From f29cb6c4fa24969f0bc33f9e8eb50fad4b1e3b4d Mon Sep 17 00:00:00 2001
From: xec-cm <70643921+xec-cm@users.noreply.github.com>
Date: Sun, 28 Jan 2024 08:56:36 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20xec-cm/b?=
 =?UTF-8?q?iocroxytest@d04127ec01a65b79837899cae533f5fc1c893802=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                                         | 2 +-
 LICENSE.html                                     | 2 +-
 articles/biocroxytest.html                       | 4 ++--
 articles/index.html                              | 2 +-
 authors.html                                     | 6 +++---
 index.html                                       | 2 +-
 news/index.html                                  | 9 ++++++++-
 pkgdown.yml                                      | 2 +-
 reference/block_to_testthat.html                 | 2 +-
 reference/index.html                             | 2 +-
 reference/internal_longtests_roclet_clean.html   | 2 +-
 reference/internal_longtests_roclet_output.html  | 2 +-
 reference/internal_longtests_roclet_process.html | 2 +-
 reference/longtests_roclet.html                  | 2 +-
 reference/made_by_biocroxytest.html              | 2 +-
 reference/process_testfiles.html                 | 2 +-
 reference/roclet_clean.roclet_longtests.html     | 2 +-
 reference/roclet_output.roclet_longtests.html    | 2 +-
 reference/roclet_process.roclet_longtests.html   | 2 +-
 reference/roxy_tag_parse.roxy_tag_longtests.html | 2 +-
 reference/use_longtests.html                     | 2 +-
 reference/verify_longtests_used.html             | 2 +-
 search.json                                      | 2 +-
 23 files changed, 33 insertions(+), 26 deletions(-)

diff --git a/404.html b/404.html
index acd5dae..3d736d6 100644
--- a/404.html
+++ b/404.html
@@ -31,7 +31,7 @@
     
     <a class="navbar-brand me-2" href="https://xec-cm.github.io/biocroxytest/index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index 6795f4d..42ec781 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/biocroxytest.html b/articles/biocroxytest.html
index 99089ee..ca983b2 100644
--- a/articles/biocroxytest.html
+++ b/articles/biocroxytest.html
@@ -37,7 +37,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -229,7 +229,7 @@ <h2 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#s
 <span><span class="co">#&gt; [13] R6_2.5.1            knitr_1.45          desc_1.4.3         </span></span>
 <span><span class="co">#&gt; [16] rprojroot_2.0.4     pillar_1.9.0        bslib_0.6.1        </span></span>
 <span><span class="co">#&gt; [19] rlang_1.1.3         utf8_1.2.4          testthat_3.2.1     </span></span>
-<span><span class="co">#&gt; [22] biocroxytest_0.99.1 cachem_1.0.8        stringi_1.8.3      </span></span>
+<span><span class="co">#&gt; [22] biocroxytest_0.99.2 cachem_1.0.8        stringi_1.8.3      </span></span>
 <span><span class="co">#&gt; [25] roxygen2_7.3.1      xfun_0.41           fs_1.6.3           </span></span>
 <span><span class="co">#&gt; [28] sass_0.4.8          pkgload_1.3.4       memoise_2.0.1      </span></span>
 <span><span class="co">#&gt; [31] cli_3.6.2           pkgdown_2.0.7.9000  withr_3.0.0        </span></span>
diff --git a/articles/index.html b/articles/index.html
index 28c14b3..53a1cb5 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index 682afc1..d317b58 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -61,13 +61,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Catala-Moll F (2024).
 <em>biocroxytest: Handle Long Tests in Bioconductor Packages</em>.
-R package version 0.99.1, <a href="https://github.com/xec-cm/biocroxytest" class="external-link">https://github.com/xec-cm/biocroxytest</a>. 
+R package version 0.99.2, <a href="https://github.com/xec-cm/biocroxytest" class="external-link">https://github.com/xec-cm/biocroxytest</a>. 
 </p>
       <pre>@Manual{,
   title = {biocroxytest: Handle Long Tests in Bioconductor Packages},
   author = {Francesc Catala-Moll},
   year = {2024},
-  note = {R package version 0.99.1},
+  note = {R package version 0.99.2},
   url = {https://github.com/xec-cm/biocroxytest},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index be5481b..b94ed9c 100644
--- a/index.html
+++ b/index.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/news/index.html b/news/index.html
index b90fc03..df4ea53 100644
--- a/news/index.html
+++ b/news/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -47,6 +47,13 @@
       <small>Source: <a href="https://github.com/xec-cm/biocroxytest/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="0.99.2" id="biocroxytest-0992">biocroxytest 0.99.2<a class="anchor" aria-label="anchor" href="#biocroxytest-0992"></a></h2>
+<div class="section level4">
+<h4 id="bug-fixes-0-99-2">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-99-2"></a></h4>
+<ul><li>Remove .Rproj file</li>
+</ul></div>
+</div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.99.1" id="biocroxytest-0991">biocroxytest 0.99.1<a class="anchor" aria-label="anchor" href="#biocroxytest-0991"></a></h2>
 <div class="section level4">
diff --git a/pkgdown.yml b/pkgdown.yml
index b80df11..569f472 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7.9000
 pkgdown_sha: 548a9493b72ff93d3ed8392d4ad30b77d8b15fa5
 articles:
   biocroxytest: biocroxytest.html
-last_built: 2024-01-28T08:52Z
+last_built: 2024-01-28T08:56Z
 urls:
   reference: https://xec-cm.github.io/biocroxytest/reference
   article: https://xec-cm.github.io/biocroxytest/articles
diff --git a/reference/block_to_testthat.html b/reference/block_to_testthat.html
index bd76c52..93b9dd8 100644
--- a/reference/block_to_testthat.html
+++ b/reference/block_to_testthat.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index bc3b0a5..543c253 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/internal_longtests_roclet_clean.html b/reference/internal_longtests_roclet_clean.html
index 52aefff..73d3f85 100644
--- a/reference/internal_longtests_roclet_clean.html
+++ b/reference/internal_longtests_roclet_clean.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/internal_longtests_roclet_output.html b/reference/internal_longtests_roclet_output.html
index c56efc2..9158239 100644
--- a/reference/internal_longtests_roclet_output.html
+++ b/reference/internal_longtests_roclet_output.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/internal_longtests_roclet_process.html b/reference/internal_longtests_roclet_process.html
index 8b89e8e..f91c938 100644
--- a/reference/internal_longtests_roclet_process.html
+++ b/reference/internal_longtests_roclet_process.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/longtests_roclet.html b/reference/longtests_roclet.html
index f3d5dc3..36f8205 100644
--- a/reference/longtests_roclet.html
+++ b/reference/longtests_roclet.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/made_by_biocroxytest.html b/reference/made_by_biocroxytest.html
index f56b6bd..ae02855 100644
--- a/reference/made_by_biocroxytest.html
+++ b/reference/made_by_biocroxytest.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/process_testfiles.html b/reference/process_testfiles.html
index 8f3bbdb..a23c407 100644
--- a/reference/process_testfiles.html
