[Genabel-commits] r2018 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Oct 6 12:34:11 CEST 2015
Author: lckarssen
Date: 2015-10-06 12:34:11 +0200 (Tue, 06 Oct 2015)
New Revision: 2018
Modified:
www/packageReviewGuidelines.html
www/packageReviewGuidelines.org
Log:
Add links to CRAN licences and GPL compatible licences to the Package Review Guidelines.
Modified: www/packageReviewGuidelines.html
===================================================================
--- www/packageReviewGuidelines.html 2015-09-21 15:27:39 UTC (rev 2017)
+++ www/packageReviewGuidelines.html 2015-10-06 10:34:11 UTC (rev 2018)
@@ -3,23 +3,30 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
+<!-- 2015-10-06 di 12:33 -->
+<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>GenABEL Project Package Review Guidelines</title>
-<!-- 2015-05-19 di 16:29 -->
-<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="generator" content="Org-mode" />
<meta name="author" content="Y. Aulchenko, L.C. Karssen" />
<style type="text/css">
<!--/*--><![CDATA[/*><!--*/
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+ .title { text-align: center;
+ margin-bottom: .2em; }
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+ font-size: medium;
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- .left { margin-left: 0px; margin-right: auto; text-align: left; }
- .center { margin-left: auto; margin-right: auto; text-align: center; }
+ .org-right { margin-left: auto; margin-right: 0px; text-align: right; }
+ .org-left { margin-left: 0px; margin-right: auto; text-align: left; }
+ .org-center { margin-left: auto; margin-right: auto; text-align: center; }
.underline { text-decoration: underline; }
#postamble p, #preamble p { font-size: 90%; margin: .2em; }
p.verse { margin-left: 3%; }
@@ -58,15 +65,14 @@
caption.t-above { caption-side: top; }
caption.t-bottom { caption-side: bottom; }
td, th { vertical-align:top; }
- th.right { text-align: center; }
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- th.center { text-align: center; }
- td.right { text-align: right; }
- td.left { text-align: left; }
- td.center { text-align: center; }
+ th.org-right { text-align: center; }
+ th.org-left { text-align: center; }
+ th.org-center { text-align: center; }
+ td.org-right { text-align: right; }
+ td.org-left { text-align: left; }
+ td.org-center { text-align: center; }
dt { font-weight: bold; }
- .footpara:nth-child(2) { display: inline; }
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+ .footpara { display: inline; }
.footdef { margin-bottom: 1em; }
.figure { padding: 1em; }
.figure p { text-align: center; }
@@ -142,53 +148,52 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
-<li><a href="#sec-1">1. Introduction</a></li>
-<li><a href="#sec-2">2. Legal issues</a>
+<li><a href="#orgheadline1">1. Introduction</a></li>
+<li><a href="#orgheadline4">2. Legal issues</a>
<ul>
-<li><a href="#sec-2-1">2.1. Is the copyright holder clearly mentioned?</a></li>
-<li><a href="#sec-2-2">2.2. Is there a clear (standard) license?</a></li>
-<li><a href="#sec-2-3">2.3. Is the license GNU GPL-compatible?</a></li>
+<li><a href="#orgheadline2">2.1. Is the copyright holder clearly mentioned?</a></li>
+<li><a href="#orgheadline3">2.2. Is there a clear (standard) license?</a></li>
</ul>
</li>
-<li><a href="#sec-3">3. Technical quality</a>
+<li><a href="#orgheadline19">3. Technical quality</a>
<ul>
-<li><a href="#sec-3-1">3.1. Is the installation procedure clearly documented? Is the code easy to compile and run?</a></li>
-<li><a href="#sec-3-2">3.2. [For R packages] Does the package pass CRAN checks ()? At minimum, run "R CMD check …" and "R CMD check –as-cran …"</a></li>
