From e064f23015f3b65a79997f24fdb31c2acee093e5 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 5 Dec 2023 00:20:35 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 64480f96c2b914190479bafb3775dd5a7eeb7c19
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2023-12-05 00:20:18 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 148112741b365ba95b0304d793b2589378fb6475
Branch  : main
Author  : Naupaka Zimmerman <naupaka@gmail.com>
Time    : 2023-11-30 21:24:06 +0000
Message : Merge pull request #241 from datacarpentry/update/packages

Update 27 packages
---
 00-introduction.html                         |   8 +-
 01-r-basics.html                             |  20 ++--
 02-data-prelude.html                         |   2 +-
 03-basics-factors-dataframes.html            |  10 +-
 04-bioconductor-vcfr.html                    |   2 +-
 05-dplyr.html                                |   2 +-
 06-data-visualization.html                   |   2 +-
 07-r-help.html                               |   2 +-
 404.html                                     |   4 +-
 CODE_OF_CONDUCT.html                         |   2 +-
 LICENSE.html                                 |   2 +-
 aio.html                                     |  36 +++---
 discuss.html                                 |   2 +-
 images.html                                  |   4 +-
 index.html                                   |   4 +-
 instructor-notes.html                        |   4 +-
 instructor/00-introduction.html              |   8 +-
 instructor/01-r-basics.html                  |  20 ++--
 instructor/02-data-prelude.html              |   2 +-
 instructor/03-basics-factors-dataframes.html |  10 +-
 instructor/04-bioconductor-vcfr.html         |   2 +-
 instructor/05-dplyr.html                     |   2 +-
 instructor/06-data-visualization.html        |   2 +-
 instructor/07-r-help.html                    |   2 +-
 instructor/404.html                          |   4 +-
 instructor/CODE_OF_CONDUCT.html              |   2 +-
 instructor/LICENSE.html                      |   2 +-
 instructor/aio.html                          |  36 +++---
 instructor/discuss.html                      |   2 +-
 instructor/images.html                       |   4 +-
 instructor/index.html                        |   4 +-
 instructor/instructor-notes.html             |   4 +-
 instructor/key-points.html                   |   4 +-
 instructor/profiles.html                     |   4 +-
 instructor/reference.html                    |   2 +-
 key-points.html                              |   4 +-
 pkgdown.yml                                  |   2 +-
 profiles.html                                |   4 +-
 reference.html                               |   2 +-
 renv.lock                                    | 111 ++++++++++---------
 40 files changed, 174 insertions(+), 171 deletions(-)

diff --git a/00-introduction.html b/00-introduction.html
index b62ba4b5..08cc1dc1 100644
--- a/00-introduction.html
+++ b/00-introduction.html
@@ -638,7 +638,7 @@ <h4 class="accordion-header" id="headingSolution1">
   Show me the solution
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>You will get the same output you did as when you ran
 <code>getwd()</code> from the source. You can run any command in the
@@ -734,7 +734,7 @@ <h4 class="accordion-header" id="headingSolution2">
   Show me the solution
   </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul><li>
 <code>dir()</code> # Lists files in the working directory</li>
@@ -881,7 +881,7 @@ <h4 class="accordion-header" id="headingSolution3">
   Show me the solution
   </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
@@ -986,7 +986,7 @@ <h3 class="callout-title">Keypoints<a class="anchor" aria-label="anchor" href="#
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/00-introduction.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2023-11-30",
-  "datePublished": "2023-11-30"
+  "datePublished": "2023-12-05"
 }
 
   </script><script>
diff --git a/01-r-basics.html b/01-r-basics.html
index 06eaa336..eec7d1fe 100644
--- a/01-r-basics.html
+++ b/01-r-basics.html
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   Show me the solution
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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 <div class="accordion-body">
 <p>Here as some possible answers to the challenge:</p>
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@@ -667,7 +667,7 @@ <h4 class="accordion-header" id="headingSolution2">
   Show me the solution
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 </button>
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 <div class="codewrapper">
 <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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   Show me the solution
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 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha"><li>False - Vectors have both of these properties<br></li>
 <li>True<br></li>
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   Show me the solution
   </h4>
 </button>
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 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
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   Show me the solution
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 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
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@@ -1498,7 +1498,7 @@ <h4 class="accordion-header" id="headingSolution9">
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 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
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@@ -1670,7 +1670,7 @@ <h3 class="callout-title">Keypoints<a class="anchor" aria-label="anchor" href="#
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/01-r-basics.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2023-11-30",
-  "datePublished": "2023-11-30"
+  "datePublished": "2023-12-05"
 }
 
   </script><script>
diff --git a/02-data-prelude.html b/02-data-prelude.html
index a8585391..b1602d99 100644
--- a/02-data-prelude.html
+++ b/02-data-prelude.html
@@ -602,7 +602,7 @@ <h3 class="callout-title">Keypoints<a class="anchor" aria-label="anchor" href="#
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/02-data-prelude.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2023-11-30",
-  "datePublished": "2023-11-30"
+  "datePublished": "2023-12-05"
 }
 
