[med-svn] [snakemake] 03/05: Skip the test_script unit test that depends on rmarkdown
chrysn
chrysn-guest at moszumanska.debian.org
Mon Dec 11 16:18:43 UTC 2017
This is an automated email from the git hooks/post-receive script.
chrysn-guest pushed a commit to branch master
in repository snakemake.
commit b21e1e99a5d085338bd1bba6445b4cf6492cd59a
Author: chrysn <chrysn at fsfe.org>
Date: Mon Dec 11 15:14:36 2017 +0100
Skip the test_script unit test that depends on rmarkdown
Note that rmarkdown is distinct from what is packaged in r-cran-markdown
(we're rather looking for an unpackaged r-cran-rmarkdown here).
---
.../patches/0010-skip-test-without-rmarkdown.patch | 278 +++++++++++++++++++++
debian/patches/series | 1 +
2 files changed, 279 insertions(+)
diff --git a/debian/patches/0010-skip-test-without-rmarkdown.patch b/debian/patches/0010-skip-test-without-rmarkdown.patch
new file mode 100644
index 0000000..8453c0f
--- /dev/null
+++ b/debian/patches/0010-skip-test-without-rmarkdown.patch
@@ -0,0 +1,278 @@
+--- a/tests/test_script/Snakefile
++++ b/tests/test_script/Snakefile
+@@ -4,7 +4,6 @@
+ rule all:
+ input:
+ "test.out",
+- "test.html"
+
+
+ rule:
+@@ -22,11 +21,3 @@
+ "test.in"
+ script:
+ "scripts/test.py"
+-
+-rule:
+- output:
+- "test.html"
+- params:
+- test="testparam"
+- script:
+- "scripts/test.Rmd"
+--- a/tests/test_script/expected-results/test.html
++++ /dev/null
+@@ -1,253 +0,0 @@
+-<!DOCTYPE html>
+-
+-<html xmlns="http://www.w3.org/1999/xhtml">
+-
+-<head>
+-
+-<meta charset="utf-8" />
+-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+-<meta name="generator" content="pandoc" />
+-
+-
+-<meta name="author" content="Mattias" />
+-
+-<meta name="date" content="2017-03-22" />
+-
+-<title>Test Report</title>
+-
+-<script src="data:application/x-javascript;base64,LyohIGpRdWVyeSB2MS4xMS4zIHwgKGMpIDIwMDUsIDIwMTUgalF1ZXJ5IEZvdW5kYXRpb24sIEluYy4gfCBqcXVlcnkub3JnL2xpY2Vuc2UgKi8KIWZ1bmN0aW9uKGEsYil7Im9iamVjdCI9PXR5cGVvZiBtb2R1bGUmJiJvYmplY3QiPT10eXBlb2YgbW9kdWxlLmV4cG9ydHM/bW9kdWxlLmV4cG9ydHM9YS5kb2N1bWVudD9iKGEsITApOmZ1bmN0aW9uKGEpe2lmKCFhLmRvY3VtZW50KXRocm93IG5ldyBFcnJvcigialF1ZXJ5IHJlcXVpcmVzIGEgd2luZG93IHdpdGggYSBkb2N1bWVudCIpO3JldHVybiBiKGEpfTpiKGEpfSgidW5kZWZpbmVkIiE9dHlwZW9mIHdpbmRvdz93aW5kb3c6d [...]
+-<meta name="viewport" content="width=device-width, initial-scale=1" />
+-<link href="data:text/css;charset=utf-8,html%7Bfont%2Dfamily%3Asans%2Dserif%3B%2Dwebkit%2Dtext%2Dsize%2Dadjust%3A100%25%3B%2Dms%2Dtext%2Dsize%2Dadjust%3A100%25%7Dbody%7Bmargin%3A0%7Darticle%2Caside%2Cdetails%2Cfigcaption%2Cfigure%2Cfooter%2Cheader%2Chgroup%2Cmain%2Cmenu%2Cnav%2Csection%2Csummary%7Bdisplay%3Ablock%7Daudio%2Ccanvas%2Cprogress%2Cvideo%7Bdisplay%3Ainline%2Dblock%3Bvertical%2Dalign%3Abaseline%7Daudio%3Anot%28%5Bcontrols%5D%29%7Bdisplay%3Anone%3Bheight%3A0%7D%5Bhidden%5D%2Cte [...]