-<li><a href="#sec-3-3">3.3. Is the package documented? What is the quality of the documentation?</a></li>
-<li><a href="#sec-3-4">3.4. [For R packages] Does <code>help(PackageName)</code> provide an adequate summary of the package and a review of the major functions?</a></li>
-<li><a href="#sec-3-5">3.5. [For R packages] Does the package use Roxygen2 for documentation?</a></li>
-<li><a href="#sec-3-6">3.6. Are examples of usage provided?</a></li>
-<li><a href="#sec-3-7">3.7. Does the package provide a tutorial/vignette? Can you comment on the tutorial?</a></li>
-<li><a href="#sec-3-8">3.8. Is the source code of the tutorial/vignette provided?</a></li>
-<li><a href="#sec-3-9">3.9. Does the package make use of unit/integration/etc. tests?</a></li>
-<li><a href="#sec-3-10">3.10. [For R packages] Does the package make use of unit tests (e.g. RUnit or testthat)?</a></li>
-<li><a href="#sec-3-11">3.11. Does the code comply with the GenABEL coding standards?</a></li>
-<li><a href="#sec-3-12">3.12. Is the code readable/understandable?</a></li>
-<li><a href="#sec-3-13">3.13. Does the code contain explanatory comments?</a></li>
-<li><a href="#sec-3-14">3.14. Were the design and methods implemented in package discussed during the development process (e.g. on the genabel-devel mailing list)?</a></li>
+<li><a href="#orgheadline5">3.1. Is the installation procedure clearly documented? Is the code easy to compile and run?</a></li>
+<li><a href="#orgheadline6">3.2. [For R packages] Does the package pass CRAN checks ()? At minimum, run "R CMD check …" and "R CMD check –as-cran …"</a></li>
+<li><a href="#orgheadline7">3.3. Is the package documented? What is the quality of the documentation?</a></li>
+<li><a href="#orgheadline8">3.4. [For R packages] Does <code>help(PackageName)</code> provide an adequate summary of the package and a review of the major functions?</a></li>
+<li><a href="#orgheadline9">3.5. [For R packages] Does the package use Roxygen2 for documentation?</a></li>
+<li><a href="#orgheadline10">3.6. Are examples of usage provided?</a></li>
+<li><a href="#orgheadline11">3.7. Does the package provide a tutorial/vignette? Can you comment on the tutorial?</a></li>
+<li><a href="#orgheadline12">3.8. Is the source code of the tutorial/vignette provided?</a></li>
+<li><a href="#orgheadline13">3.9. Does the package make use of unit/integration/etc. tests?</a></li>
+<li><a href="#orgheadline14">3.10. [For R packages] Does the package make use of unit tests (e.g. RUnit or testthat)?</a></li>
+<li><a href="#orgheadline15">3.11. Does the code comply with the GenABEL coding standards?</a></li>
+<li><a href="#orgheadline16">3.12. Is the code readable/understandable?</a></li>
+<li><a href="#orgheadline17">3.13. Does the code contain explanatory comments?</a></li>
+<li><a href="#orgheadline18">3.14. Were the design and methods implemented in package discussed during the development process (e.g. on the genabel-devel mailing list)?</a></li>
</ul>
</li>
-<li><a href="#sec-4">4. Content</a>
+<li><a href="#orgheadline25">4. Content</a>
<ul>
-<li><a href="#sec-4-1">4.1. Does the package address a problem in the domain of statistical genomics?</a></li>
-<li><a href="#sec-4-2">4.2. Is it streamlining analyses not covered elsewhere in the GenABEL suite? If not, does it improve the analysis already covered?</a></li>
-<li><a href="#sec-4-3">4.3. Should it become a separate package or rather be incorporated into an existing package?</a></li>
-<li><a href="#sec-4-4">4.4. Does the package use any of the data types defined in other GenABEL packages?</a></li>
-<li><a href="#sec-4-5">4.5. Does the package use code/functions/data defined in other GenABEL packages?</a></li>