+++ b/reference/process_testfiles.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/roclet_clean.roclet_longtests.html b/reference/roclet_clean.roclet_longtests.html
index 3e9aa4a..9f0b162 100644
--- a/reference/roclet_clean.roclet_longtests.html
+++ b/reference/roclet_clean.roclet_longtests.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/roclet_output.roclet_longtests.html b/reference/roclet_output.roclet_longtests.html
index 48885d7..226622c 100644
--- a/reference/roclet_output.roclet_longtests.html
+++ b/reference/roclet_output.roclet_longtests.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/roclet_process.roclet_longtests.html b/reference/roclet_process.roclet_longtests.html
index 6c92e1c..664a38e 100644
--- a/reference/roclet_process.roclet_longtests.html
+++ b/reference/roclet_process.roclet_longtests.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/roxy_tag_parse.roxy_tag_longtests.html b/reference/roxy_tag_parse.roxy_tag_longtests.html
index cb2a2ed..c771727 100644
--- a/reference/roxy_tag_parse.roxy_tag_longtests.html
+++ b/reference/roxy_tag_parse.roxy_tag_longtests.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/use_longtests.html b/reference/use_longtests.html
index d72e5ba..b1b67d5 100644
--- a/reference/use_longtests.html
+++ b/reference/use_longtests.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/verify_longtests_used.html b/reference/verify_longtests_used.html
index 36b116f..c4d3cc6 100644
--- a/reference/verify_longtests_used.html
+++ b/reference/verify_longtests_used.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">biocroxytest</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index 2f69aae..9fa1b29 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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States allow patents restrict development use software general-purpose computers, , wish avoid special danger patents applied free program make effectively proprietary. prevent , GPL assures patents used render program non-free. precise terms conditions copying, distribution modification follow.","code":""},{"path":[]},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_0-definitions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"0. Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. 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GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"biocroxytest-setup","dir":"Articles","previous_headings":"","what":"biocroxytest setup","title":"Introduction to biocroxytest","text":"biocroxytest package installed, need carry two steps correctly set long tests package: 1 - Add new roclet Description file: need add biocroxytest::longtests_roclet Roxygen section Description file. enable roxygen2::roxygenize() generate long tests @longtest tag. Description file line similar : 2 - Run biocroxytest::use_longtests() function: function sets overall infrastructure long tests. run, creates longtests/testthat directory longtests/testthat.R file, necessary storing running long tests. Additionally, generates file named .BBSoptions contains RunLongTests: TRUE parameter, indicating long tests run Bioconductor server. two steps, package set write, document, store long tests directly roxygen2 comments, improving efficiency organization test code.","code":"Roxygen: list(roclets = c(\"namespace\", \"rd\", \"biocroxytest::longtests_roclet\")) # Create the longtests directory and .BBSoptions file biocroxytest::use_longtests()"},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"basic-process","dir":"Articles","previous_headings":"","what":"Basic Process","title":"Introduction to biocroxytest","text":"biocroxytest package allows add extensive tests functions using @longtests tag roxygen comments. ’s detailed explanation use : 1 - Add @longtests tag function documentation: roxygen comments function, can add @longtests tag followed tests want run. tests written testthat::test_that() call. example: example, function foo() two long tests associated : expect_equal(foo(2),    sqrt(2)) expect_error(foo(\"string\")). 2 - Run roxygen2::roxygenise(): adding @longtests tags functions, need run roxygen2::roxygenise(). generate new file longtests/testthat directory R script contains functions @longtests tags. generated files contain testthat::test_that() calls set long tests. instance, foo() function file named R/functions.R, roxygen2::roxygenise() generate file named longtests/test-biocroxytest-tests-functions.R following content: file contains long tests foo() function, ready run testthat.","code":"#' A function to do x #'  #' @param x A number #'  #' @longtests  #' expect_equal(foo(2), sqrt(2)) #' expect_error(foo(\"a string\")) #'  #' @return something foo <- function(x) {   return(sqrt(x)) } # Generated by biocroxytest: do not edit by hand!  # File R/functions.R: @longtests  testthat::test_that(\"Function foo() @ L11\", {   testthat::expect_equal(foo(2), sqrt(2))   testthat::expect_error(foo(\"a string\")) })"},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"Introduction to biocroxytest","text":"","code":"utils::sessionInfo() #> R Under development (unstable) (2024-01-23 r85822) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.3 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               #>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     #>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    #>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  #>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> loaded via a namespace (and not attached): #>  [1] BiocStyle_2.31.0    jsonlite_1.8.8      compiler_4.4.0      #>  [4] BiocManager_1.30.22 brio_1.1.4          xml2_1.3.6          #>  [7] stringr_1.5.1       jquerylib_0.1.4     systemfonts_1.0.5   #> [10] textshaping_0.3.7   yaml_2.3.8          fastmap_1.1.1       #> [13] R6_2.5.1            knitr_1.45          desc_1.4.3          #> [16] rprojroot_2.0.4     pillar_1.9.0        bslib_0.6.1         #> [19] rlang_1.1.3         utf8_1.2.4          testthat_3.2.1      #> [22] biocroxytest_0.99.1 cachem_1.0.8        stringi_1.8.3       #> [25] roxygen2_7.3.1      xfun_0.41           fs_1.6.3            #> [28] sass_0.4.8          pkgload_1.3.4       memoise_2.0.1       #> [31] cli_3.6.2           pkgdown_2.0.7.9000  withr_3.0.0         #> [34] magrittr_2.0.3      digest_0.6.34       lifecycle_1.0.4     #> [37] waldo_0.5.2         vctrs_0.6.5         evaluate_0.23       #> [40] glue_1.7.0          ragg_1.2.7          fansi_1.0.6         #> [43] rmarkdown_2.25      purrr_1.0.2         tools_4.4.0         #> [46] htmltools_0.5.7"},{"path":"https://xec-cm.github.io/biocroxytest/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Francesc Catala-Moll. Author, maintainer.