+-<script src="data:application/x-javascript;base64,LyohCiAqIEJvb3RzdHJhcCB2My4zLjUgKGh0dHA6Ly9nZXRib290c3RyYXAuY29tKQogKiBDb3B5cmlnaHQgMjAxMS0yMDE1IFR3aXR0ZXIsIEluYy4KICogTGljZW5zZWQgdW5kZXIgdGhlIE1JVCBsaWNlbnNlCiAqLwppZigidW5kZWZpbmVkIj09dHlwZW9mIGpRdWVyeSl0aHJvdyBuZXcgRXJyb3IoIkJvb3RzdHJhcCdzIEphdmFTY3JpcHQgcmVxdWlyZXMgalF1ZXJ5Iik7K2Z1bmN0aW9uKGEpeyJ1c2Ugc3RyaWN0Ijt2YXIgYj1hLmZuLmpxdWVyeS5zcGxpdCgiICIpWzBdLnNwbGl0KCIuIik7aWYoYlswXTwyJiZiWzFdPDl8fDE9PWJbMF0mJjk9PWJbMV0mJmJbMl08MSl0aHJvd [...]
+-<script src="data:application/x-javascript;base64,LyoqCiogQHByZXNlcnZlIEhUTUw1IFNoaXYgMy43LjIgfCBAYWZhcmthcyBAamRhbHRvbiBAam9uX25lYWwgQHJlbSB8IE1JVC9HUEwyIExpY2Vuc2VkCiovCi8vIE9ubHkgcnVuIHRoaXMgY29kZSBpbiBJRSA4CmlmICghIXdpbmRvdy5uYXZpZ2F0b3IudXNlckFnZW50Lm1hdGNoKCJNU0lFIDgiKSkgewohZnVuY3Rpb24oYSxiKXtmdW5jdGlvbiBjKGEsYil7dmFyIGM9YS5jcmVhdGVFbGVtZW50KCJwIiksZD1hLmdldEVsZW1lbnRzQnlUYWdOYW1lKCJoZWFkIilbMF18fGEuZG9jdW1lbnRFbGVtZW50O3JldHVybiBjLmlubmVySFRNTD0ieDxzdHlsZT4iK2IrIjwvc3R5bGU+IixkL [...]
+-<script src="data:application/x-javascript;base64,LyohIFJlc3BvbmQuanMgdjEuNC4yOiBtaW4vbWF4LXdpZHRoIG1lZGlhIHF1ZXJ5IHBvbHlmaWxsICogQ29weXJpZ2h0IDIwMTMgU2NvdHQgSmVobAogKiBMaWNlbnNlZCB1bmRlciBodHRwczovL2dpdGh1Yi5jb20vc2NvdHRqZWhsL1Jlc3BvbmQvYmxvYi9tYXN0ZXIvTElDRU5TRS1NSVQKICogICovCgovLyBPbmx5IHJ1biB0aGlzIGNvZGUgaW4gSUUgOAppZiAoISF3aW5kb3cubmF2aWdhdG9yLnVzZXJBZ2VudC5tYXRjaCgiTVNJRSA4IikpIHsKIWZ1bmN0aW9uKGEpeyJ1c2Ugc3RyaWN0IjthLm1hdGNoTWVkaWE9YS5tYXRjaE1lZGlhfHxmdW5jdGlvbihhKXt2YXIgYixjPWEuZ [...]
+-<script src="data:application/x-javascript;base64,LyohIGpRdWVyeSBVSSAtIHYxLjExLjQgLSAyMDE2LTAxLTA1CiogaHR0cDovL2pxdWVyeXVpLmNvbQoqIEluY2x1ZGVzOiBjb3JlLmpzLCB3aWRnZXQuanMsIG1vdXNlLmpzLCBwb3NpdGlvbi5qcywgZHJhZ2dhYmxlLmpzLCBkcm9wcGFibGUuanMsIHJlc2l6YWJsZS5qcywgc2VsZWN0YWJsZS5qcywgc29ydGFibGUuanMsIGFjY29yZGlvbi5qcywgYXV0b2NvbXBsZXRlLmpzLCBidXR0b24uanMsIGRpYWxvZy5qcywgbWVudS5qcywgcHJvZ3Jlc3NiYXIuanMsIHNlbGVjdG1lbnUuanMsIHNsaWRlci5qcywgc3Bpbm5lci5qcywgdGFicy5qcywgdG9vbHRpcC5qcywgZWZmZWN0LmpzL [...]
