>This currently results in 23286, 23199, 20744 binary packages from CRAN in "focal", "jammy", and
"noble", respectively, and 412, 411, and 428 BioConductor packages, respectively, from the 3.19 and
3.18 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 two packages we cannot build (as we do not have the required commercial
software it accessess) plus less than a handful of 'odd builds' that fail and
are skipped.</p>
<h3 id="what-is-it-based-on">What is it Based On?</h3>
<p>For the CRAN binaries we either repackage
<a href="https://packagemanager.rstudio.com/client/#/repos/2/packages/">RSPM/PPM</a> builds (where available)
or build natively. All selected BioConductor 3.18 packages are built natively. For all of these,
full dependency resolution and integration with the system is a key feature.</p>
<a href="https://packagemanager.rstudio.com/client/#/repos/2/packages/">P3M/RSPM/PPM</a> builds (where
available) or build natively. All selected BioConductor packages are built natively. For all of
these, full dependency resolution and integration with the system is a key feature.</p>
<p>Everything is provided as <code>.deb</code> binary files with proper dependency
resolution by using a proper <code>apt</code> repo which also has a signed Release file.</p>
<h3 id="usage-and-setup">Usage and Setup</h3>
Expand Down Expand Up @@ -1169,14 +1173,14 @@ <h3 id="about-pinning">About Pinning</h3>
give the r2u / cranapt repo a weight of 700 which is higher than the package default value of
500.</p>
<h3 id="docker">Docker</h3>
<p>There are also two Docker containers for Ubuntu 20.04 'focal' and 22.04 'jammy', respectively.
Initially published as
<p>There are also Docker containers for Ubuntu 20.04 'focal', 22.04 'jammy', and 24.04 'noble',
respectively. Initially published as
<a href="https://hub.docker.com/repository/docker/eddelbuettel/r2u">eddelbuettel/r2u</a>, these are now also
available also as <a href="https://github.com/rocker-org/r2u">rocker/r2u</a>. They all have the features
detailed above, including pinning and <a href="https://cran.r-project.org/package=bspm">bspm</a> support,
already set up. </p>
already set up.</p>
<p>Each of the Ubuntu LTS flavors, <em>i.e.</em>, 'focal' and 'jammy' is also available as an identical image
using the release version, <em>i.e.</em>, '20.04' and '22.04', respectively.</p>
using the release version, <em>i.e.</em>, '20.04', '22.04', and '24.04', respectively.</p>
<p>Note that with some builds of Docker (and possibly related to Ubuntu hosts) you may have to add
the <code>--security-opt seccomp=unconfined</code> option to your Docker invocation to take advantage of bspm
and the full system integration inside the container.
Expand Down
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<h1>News</h1>

<section id="NEWS" class="container">
<h2>News for Package <code>r2u</code></h2>
<div class="container">
<div role="main">
<h3 id="version-0.0.7-2024-05-12">Version 0.0.7 (2024-05-12)</h3>
<ul>
<li><p>Add support for Ubuntu 24.04 aka 'noble'</p></li>
<li><p>Switch to BioConductor 3.19 and rebuild all r-bioc-* packages (in
'noble' aks 24.04, jammy to follow)</p></li>
</ul>
<h3 id="version-0.0.6-2023-11-04">Version 0.0.6 (2023-11-04)</h3>
<ul>
<li><p>Switch to BioConductor 3.18 and rebuild all r-bioc-*
Expand Down Expand Up @@ -627,7 +633,8 @@ <h3 id="version-0.0.1-2022-05-04">Version 0.0.1 (2022-05-04)</h3>
<ul>
<li><p>Initial release for Ubuntu 20.04</p></li>
</ul>
</section>
</div>
</div>



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