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Catala-Moll F (2024). biocroxytest: Handle Long Tests Bioconductor Packages. R package version 0.99.1, https://github.com/xec-cm/biocroxytest.","code":"@Manual{,   title = {biocroxytest: Handle Long Tests in Bioconductor Packages},   author = {Francesc Catala-Moll},   year = {2024},   note = {R package version 0.99.1},   url = {https://github.com/xec-cm/biocroxytest}, }"},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"biocroxytest-","dir":"","previous_headings":"","what":"Handle Long Tests in Bioconductor Packages","title":"Handle Long Tests in Bioconductor Packages","text":"biocroxytest package novel tool enhances efficiency test writing R, particularly Bioconductor software packages. leverages structure roxygen2 test writing, improves readability, code organization, integrates seamlessly package documentation. Bioconductor, daily tests run part nightly builds, maximum limit 40 minutes per package. tests exceed limit, developers can set “long tests” add package Bioconductor Long Tests builds. However, traditionally separating tests long tests can cumbersome. biocroxytest addresses issue introducing new roclet, @longtests, inspired roxytest. allows developers document store long tests directly within roxygen2 comments. using @longtests roclet, extensive tests run checked regularly without impacting efficiency daily build process. @longtests roclet provides dedicated space extensive tests, ensuring easily accessible well-documented. improves package’s reliability also maintainability. Thus, biocroxytest contributes creation robust, reliable, efficient Bioconductor packages.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"installation-instructions","dir":"","previous_headings":"","what":"Installation instructions","title":"Handle Long Tests in Bioconductor Packages","text":"Get latest stable R release CRAN. install biocroxytest Bioconductor using following code: development version GitHub :","code":"# Not yet on Bioconductor # if (!requireNamespace(\"BiocManager\", quietly = TRUE)) { #     install.packages(\"BiocManager\") # } #  # BiocManager::install(\"biocroxytest\") BiocManager::install(\"xec-cm/biocroxytest\")"},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Handle Long Tests in Bioconductor Packages","text":"can use biocroxytest create new package long tests: use package package need add additional dependencies package’s DESCRIPTION file. Simply add following lines package’s DESCRIPTION file (along Suggests: testthat): add @longtests roxygen comments functions want test. example, file R/functions.R contains code: roxygen2::roxygenise() generate (longtests_roclet roclet) file longtests/test-biocroxytest-tests-functions.R content:","code":"Roxygen: list(roclets = c(\"namespace\", \"rd\", \"biocroxytest::longtests_roclet\")) #' A function to do x #'  #' @param x A number #'  #' @longtests  #' expect_equal(foo(2), sqrt(2)) #' expect_error(foo(\"a string\")) #'  #' @return something foo <- function(x) {   return(sqrt(x)) }  #' A function to do y #'  #' @param x Character vector #' @param y Character vector #'  #' @longtests  #' expect_equal(bar(\"A\", \"B\"), paste(\"A\", \"B\", sep = \"/\")) #'  #' @export bar <- function(x, y) {   paste0(x, \"/\", y) } # Generated by biocroxytest: do not edit by hand!  # File R/functions.R: @longtests  test_that(\"Function foo() @ L11\", {   expect_equal(foo(2), sqrt(2))   expect_error(foo(\"a string\")) })   test_that(\"Function bar() @ L27\", {   expect_equal(bar(\"A\", \"B\"), paste(\"A\", \"B\", sep = \"/\")) })"},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Handle Long Tests in Bioconductor Packages","text":"think encountered bug, please submit issue. Either way, learn create share reprex (minimal, reproducible example), clearly communicate code. Working first Pull Request? can learn free series Contribute Open Source Project GitHub","code":""},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Handle Long Tests in Bioconductor Packages","text":"Please note biocroxytest project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a roxygen2 block to a testthat file — block_to_testthat","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"internal function converts roxygen2 block testthat file. first checks block 'longtests' tags. , returns NULL. , extracts 'longtests' 'examples' tags block assigns 'longtests' 'examples' fields testthat file, respectively. also assigns basename block's file 'filename' field, alias block's object 'functionname' field. block's line NULL, appends 'functionname' field.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"","code":"block_to_testthat(block)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"block roxygen2 block.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"list representing testthat file, NULL block 'longtests' tags.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"internal function cleans test files generated biocroxytest. checks file provided list test files. file generated biocroxytest, removed. file generated biocroxytest, message printed inform user, file removed.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"","code":"internal_longtests_roclet_clean(testfiles)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"testfiles character vector representing paths test files check clean.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"invisible","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":null,"dir":"Reference","previous_headings":"","what":"Write long test results to files — internal_longtests_roclet_output","title":"Write long test results to files — internal_longtests_roclet_output","text":"function takes three arguments: results, base_path, prefix. function iterates elements results writes content element file directory specified base_path prefix. file created biocroxytest, function informs user files removed.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write long test results to files — internal_longtests_roclet_output","text":"","code":"internal_longtests_roclet_output(   results,   base_path,   prefix = \"test-biocroxytest\" )"},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write long test results to files — internal_longtests_roclet_output","text":"results list results. base_path base path files written. prefix prefix used name files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Write long test results to files — internal_longtests_roclet_output","text":"list file paths.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"internal function processes list blocks 'longtests' roclet. first collects annotates 'rdname' blocks. , loops block converts testthat file using 'block_to_testthat' function. resulting testthat file filename contains 'longtests', added list test files. Finally, processes test files using 'process_testfiles' function.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"","code":"internal_longtests_roclet_process(blocks, ...)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"blocks list roxygen2 blocks. ... Additional arguments.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"list single element 'longtests', contains processed test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":null,"dir":"Reference","previous_headings":"","what":"Roclet for Long Tests — longtests_roclet","title":"Roclet for Long Tests — longtests_roclet","text":"roclet used identify process code blocks documentation marked @longtests. longtests_roclet function creates new roclet, plugin roxygen2 package. Roclets responsible parsing R scripts package producing relevant documentation files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Roclet for Long Tests — longtests_roclet","text":"","code":"longtests_roclet()"},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Roclet for Long Tests — longtests_roclet","text":"roclet can used roxygen2 process code blocks marked @longtests. roclet produce set test files separate directory, can run independently rest test suite.