+-<link href="data:text/css;charset=utf-8,%0A%0A%2Etocify%20%7B%0Awidth%3A%2020%25%3B%0Amax%2Dheight%3A%2090%25%3B%0Aoverflow%3A%20auto%3B%0Amargin%2Dleft%3A%202%25%3B%0Aposition%3A%20fixed%3B%0Aborder%3A%201px%20solid%20%23ccc%3B%0Awebkit%2Dborder%2Dradius%3A%206px%3B%0Amoz%2Dborder%2Dradius%3A%206px%3B%0Aborder%2Dradius%3A%206px%3B%0A%7D%0A%0A%2Etocify%20ul%2C%20%2Etocify%20li%20%7B%0Alist%2Dstyle%3A%20none%3B%0Amargin%3A%200%3B%0Apadding%3A%200%3B%0Aborder%3A%20none%3B%0Aline%2Dheight% [...]
+-<script src="data:application/x-javascript;base64,LyoganF1ZXJ5IFRvY2lmeSAtIHYxLjkuMSAtIDIwMTMtMTAtMjIKICogaHR0cDovL3d3dy5ncmVnZnJhbmtvLmNvbS9qcXVlcnkudG9jaWZ5LmpzLwogKiBDb3B5cmlnaHQgKGMpIDIwMTMgR3JlZyBGcmFua287IExpY2Vuc2VkIE1JVCAqLwoKLy8gSW1tZWRpYXRlbHktSW52b2tlZCBGdW5jdGlvbiBFeHByZXNzaW9uIChJSUZFKSBbQmVuIEFsbWFuIEJsb2cgUG9zdF0oaHR0cDovL2JlbmFsbWFuLmNvbS9uZXdzLzIwMTAvMTEvaW1tZWRpYXRlbHktaW52b2tlZC1mdW5jdGlvbi1leHByZXNzaW9uLykgdGhhdCBjYWxscyBhbm90aGVyIElJRkUgdGhhdCBjb250YWlucyBhbGwgb2Ygd [...]
+-<script src="data:application/x-javascript;base64,CgovKioKICogalF1ZXJ5IFBsdWdpbjogU3RpY2t5IFRhYnMKICoKICogQGF1dGhvciBBaWRhbiBMaXN0ZXIgPGFpZGFuQHBocC5uZXQ+CiAqIGFkYXB0ZWQgYnkgUnViZW4gQXJzbGFuIHRvIGFjdGl2YXRlIHBhcmVudCB0YWJzIHRvbwogKiBodHRwOi8vd3d3LmFpZGFubGlzdGVyLmNvbS8yMDE0LzAzL3BlcnNpc3RpbmctdGhlLXRhYi1zdGF0ZS1pbi1ib290c3RyYXAvCiAqLwooZnVuY3Rpb24oJCkgewogICJ1c2Ugc3RyaWN0IjsKICAkLmZuLnJtYXJrZG93blN0aWNreVRhYnMgPSBmdW5jdGlvbigpIHsKICAgIHZhciBjb250ZXh0ID0gdGhpczsKICAgIC8vIFNob3cgdGhlIHRhY [...]