+<li><a href="#orgheadline20">4.1. Does the package address a problem in the domain of statistical genomics?</a></li>
+<li><a href="#orgheadline21">4.2. Is it streamlining analyses not covered elsewhere in the GenABEL suite? If not, does it improve the analysis already covered?</a></li>
+<li><a href="#orgheadline22">4.3. Should it become a separate package or rather be incorporated into an existing package?</a></li>
+<li><a href="#orgheadline23">4.4. Does the package use any of the data types defined in other GenABEL packages?</a></li>
+<li><a href="#orgheadline24">4.5. Does the package use code/functions/data defined in other GenABEL packages?</a></li>
</ul>
</li>
-<li><a href="#sec-5">5. Recommendations</a>
+<li><a href="#orgheadline28">5. Recommendations</a>
<ul>
-<li><a href="#sec-5-1">5.1. What are the major issues that should be addressed?</a></li>
-<li><a href="#sec-5-2">5.2. What other (optional) suggestions do you have for the author?</a></li>
+<li><a href="#orgheadline26">5.1. What are the major issues that should be addressed?</a></li>
+<li><a href="#orgheadline27">5.2. What other (optional) suggestions do you have for the author?</a></li>
</ul>
</li>
</ul>
</div>
</div>
-<div id="outline-container-sec-1" class="outline-2">
-<h2 id="sec-1"><span class="section-number-2">1</span> Introduction</h2>
+<div id="outline-container-orgheadline1" class="outline-2">
+<h2 id="orgheadline1"><span class="section-number-2">1</span> Introduction</h2>
<div class="outline-text-2" id="text-1">
<p>
One of the goals of the GenABEL project is to be an environment in
@@ -206,12 +211,10 @@
</p>
<ul class="org-ul">
<li><i>Maintainability of the package</i>: is the code understandable? Does
-it follow <a href="codingstyle.html">our coding standards</a>? Is the code documented?
-</li>
+it follow <a href="codingstyle.html">our coding standards</a>? Is the code documented?</li>
<li><i>User-friendliness</i>: What is the quality of the user
documentation? Are there any examples? Is the user interface
-compatible with what is to be expected?
-</li>
+compatible with what is to be expected?</li>
</ul>
<p>
@@ -235,99 +238,108 @@
</div>
</div>
-<div id="outline-container-sec-2" class="outline-2">
-<h2 id="sec-2"><span class="section-number-2">2</span> Legal issues</h2>
+<div id="outline-container-orgheadline4" class="outline-2">
+<h2 id="orgheadline4"><span class="section-number-2">2</span> Legal issues</h2>
<div class="outline-text-2" id="text-2">
-</div><div id="outline-container-sec-2-1" class="outline-3">
-<h3 id="sec-2-1"><span class="section-number-3">2.1</span> Is the copyright holder clearly mentioned?</h3>
+</div><div id="outline-container-orgheadline2" class="outline-3">
+<h3 id="orgheadline2"><span class="section-number-3">2.1</span> Is the copyright holder clearly mentioned?</h3>
</div>
-<div id="outline-container-sec-2-2" class="outline-3">
-<h3 id="sec-2-2"><span class="section-number-3">2.2</span> Is there a clear (standard) license?</h3>
+<div id="outline-container-orgheadline3" class="outline-3">
+<h3 id="orgheadline3"><span class="section-number-3">2.2</span> Is there a clear (standard) license?</h3>
+<div class="outline-text-3" id="text-2-2">
+<p>
+If yes:
+</p>
+<ul class="org-ul">
+<li>is it on the list of licences accepted by CRAN
+(<a href="https://svn.r-project.org/R/trunk/share/licenses/license.db">https://svn.r-project.org/R/trunk/share/licenses/license.db</a>)?</li>
+<li>is it on the list of GPL compatible licences
+(<a href="http://www.gnu.org/licenses/license-list.en.html#GPLCompatibleLicenses">http://www.gnu.org/licenses/license-list.en.html#GPLCompatibleLicenses</a>)?