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Roclet for Long Tests — longtests_roclet","text":"longtests_roclet specifically looks code blocks documentation annotated @longtests tag. code blocks contain tests take long time run, thus included regular test suite package. run roxygen2::roxygenise longtests_roclet, extract long tests documentation save separate directory. allows run long tests separately rest tests, example, continuous integration server set run long tests.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Roclet for Long Tests — longtests_roclet","text":"","code":"# Create a new roclet longtests_roclet() #> list() #> attr(,\"class\") #> [1] \"roclet_longtests\" \"roclet\""},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if a file is generated by biocroxytest — made_by_biocroxytest","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"internal function checks file given path generated biocroxytest. checks file exists, name matches pattern \"test-biocroxytest-.*\\.R$\", header file starts \"Generated biocroxytest\". file exists name matches pattern header start \"Generated biocroxytest\", function return FALSE.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"","code":"made_by_biocroxytest(path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"path character string representing path file check.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"TRUE checks pass, FALSE otherwise.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":null,"dir":"Reference","previous_headings":"","what":"Process test files for 'longtests' — process_testfiles","title":"Process test files for 'longtests' — process_testfiles","text":"internal function processes list test files 'longtests'. loops test file extracts 'longtests' 'functionname' fields. prepares tests, optionally indents code, formats tests string optional 'test_that' boilerplate. function also constructs header content, including 'context' line specified. resulting content strings returned named list, names paths test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process test files for 'longtests' — process_testfiles","text":"","code":"process_testfiles(   testfiles,   indent_code = FALSE,   add_testthat_boilerplate = FALSE,   add_context_header = FALSE )"},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process test files for 'longtests' — process_testfiles","text":"testfiles named list test files, names paths files. indent_code logical value indicating whether indent code tests. add_testthat_boilerplate logical value indicating whether add 'test_that' boilerplate tests. add_context_header logical value indicating whether add 'context' line header.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process test files for 'longtests' — process_testfiles","text":"named list content strings test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"function cleans test files 'longtests' directory given base path. first verifies 'longtests' used package calling verify_longtests_used(). , finds test files 'longtests' directory match pattern \"test-biocroxytest-.*\\.R$\". Finally, calls internal_longtests_roclet_clean(testfiles) remove test files generated biocroxytest.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"","code":"# S3 method for roclet_longtests roclet_clean(x, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"x object class 'roclet_longtests'. base_path character string representing base path package.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"Invisible NULL.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"","code":"# Set up a temporary directory base_path <- tempdir() longtests_path <- file.path(base_path, \"longtests\") unlink(longtests_path, recursive = TRUE, force = TRUE) dir.create(longtests_path, recursive = TRUE, showWarnings = FALSE)  # Create dummy inputs obj <- longtests_roclet()  # Run the roclet_output function result <- roxygen2::roclet_clean(obj, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"function processes list blocks 'longtests' roclet. calls 'internal_longtests_roclet_process' function specified blocks additional arguments. code tests indented, 'test_that' boilerplate added tests, 'context' line added header.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"","code":"# S3 method for roclet_longtests roclet_output(x, results, base_path, ...)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"x object class 'roclet_longtests'. package. results list single element 'longtests', contains base_path character string representing base path ... Additional arguments passed function.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"list single element 'longtests', contains processed test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"","code":"# Set up a temporary directory base_path <- tempdir() longtests_path <- file.path(base_path, \"longtests\", \"testthat\") unlink(longtests_path, recursive = TRUE, force = TRUE) dir.create(longtests_path, recursive = TRUE, showWarnings = FALSE)  # Create dummy inputs obj <- longtests_roclet() results <- list(longtests = list())  # Run the roclet_output function result <- roxygen2::roclet_output(obj, results, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"function processes list blocks 'longtests' roclet. calls 'internal_longtests_roclet_process' function specified blocks additional arguments. code tests indented, 'test_that' boilerplate added tests, 'context' line added header.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"","code":"# S3 method for roclet_longtests roclet_process(x, blocks, env, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"x object class 'roclet_longtests'. blocks list roxygen2 blocks. env environment roxygen2 blocks parsed. base_path character string representing base path package.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"list single element 'longtests', contains processed test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"","code":"# Create a dummy block function block <- function(roclet, value) {   list(roclet = roclet, value = value) }  # Create a new roclet_longtests object x <- longtests_roclet()  # Define some roxygen2 blocks blocks <- list(   block(     roclet = \"longtests\",     value = list(       raw = \"test_that('this is a test', { expect_equal(1, 1) })\"     )   ) )  blocks <- structure(blocks, class = \"roclet_longtests\")  # Define the environment and base path env <- globalenv() base_path <- tempdir()  # Process the blocks roxygen2::roclet_process(x, blocks, env, base_path) #> $longtests #> list() #>"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"function parses 'roxy_tag_longtests' object. first checks object inherits 'roxy_tag_longtests' 'roxy_tag'. , aborts error message. , checks 'raw' field object empty. , returns warning value required. Finally, removes leading newline characters 'raw' field assigns result 'val' field object.