+-
+-
+-
+-
+-<style type="text/css">
+-h1 {
+- font-size: 34px;
+-}
+-h1.title {
+- font-size: 38px;
+-}
+-h2 {
+- font-size: 30px;
+-}
+-h3 {
+- font-size: 24px;
+-}
+-h4 {
+- font-size: 18px;
+-}
+-h5 {
+- font-size: 16px;
+-}
+-h6 {
+- font-size: 12px;
+-}
+-.table th:not([align]) {
+- text-align: left;
+-}
+-</style>
+-
+-
+-</head>
+-
+-<body>
+-
+-<style type="text/css">
+-.main-container {
+- max-width: 940px;
+- margin-left: auto;
+- margin-right: auto;
+-}
+-code {
+- color: inherit;
+- background-color: rgba(0, 0, 0, 0.04);
+-}
+-img {
+- max-width:100%;
+- height: auto;
+-}
+-.tabbed-pane {
+- padding-top: 12px;
+-}
+-button.code-folding-btn:focus {
+- outline: none;
+-}
+-</style>
+-
+-
+-
+-<div class="container-fluid main-container">
+-
+-<!-- tabsets -->
+-<script>
+-$(document).ready(function () {
+- window.buildTabsets("TOC");
+-});
+-</script>
+-
+-<!-- code folding -->
+-
+-
+-
+-
+-<script>
+-$(document).ready(function () {
+-
+- // move toc-ignore selectors from section div to header
+- $('div.section.toc-ignore')
+- .removeClass('toc-ignore')
+- .children('h1,h2,h3,h4,h5').addClass('toc-ignore');
+-
+- // establish options
+- var options = {
+- selectors: "h1,h2,h3",
+- theme: "bootstrap3",
+- context: '.toc-content',
+- hashGenerator: function (text) {
+- return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
+- },
+- ignoreSelector: ".toc-ignore",
+- scrollTo: 0
+- };
+- options.showAndHide = false;
+- options.smoothScroll = true;
+-
+- // tocify
+- var toc = $("#TOC").tocify(options).data("toc-tocify");
+-});
+-</script>
+-
+-<style type="text/css">
+-
+-#TOC {
+- margin: 25px 0px 20px 0px;
+-}
+- at media (max-width: 768px) {
+-#TOC {
+- position: relative;
+- width: 100%;
+-}
+-}
+-
+-
+-.toc-content {
+- padding-left: 30px;
+- padding-right: 40px;
+-}
+-
+-div.main-container {
+- max-width: 1200px;
+-}
+-
+-div.tocify {
+- width: 20%;
+- max-width: 260px;
+- max-height: 85%;
+-}
+-
+- at media (min-width: 768px) and (max-width: 991px) {
+- div.tocify {
+- width: 25%;
+- }
+-}
+-
+- at media (max-width: 767px) {
+- div.tocify {
+- width: 100%;
+- max-width: none;
+- }
+-}
+-
+-.tocify ul, .tocify li {
+- line-height: 20px;
+-}
+-
+-.tocify-subheader .tocify-item {
+- font-size: 0.90em;
+- padding-left: 25px;
+- text-indent: 0;
+-}
+-
+-.tocify .list-group-item {
+- border-radius: 0px;
+-}
+-
+-.tocify-subheader {
+- display: inline;
+-}
+-.tocify-subheader .tocify-item {
+- font-size: 0.95em;
+-}
+-
+-</style>
+-
+-<!-- setup 3col/9col grid for toc_float and main content -->
+-<div class="row-fluid">
+-<div class="col-xs-12 col-sm-4 col-md-3">
+-<div id="TOC" class="tocify">
+-</div>
+-</div>
+-
+-<div class="toc-content col-xs-12 col-sm-8 col-md-9">
+-
+-
+-
+-
+-<div class="fluid-row" id="header">
+-
+-
+-
+-<h1 class="title toc-ignore">Test Report</h1>
+-<h4 class="author"><em>Mattias</em></h4>
+-<h4 class="date"><em>March 22, 2017</em></h4>
+-
+-</div>
+-
+-
+-<div id="r-markdown" class="section level2">
+-<h2>R Markdown</h2>
+-<p>This is an R Markdown document.</p>
+-<p>Test include from snakemake testparam.</p>
+-</div>
+-
+-
+-
+-</div>
+-</div>
+-
+-</div>
+-
+-<script>
+-
+-// add bootstrap table styles to pandoc tables
+-function bootstrapStylePandocTables() {
+- $('tr.header').parent('thead').parent('table').addClass('table table-condensed');
+-}
+-$(document).ready(function () {
+- bootstrapStylePandocTables();
+-});
+-
+-
+-</script>
+-
+-<!-- dynamically load mathjax for compatibility with self-contained -->
+-<script>
+- (function () {
+- var script = document.createElement("script");
+- script.type = "text/javascript";
+- script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
+- document.getElementsByTagName("head")[0].appendChild(script);
+- })();
+-</script>
+-
+-</body>
+-</html>
diff --git a/debian/patches/series b/debian/patches/series
index 186b8ab..f1e5f3c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -7,3 +7,4 @@
# 0007-noop-rate-limiter.patch - broken and obsolete with https://bugs.debian.org/880661
0008-remove_sphinx.ext.patch
0009-skip-test-without-google-cloud-sdk.patch
+0010-skip-test-without-rmarkdown.patch
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