+This is optional to package acceptance.</li>
+</ul>
</div>
-<div id="outline-container-sec-2-3" class="outline-3">
-<h3 id="sec-2-3"><span class="section-number-3">2.3</span> Is the license GNU GPL-compatible?</h3>
</div>
</div>
-<div id="outline-container-sec-3" class="outline-2">
-<h2 id="sec-3"><span class="section-number-2">3</span> Technical quality</h2>
+<div id="outline-container-orgheadline19" class="outline-2">
+<h2 id="orgheadline19"><span class="section-number-2">3</span> Technical quality</h2>
<div class="outline-text-2" id="text-3">
-</div><div id="outline-container-sec-3-1" class="outline-3">
-<h3 id="sec-3-1"><span class="section-number-3">3.1</span> Is the installation procedure clearly documented? Is the code easy to compile and run?</h3>
+</div><div id="outline-container-orgheadline5" class="outline-3">
+<h3 id="orgheadline5"><span class="section-number-3">3.1</span> Is the installation procedure clearly documented? Is the code easy to compile and run?</h3>
</div>
-<div id="outline-container-sec-3-2" class="outline-3">
-<h3 id="sec-3-2"><span class="section-number-3">3.2</span> [For R packages] Does the package pass CRAN checks (<a href="http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Checking-packages">http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Checking-packages</a>)? At minimum, run "R CMD check …" and "R CMD check –as-cran …"</h3>
+<div id="outline-container-orgheadline6" class="outline-3">
+<h3 id="orgheadline6"><span class="section-number-3">3.2</span> [For R packages] Does the package pass CRAN checks (<a href="http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Checking-packages">http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Checking-packages</a>)? At minimum, run "R CMD check …" and "R CMD check –as-cran …"</h3>
</div>
-<div id="outline-container-sec-3-3" class="outline-3">
-<h3 id="sec-3-3"><span class="section-number-3">3.3</span> Is the package documented? What is the quality of the documentation?</h3>
+<div id="outline-container-orgheadline7" class="outline-3">
+<h3 id="orgheadline7"><span class="section-number-3">3.3</span> Is the package documented? What is the quality of the documentation?</h3>
</div>
-<div id="outline-container-sec-3-4" class="outline-3">
-<h3 id="sec-3-4"><span class="section-number-3">3.4</span> [For R packages] Does <code>help(PackageName)</code> provide an adequate summary of the package and a review of the major functions?</h3>
+<div id="outline-container-orgheadline8" class="outline-3">
+<h3 id="orgheadline8"><span class="section-number-3">3.4</span> [For R packages] Does <code>help(PackageName)</code> provide an adequate summary of the package and a review of the major functions?</h3>
</div>
-<div id="outline-container-sec-3-5" class="outline-3">
-<h3 id="sec-3-5"><span class="section-number-3">3.5</span> [For R packages] Does the package use Roxygen2 for documentation?</h3>
+<div id="outline-container-orgheadline9" class="outline-3">
+<h3 id="orgheadline9"><span class="section-number-3">3.5</span> [For R packages] Does the package use Roxygen2 for documentation?</h3>
</div>
-<div id="outline-container-sec-3-6" class="outline-3">
-<h3 id="sec-3-6"><span class="section-number-3">3.6</span> Are examples of usage provided?</h3>
+<div id="outline-container-orgheadline10" class="outline-3">
+<h3 id="orgheadline10"><span class="section-number-3">3.6</span> Are examples of usage provided?</h3>
</div>
-<div id="outline-container-sec-3-7" class="outline-3">
-<h3 id="sec-3-7"><span class="section-number-3">3.7</span> Does the package provide a tutorial/vignette? Can you comment on the tutorial?</h3>
+<div id="outline-container-orgheadline11" class="outline-3">
+<h3 id="orgheadline11"><span class="section-number-3">3.7</span> Does the package provide a tutorial/vignette? Can you comment on the tutorial?</h3>
</div>
-<div id="outline-container-sec-3-8" class="outline-3">