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"","code":"# S3 method for roxy_tag_longtests roxy_tag_parse(x)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"x object class 'roxy_tag_longtests'.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"input object 'val' field updated.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Sets up overall longtests infrastructure — use_longtests","title":"Sets up overall longtests infrastructure — use_longtests","text":"function used set environment running long tests. calls two helper functions: setup_bboptions() setup_longtetsts().","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sets up overall longtests infrastructure — use_longtests","text":"","code":"use_longtests()"},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sets up overall longtests infrastructure — use_longtests","text":"function return value. used side effects setting environment running long tests.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sets up overall longtests infrastructure — use_longtests","text":"use_longtests() function wrapper function calls setup_bboptions() setup_longtetsts(). setup_bboptions() function checks .BBSoptions file exists creates . checks contents .BBSoptions file adds modifies 'RunLongTests: TRUE' line needed. setup_longtetsts() function creates 'longtests/testthat' directory exist copies 'tests/testthat.R' file . 'tests/testthat.R' file exist, creates new one default content.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sets up overall longtests infrastructure — use_longtests","text":"","code":"# Create the longtests directory and .BBSoptions file use_longtests() #> ✔ The .BBSoptions file has been created. #> ✔ Adding RunLongTests: TRUE to the .BBSoptions file. #> ✔ The longtests directory has been created. #> ✔ Adding testthat.R to the longtests directory.  # Remove the longtests directory and .BBSoptions file unlink(file.path(\".BBSoptions\"), recursive = TRUE, force = TRUE) unlink(file.path(\"longtests\"), recursive = TRUE, force = TRUE)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if longtests are used in the package — verify_longtests_used","title":"Check if longtests are used in the package — verify_longtests_used","text":"function checks directory \"longtests\" exists current package. exist, function throw error message suggest setting using biocroxytest::use_longtests() function.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if longtests are used in the package — verify_longtests_used","text":"","code":"verify_longtests_used(base_path = \".\")"},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if longtests are used in the package — verify_longtests_used","text":"base_path base path package.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if longtests are used in the package — verify_longtests_used","text":"TRUE \"longtests\" directory exists, FALSE otherwise.","code":""},{"path":[]},{"path":"https://xec-cm.github.io/biocroxytest/news/index.html","id":"bug-fixes-0-99-1","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"biocroxytest 0.99.1","text":"Add files .gitignore","code":""},{"path":[]},{"path":"https://xec-cm.github.io/biocroxytest/news/index.html","id":"new-features-0-99-0","dir":"Changelog","previous_headings":"","what":"New features","title":"biocroxytest 0.99.0","text":"Initial Bioconductor submission","code":""}]
+[{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. 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States allow patents restrict development use software general-purpose computers, , wish avoid special danger patents applied free program make effectively proprietary. prevent , GPL assures patents used render program non-free. precise terms conditions copying, distribution modification follow.","code":""},{"path":[]},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"id_0-definitions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"0. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://xec-cm.github.io/biocroxytest/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. 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GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"biocroxytest-setup","dir":"Articles","previous_headings":"","what":"biocroxytest setup","title":"Introduction to biocroxytest","text":"biocroxytest package installed, need carry two steps correctly set long tests package: 1 - Add new roclet Description file: need add biocroxytest::longtests_roclet Roxygen section Description file. enable roxygen2::roxygenize() generate long tests @longtest tag. Description file line similar : 2 - Run biocroxytest::use_longtests() function: function sets overall infrastructure long tests. run, creates longtests/testthat directory longtests/testthat.R file, necessary storing running long tests. Additionally, generates file named .BBSoptions contains RunLongTests: TRUE parameter, indicating long tests run Bioconductor server. two steps, package set write, document, store long tests directly roxygen2 comments, improving efficiency organization test code.","code":"Roxygen: list(roclets = c(\"namespace\", \"rd\", \"biocroxytest::longtests_roclet\")) # Create the longtests directory and .BBSoptions file biocroxytest::use_longtests()"},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"basic-process","dir":"Articles","previous_headings":"","what":"Basic Process","title":"Introduction to biocroxytest","text":"biocroxytest package allows add extensive tests functions using @longtests tag roxygen comments. ’s detailed explanation use : 1 - Add @longtests tag function documentation: roxygen comments function, can add @longtests tag followed tests want run. tests written testthat::test_that() call. example: example, function foo() two long tests associated : expect_equal(foo(2),    sqrt(2)) expect_error(foo(\"string\")). 2 - Run roxygen2::roxygenise(): adding @longtests tags functions, need run roxygen2::roxygenise(). generate new file longtests/testthat directory R script contains functions @longtests tags. generated files contain testthat::test_that() calls set long tests. instance, foo() function file named R/functions.R, roxygen2::roxygenise() generate file named longtests/test-biocroxytest-tests-functions.R following content: file contains long tests foo() function, ready run testthat.","code":"#' A function to do x #'  #' @param x A number #'  #' @longtests  #' expect_equal(foo(2), sqrt(2)) #' expect_error(foo(\"a string\")) #'  #' @return something foo <- function(x) {   return(sqrt(x)) } # Generated by biocroxytest: do not edit by hand!  # File R/functions.R: @longtests  testthat::test_that(\"Function foo() @ L11\", {   testthat::expect_equal(foo(2), sqrt(2))   testthat::expect_error(foo(\"a string\")) })"},{"path":"https://xec-cm.github.io/biocroxytest/articles/biocroxytest.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"Introduction to biocroxytest","text":"","code":"utils::sessionInfo() #> R Under development (unstable) (2024-01-23 r85822) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.3 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               #>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     #>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    #>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  #>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> loaded via a namespace (and not attached): #>  [1] BiocStyle_2.31.0    jsonlite_1.8.8      compiler_4.4.0      #>  [4] BiocManager_1.30.22 brio_1.1.4          xml2_1.3.6          #>  [7] stringr_1.5.1       jquerylib_0.1.4     systemfonts_1.0.5   #> [10] textshaping_0.3.7   yaml_2.3.8          fastmap_1.1.1       #> [13] R6_2.5.1            knitr_1.45          desc_1.4.3          #> [16] rprojroot_2.0.4     pillar_1.9.0        bslib_0.6.1         #> [19] rlang_1.1.3         utf8_1.2.4          testthat_3.2.1      #> [22] biocroxytest_0.99.2 cachem_1.0.8        stringi_1.8.3       #> [25] roxygen2_7.3.1      xfun_0.41           fs_1.6.3            #> [28] sass_0.4.8          pkgload_1.3.4       memoise_2.0.1       #> [31] cli_3.6.2           pkgdown_2.0.7.9000  withr_3.0.0         #> [34] magrittr_2.0.3      digest_0.6.34       lifecycle_1.0.4     #> [37] waldo_0.5.2         vctrs_0.6.5         evaluate_0.23       #> [40] glue_1.7.0          ragg_1.2.7          fansi_1.0.6         #> [43] rmarkdown_2.25      purrr_1.0.2         tools_4.4.0         #> [46] htmltools_0.5.7"},{"path":"https://xec-cm.github.io/biocroxytest/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Francesc Catala-Moll. Author, maintainer.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Catala-Moll F (2024). biocroxytest: Handle Long Tests Bioconductor Packages. R package version 0.99.2, https://github.com/xec-cm/biocroxytest.","code":"@Manual{,   title = {biocroxytest: Handle Long Tests in Bioconductor Packages},   author = {Francesc Catala-Moll},   year = {2024},   note = {R package version 0.99.2},   url = {https://github.com/xec-cm/biocroxytest}, }"},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"biocroxytest-","dir":"","previous_headings":"","what":"Handle Long Tests in Bioconductor Packages","title":"Handle Long Tests in Bioconductor Packages","text":"biocroxytest package novel tool enhances efficiency test writing R, particularly Bioconductor software packages. leverages structure roxygen2 test writing, improves readability, code organization, integrates seamlessly package documentation. Bioconductor, daily tests run part nightly builds, maximum limit 40 minutes per package. tests exceed limit, developers can set “long tests” add package Bioconductor Long Tests builds. However, traditionally separating tests long tests can cumbersome. biocroxytest addresses issue introducing new roclet, @longtests, inspired roxytest. allows developers document store long tests directly within roxygen2 comments. using @longtests roclet, extensive tests run checked regularly without impacting efficiency daily build process. @longtests roclet provides dedicated space extensive tests, ensuring easily accessible well-documented. improves package’s reliability also maintainability. Thus, biocroxytest contributes creation robust, reliable, efficient Bioconductor packages.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"installation-instructions","dir":"","previous_headings":"","what":"Installation instructions","title":"Handle Long Tests in Bioconductor Packages","text":"Get latest stable R release CRAN. install biocroxytest Bioconductor using following code: development version GitHub :","code":"# Not yet on Bioconductor # if (!requireNamespace(\"BiocManager\", quietly = TRUE)) { #     install.packages(\"BiocManager\") # } #  # BiocManager::install(\"biocroxytest\") BiocManager::install(\"xec-cm/biocroxytest\")"},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Handle Long Tests in Bioconductor Packages","text":"can use biocroxytest create new package long tests: use package package need add additional dependencies package’s DESCRIPTION file. Simply add following lines package’s DESCRIPTION file (along Suggests: testthat): add @longtests roxygen comments functions want test. example, file R/functions.R contains code: roxygen2::roxygenise() generate (longtests_roclet roclet) file longtests/test-biocroxytest-tests-functions.R content:","code":"Roxygen: list(roclets = c(\"namespace\", \"rd\", \"biocroxytest::longtests_roclet\")) #' A function to do x #'  #' @param x A number #'  #' @longtests  #' expect_equal(foo(2), sqrt(2)) #' expect_error(foo(\"a string\")) #'  #' @return something foo <- function(x) {   return(sqrt(x)) }  #' A function to do y #'  #' @param x Character vector #' @param y Character vector #'  #' @longtests  #' expect_equal(bar(\"A\", \"B\"), paste(\"A\", \"B\", sep = \"/\")) #'  #' @export bar <- function(x, y) {   paste0(x, \"/\", y) } # Generated by biocroxytest: do not edit by hand!  # File R/functions.R: @longtests  test_that(\"Function foo() @ L11\", {   expect_equal(foo(2), sqrt(2))   expect_error(foo(\"a string\")) })   test_that(\"Function bar() @ L27\", {   expect_equal(bar(\"A\", \"B\"), paste(\"A\", \"B\", sep = \"/\")) })"},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Handle Long Tests in Bioconductor Packages","text":"think encountered bug, please submit issue. Either way, learn create share reprex (minimal, reproducible example), clearly communicate code. Working first Pull Request? can learn free series Contribute Open Source Project GitHub","code":""},{"path":"https://xec-cm.github.io/biocroxytest/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Handle Long Tests in Bioconductor Packages","text":"Please note biocroxytest project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a roxygen2 block to a testthat file — block_to_testthat","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"internal function converts roxygen2 block testthat file. first checks block 'longtests' tags. , returns NULL. , extracts 'longtests' 'examples' tags block assigns 'longtests' 'examples' fields testthat file, respectively. also assigns basename block's file 'filename' field, alias block's object 'functionname' field. block's line NULL, appends 'functionname' field.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"","code":"block_to_testthat(block)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"block roxygen2 block.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/block_to_testthat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a roxygen2 block to a testthat file — block_to_testthat","text":"list representing testthat file, NULL block 'longtests' tags.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"internal function cleans test files generated biocroxytest. checks file provided list test files. file generated biocroxytest, removed. file generated biocroxytest, message printed inform user, file removed.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"","code":"internal_longtests_roclet_clean(testfiles)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"testfiles character vector representing paths test files check clean.