-<h3 id="sec-3-8"><span class="section-number-3">3.8</span> Is the source code of the tutorial/vignette provided?</h3>
+<div id="outline-container-orgheadline12" class="outline-3">
+<h3 id="orgheadline12"><span class="section-number-3">3.8</span> Is the source code of the tutorial/vignette provided?</h3>
</div>
-<div id="outline-container-sec-3-9" class="outline-3">
-<h3 id="sec-3-9"><span class="section-number-3">3.9</span> Does the package make use of unit/integration/etc. tests?</h3>
+<div id="outline-container-orgheadline13" class="outline-3">
+<h3 id="orgheadline13"><span class="section-number-3">3.9</span> Does the package make use of unit/integration/etc. tests?</h3>
</div>
-<div id="outline-container-sec-3-10" class="outline-3">
-<h3 id="sec-3-10"><span class="section-number-3">3.10</span> [For R packages] Does the package make use of unit tests (e.g. RUnit or testthat)?</h3>
+<div id="outline-container-orgheadline14" class="outline-3">
+<h3 id="orgheadline14"><span class="section-number-3">3.10</span> [For R packages] Does the package make use of unit tests (e.g. RUnit or testthat)?</h3>
</div>
-<div id="outline-container-sec-3-11" class="outline-3">
-<h3 id="sec-3-11"><span class="section-number-3">3.11</span> Does the code comply with the <a href="codingstyle.html">GenABEL coding standards</a>?</h3>
+<div id="outline-container-orgheadline15" class="outline-3">
+<h3 id="orgheadline15"><span class="section-number-3">3.11</span> Does the code comply with the <a href="codingstyle.html">GenABEL coding standards</a>?</h3>
</div>
-<div id="outline-container-sec-3-12" class="outline-3">
-<h3 id="sec-3-12"><span class="section-number-3">3.12</span> Is the code readable/understandable?</h3>
+<div id="outline-container-orgheadline16" class="outline-3">
+<h3 id="orgheadline16"><span class="section-number-3">3.12</span> Is the code readable/understandable?</h3>
</div>
-<div id="outline-container-sec-3-13" class="outline-3">
-<h3 id="sec-3-13"><span class="section-number-3">3.13</span> Does the code contain explanatory comments?</h3>
+<div id="outline-container-orgheadline17" class="outline-3">
+<h3 id="orgheadline17"><span class="section-number-3">3.13</span> Does the code contain explanatory comments?</h3>
</div>
-<div id="outline-container-sec-3-14" class="outline-3">
-<h3 id="sec-3-14"><span class="section-number-3">3.14</span> Were the design and methods implemented in package discussed during the development process (e.g. on the genabel-devel mailing list)?</h3>
+<div id="outline-container-orgheadline18" class="outline-3">
+<h3 id="orgheadline18"><span class="section-number-3">3.14</span> Were the design and methods implemented in package discussed during the development process (e.g. on the genabel-devel mailing list)?</h3>
</div>
</div>
-<div id="outline-container-sec-4" class="outline-2">
-<h2 id="sec-4"><span class="section-number-2">4</span> Content</h2>
+<div id="outline-container-orgheadline25" class="outline-2">
+<h2 id="orgheadline25"><span class="section-number-2">4</span> Content</h2>
<div class="outline-text-2" id="text-4">
-</div><div id="outline-container-sec-4-1" class="outline-3">
-<h3 id="sec-4-1"><span class="section-number-3">4.1</span> Does the package address a problem in the domain of statistical genomics?</h3>
+</div><div id="outline-container-orgheadline20" class="outline-3">
+<h3 id="orgheadline20"><span class="section-number-3">4.1</span> Does the package address a problem in the domain of statistical genomics?</h3>
</div>
-<div id="outline-container-sec-4-2" class="outline-3">
-<h3 id="sec-4-2"><span class="section-number-3">4.2</span> Is it streamlining analyses not covered elsewhere in the GenABEL suite? If not, does it improve the analysis already covered?</h3>
+<div id="outline-container-orgheadline21" class="outline-3">
+<h3 id="orgheadline21"><span class="section-number-3">4.2</span> Is it streamlining analyses not covered elsewhere in the GenABEL suite? If not, does it improve the analysis already covered?</h3>
</div>
-<div id="outline-container-sec-4-3" class="outline-3">
-<h3 id="sec-4-3"><span class="section-number-3">4.3</span> Should it become a separate package or rather be incorporated into an existing package?</h3>
+<div id="outline-container-orgheadline22" class="outline-3">
+<h3 id="orgheadline22"><span class="section-number-3">4.3</span> Should it become a separate package or rather be incorporated into an existing package?</h3>
</div>
-<div id="outline-container-sec-4-4" class="outline-3">
-<h3 id="sec-4-4"><span class="section-number-3">4.4</span> Does the package use any of the data types defined in other GenABEL packages?</h3>
+<div id="outline-container-orgheadline23" class="outline-3">
+<h3 id="orgheadline23"><span class="section-number-3">4.4</span> Does the package use any of the data types defined in other GenABEL packages?</h3>
</div>
-<div id="outline-container-sec-4-5" class="outline-3">
-<h3 id="sec-4-5"><span class="section-number-3">4.5</span> Does the package use code/functions/data defined in other GenABEL packages?</h3>
+<div id="outline-container-orgheadline24" class="outline-3">
+<h3 id="orgheadline24"><span class="section-number-3">4.5</span> Does the package use code/functions/data defined in other GenABEL packages?</h3>
</div>
</div>
-<div id="outline-container-sec-5" class="outline-2">
-<h2 id="sec-5"><span class="section-number-2">5</span> Recommendations</h2>
+<div id="outline-container-orgheadline28" class="outline-2">
+<h2 id="orgheadline28"><span class="section-number-2">5</span> Recommendations</h2>
<div class="outline-text-2" id="text-5">
-</div><div id="outline-container-sec-5-1" class="outline-3">
-<h3 id="sec-5-1"><span class="section-number-3">5.1</span> What are the major issues that should be addressed?</h3>
+</div><div id="outline-container-orgheadline26" class="outline-3">
+<h3 id="orgheadline26"><span class="section-number-3">5.1</span> What are the major issues that should be addressed?</h3>
</div>
-<div id="outline-container-sec-5-2" class="outline-3">
-<h3 id="sec-5-2"><span class="section-number-3">5.2</span> What other (optional) suggestions do you have for the author?</h3>
+<div id="outline-container-orgheadline27" class="outline-3">
+<h3 id="orgheadline27"><span class="section-number-3">5.2</span> What other (optional) suggestions do you have for the author?</h3>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="date">Date: <span class="timestamp-wrapper"><span class="timestamp"><2015-01-14 wo></span></span></p>
<p class="author">Author: Y. Aulchenko, L.C. Karssen</p>
-<p class="date">Created: 2015-05-19 di 16:29</p>
+<p class="date">Created: 2015-10-06 di 12:33</p>
<p class="creator">Emacs 24.3.1 (Org mode 8.2.4)</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
Modified: www/packageReviewGuidelines.org
===================================================================
--- www/packageReviewGuidelines.org 2015-09-21 15:27:39 UTC (rev 2017)
+++ www/packageReviewGuidelines.org 2015-10-06 10:34:11 UTC (rev 2018)
@@ -46,7 +46,12 @@
* Legal issues
** Is the copyright holder clearly mentioned?
** Is there a clear (standard) license?
-** Is the license GNU GPL-compatible?
+ If yes:
+ - is it on the list of licences accepted by CRAN
+ (https://svn.r-project.org/R/trunk/share/licenses/license.db)?
+ - is it on the list of GPL compatible licences
+ (http://www.gnu.org/licenses/license-list.en.html#GPLCompatibleLicenses)?
+ This is optional to package acceptance.
* Technical quality
** Is the installation procedure clearly documented? Is the code easy to compile and run?
** [For R packages] Does the package pass CRAN checks (http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Checking-packages)? At minimum, run "R CMD check ..." and "R CMD check --as-cran ..."
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