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_clean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean up longtest files generated by biocroxytest — internal_longtests_roclet_clean","text":"invisible","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":null,"dir":"Reference","previous_headings":"","what":"Write long test results to files — internal_longtests_roclet_output","title":"Write long test results to files — internal_longtests_roclet_output","text":"function takes three arguments: results, base_path, prefix. function iterates elements results writes content element file directory specified base_path prefix. file created biocroxytest, function informs user files removed.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write long test results to files — internal_longtests_roclet_output","text":"","code":"internal_longtests_roclet_output(   results,   base_path,   prefix = \"test-biocroxytest\" )"},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write long test results to files — internal_longtests_roclet_output","text":"results list results. base_path base path files written. prefix prefix used name files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_output.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Write long test results to files — internal_longtests_roclet_output","text":"list file paths.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"internal function processes list blocks 'longtests' roclet. first collects annotates 'rdname' blocks. , loops block converts testthat file using 'block_to_testthat' function. resulting testthat file filename contains 'longtests', added list test files. Finally, processes test files using 'process_testfiles' function.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"","code":"internal_longtests_roclet_process(blocks, ...)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"blocks list roxygen2 blocks. ... Additional arguments.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/internal_longtests_roclet_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process blocks for 'longtests' roclet — internal_longtests_roclet_process","text":"list single element 'longtests', contains processed test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":null,"dir":"Reference","previous_headings":"","what":"Roclet for Long Tests — longtests_roclet","title":"Roclet for Long Tests — longtests_roclet","text":"roclet used identify process code blocks documentation marked @longtests. longtests_roclet function creates new roclet, plugin roxygen2 package. Roclets responsible parsing R scripts package producing relevant documentation files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Roclet for Long Tests — longtests_roclet","text":"","code":"longtests_roclet()"},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Roclet for Long Tests — longtests_roclet","text":"roclet can used roxygen2 process code blocks marked @longtests. roclet produce set test files separate directory, can run independently rest test suite.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Roclet for Long Tests — longtests_roclet","text":"longtests_roclet specifically looks code blocks documentation annotated @longtests tag. code blocks contain tests take long time run, thus included regular test suite package. run roxygen2::roxygenise longtests_roclet, extract long tests documentation save separate directory. allows run long tests separately rest tests, example, continuous integration server set run long tests.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/longtests_roclet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Roclet for Long Tests — longtests_roclet","text":"","code":"# Create a new roclet longtests_roclet() #> list() #> attr(,\"class\") #> [1] \"roclet_longtests\" \"roclet\""},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if a file is generated by biocroxytest — made_by_biocroxytest","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"internal function checks file given path generated biocroxytest. checks file exists, name matches pattern \"test-biocroxytest-.*\\.R$\", header file starts \"Generated biocroxytest\". file exists name matches pattern header start \"Generated biocroxytest\", function return FALSE.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"","code":"made_by_biocroxytest(path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"path character string representing path file check.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/made_by_biocroxytest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if a file is generated by biocroxytest — made_by_biocroxytest","text":"TRUE checks pass, FALSE otherwise.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":null,"dir":"Reference","previous_headings":"","what":"Process test files for 'longtests' — process_testfiles","title":"Process test files for 'longtests' — process_testfiles","text":"internal function processes list test files 'longtests'. loops test file extracts 'longtests' 'functionname' fields. prepares tests, optionally indents code, formats tests string optional 'test_that' boilerplate. function also constructs header content, including 'context' line specified. resulting content strings returned named list, names paths test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process test files for 'longtests' — process_testfiles","text":"","code":"process_testfiles(   testfiles,   indent_code = FALSE,   add_testthat_boilerplate = FALSE,   add_context_header = FALSE )"},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process test files for 'longtests' — process_testfiles","text":"testfiles named list test files, names paths files. indent_code logical value indicating whether indent code tests. add_testthat_boilerplate logical value indicating whether add 'test_that' boilerplate tests. add_context_header logical value indicating whether add 'context' line header.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/process_testfiles.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process test files for 'longtests' — process_testfiles","text":"named list content strings test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"function cleans test files 'longtests' directory given base path. first verifies 'longtests' used package calling verify_longtests_used(). , finds test files 'longtests' directory match pattern \"test-biocroxytest-.*\\.R$\". Finally, calls internal_longtests_roclet_clean(testfiles) remove test files generated biocroxytest.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"","code":"# S3 method for roclet_longtests roclet_clean(x, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"x object class 'roclet_longtests'. base_path character string representing base path package.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"Invisible NULL.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_clean.roclet_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean up test files in the 'longtests' directory — roclet_clean.roclet_longtests","text":"","code":"# Set up a temporary directory base_path <- tempdir() longtests_path <- file.path(base_path, \"longtests\") unlink(longtests_path, recursive = TRUE, force = TRUE) dir.create(longtests_path, recursive = TRUE, showWarnings = FALSE)  # Create dummy inputs obj <- longtests_roclet()  # Run the roclet_output function result <- roxygen2::roclet_clean(obj, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"function processes list blocks 'longtests' roclet. calls 'internal_longtests_roclet_process' function specified blocks additional arguments. code tests indented, 'test_that' boilerplate added tests, 'context' line added header.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"","code":"# S3 method for roclet_longtests roclet_output(x, results, base_path, ...)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"x object class 'roclet_longtests'. package. results list single element 'longtests', contains base_path character string representing base path ... Additional arguments passed function.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"list single element 'longtests', contains processed test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_output.roclet_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Process blocks for 'longtests' roclet — roclet_output.roclet_longtests","text":"","code":"# Set up a temporary directory base_path <- tempdir() longtests_path <- file.path(base_path, \"longtests\", \"testthat\") unlink(longtests_path, recursive = TRUE, force = TRUE) dir.create(longtests_path, recursive = TRUE, showWarnings = FALSE)  # Create dummy inputs obj <- longtests_roclet() results <- list(longtests = list())  # Run the roclet_output function result <- roxygen2::roclet_output(obj, results, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"function processes list blocks 'longtests' roclet. calls 'internal_longtests_roclet_process' function specified blocks additional arguments. code tests indented, 'test_that' boilerplate added tests, 'context' line added header.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"","code":"# S3 method for roclet_longtests roclet_process(x, blocks, env, base_path)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"x object class 'roclet_longtests'. blocks list roxygen2 blocks. env environment roxygen2 blocks parsed. base_path character string representing base path package.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"list single element 'longtests', contains processed test files.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roclet_process.roclet_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Process blocks for 'longtests' roclet — roclet_process.roclet_longtests","text":"","code":"# Create a dummy block function block <- function(roclet, value) {   list(roclet = roclet, value = value) }  # Create a new roclet_longtests object x <- longtests_roclet()  # Define some roxygen2 blocks blocks <- list(   block(     roclet = \"longtests\",     value = list(       raw = \"test_that('this is a test', { expect_equal(1, 1) })\"     )   ) )  blocks <- structure(blocks, class = \"roclet_longtests\")  # Define the environment and base path env <- globalenv() base_path <- tempdir()  # Process the blocks roxygen2::roclet_process(x, blocks, env, base_path) #> $longtests #> list() #>"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"function parses 'roxy_tag_longtests' object. first checks object inherits 'roxy_tag_longtests' 'roxy_tag'. , aborts error message. , checks 'raw' field object empty. , returns warning value required. Finally, removes leading newline characters 'raw' field assigns result 'val' field object.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"","code":"# S3 method for roxy_tag_longtests roxy_tag_parse(x)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"x object class 'roxy_tag_longtests'.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/roxy_tag_parse.roxy_tag_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse a roxy_tag_longtests object — roxy_tag_parse.roxy_tag_longtests","text":"input object 'val' field updated.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":null,"dir":"Reference","previous_headings":"","what":"Sets up overall longtests infrastructure — use_longtests","title":"Sets up overall longtests infrastructure — use_longtests","text":"function used set environment running long tests. calls two helper functions: setup_bboptions() setup_longtetsts().","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sets up overall longtests infrastructure — use_longtests","text":"","code":"use_longtests()"},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sets up overall longtests infrastructure — use_longtests","text":"function return value. used side effects setting environment running long tests.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sets up overall longtests infrastructure — use_longtests","text":"use_longtests() function wrapper function calls setup_bboptions() setup_longtetsts(). setup_bboptions() function checks .BBSoptions file exists creates . checks contents .BBSoptions file adds modifies 'RunLongTests: TRUE' line needed. setup_longtetsts() function creates 'longtests/testthat' directory exist copies 'tests/testthat.R' file . 'tests/testthat.R' file exist, creates new one default content.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/use_longtests.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sets up overall longtests infrastructure — use_longtests","text":"","code":"# Create the longtests directory and .BBSoptions file use_longtests() #> ✔ The .BBSoptions file has been created. #> ✔ Adding RunLongTests: TRUE to the .BBSoptions file. #> ✔ The longtests directory has been created. #> ✔ Adding testthat.R to the longtests directory.  # Remove the longtests directory and .BBSoptions file unlink(file.path(\".BBSoptions\"), recursive = TRUE, force = TRUE) unlink(file.path(\"longtests\"), recursive = TRUE, force = TRUE)"},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if longtests are used in the package — verify_longtests_used","title":"Check if longtests are used in the package — verify_longtests_used","text":"function checks directory \"longtests\" exists current package. exist, function throw error message suggest setting using biocroxytest::use_longtests() function.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if longtests are used in the package — verify_longtests_used","text":"","code":"verify_longtests_used(base_path = \".\")"},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if longtests are used in the package — verify_longtests_used","text":"base_path base path package.","code":""},{"path":"https://xec-cm.github.io/biocroxytest/reference/verify_longtests_used.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if longtests are used in the package — verify_longtests_used","text":"TRUE \"longtests\" directory exists, FALSE otherwise.","code":""},{"path":[]},{"path":"https://xec-cm.github.io/biocroxytest/news/index.html","id":"bug-fixes-0-99-2","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"biocroxytest 0.99.2","text":"Remove .Rproj file","code":""},{"path":[]},{"path":"https://xec-cm.github.io/biocroxytest/news/index.html","id":"bug-fixes-0-99-1","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"biocroxytest 0.99.1","text":"Add files .gitignore","code":""},{"path":[]},{"path":"https://xec-cm.github.io/biocroxytest/news/index.html","id":"new-features-0-99-0","dir":"Changelog","previous_headings":"","what":"New features","title":"biocroxytest 0.99.0","text":"Initial Bioconductor submission","code":""}]