   </script><script>
diff --git a/03-basics-factors-dataframes.html b/03-basics-factors-dataframes.html
index 44a863ea..50f5697a 100644
--- a/03-basics-factors-dataframes.html
+++ b/03-basics-factors-dataframes.html
@@ -438,7 +438,7 @@ <h4 class="accordion-header" id="headingSolution1">
   Show me the solution
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha"><li><p>The <code>read.csv()</code> function has the argument ‘header’
 set to TRUE by default, this means the function always assumes the first
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   Show me the solution
   </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
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 <ol style="list-style-type: lower-alpha"><li>
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   Show me the solution
   </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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   Show me the solution
   </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1880,7 +1880,7 @@ <h3 class="callout-title">Keypoints<a class="anchor" aria-label="anchor" href="#
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/03-basics-factors-dataframes.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2023-11-30",
-  "datePublished": "2023-11-30"
+  "datePublished": "2023-12-05"
 }
 
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diff --git a/04-bioconductor-vcfr.html b/04-bioconductor-vcfr.html
index 17b7b6a2..4a92eed8 100644
--- a/04-bioconductor-vcfr.html
+++ b/04-bioconductor-vcfr.html
@@ -576,7 +576,7 @@ <h3 class="callout-title">Keypoints<a class="anchor" aria-label="anchor" href="#
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   "dateCreated": "2018-03-12",
   "dateModified": "2023-11-30",
-  "datePublished": "2023-11-30"
+  "datePublished": "2023-12-05"
 }
 
   </script><script>
diff --git a/05-dplyr.html b/05-dplyr.html
index afc1f59c..2c2ab686 100644
--- a/05-dplyr.html
+++ b/05-dplyr.html
@@ -1551,7 +1551,7 @@ <h3 class="callout-title">Keypoints<a class="anchor" aria-label="anchor" href="#
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/05-dplyr.html",
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   "dateModified": "2023-11-30",
-  "datePublished": "2023-11-30"
+  "datePublished": "2023-12-05"
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diff --git a/06-data-visualization.html b/06-data-visualization.html
index d37bc8dc..44e329c0 100644
--- a/06-data-visualization.html
+++ b/06-data-visualization.html
@@ -1256,7 +1256,7 @@ <h3 class="callout-title">Keypoints<a class="anchor" aria-label="anchor" href="#
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   "dateCreated": "2018-03-12",
   "dateModified": "2023-11-30",
-  "datePublished": "2023-11-30"
+  "datePublished": "2023-12-05"
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diff --git a/07-r-help.html b/07-r-help.html
index 250f6766..57d3fc9b 100644
--- a/07-r-help.html
+++ b/07-r-help.html
@@ -548,7 +548,7 @@ <h3 class="callout-title">Keypoints<a class="anchor" aria-label="anchor" href="#
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   "dateCreated": "2018-03-12",
   "dateModified": "2023-11-30",
-  "datePublished": "2023-11-30"
+  "datePublished": "2023-12-05"
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diff --git a/404.html b/404.html
index 41aace87..6594a93c 100644
--- a/404.html
+++ b/404.html
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   "identifier": "https://datacarpentry.github.io/genomics-r-intro/404.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2023-11-30",
-  "datePublished": "2023-11-30"
+  "dateModified": "2023-12-05",
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index eabcb314..b66e5b92 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
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   "dateCreated": "2018-03-12",
   "dateModified": "2023-11-30",
-  "datePublished": "2023-11-30"
+  "datePublished": "2023-12-05"
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diff --git a/LICENSE.html b/LICENSE.html
index 85d0c3e4..05202e0a 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -406,7 +406,7 @@ <h1>Licenses</h1>
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   "dateCreated": "2018-03-12",
   "dateModified": "2023-11-30",
-  "datePublished": "2023-11-30"
+  "datePublished": "2023-12-05"
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index 203c4639..f32aaeaa 100644
--- a/aio.html
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-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
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 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
@@ -1223,7 +1223,7 @@ <h4 class="accordion-header" id="headingSolution1">
   Show me the solution
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Here as some possible answers to the challenge:</p>
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@@ -1419,7 +1419,7 @@ <h4 class="accordion-header" id="headingSolution2">
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   </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper">
 <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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   </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
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 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1861,7 +1861,7 @@ <h4 class="accordion-header" id="headingSolution4">
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   </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha">
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@@ -2100,7 +2100,7 @@ <h4 class="accordion-header" id="headingSolution5">
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 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
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 <div class="codewrapper sourceCode" id="cb65">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2161,7 +2161,7 @@ <h4 class="accordion-header" id="headingSolution6">
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   </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
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 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
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-<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
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-<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
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-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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   </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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diff --git a/key-points.html b/key-points.html
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-      "Version": "2.24",
+      "Version": "2.25",
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@@ -1145,7 +1148,7 @@
         "xfun",
         "yaml"
       ],
-      "Hash": "3854c37590717c08c32ec8542a2e0a35"
+      "Hash": "d65e35823c817f09f4de424fcdfa812a"
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       "Package": "rstudioapi",
@@ -1258,18 +1261,18 @@
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     "systemfonts": {
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-      "Version": "1.0.4",
+      "Version": "1.0.5",
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       "Repository": "RSPM",
       "Requirements": [
         "R",
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-      "Hash": "90b28393209827327de889f49935140a"
+      "Hash": "15b594369e70b975ba9f064295983499"
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     "textshaping": {
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+      "Version": "0.3.7",
       "Source": "Repository",
       "Repository": "RSPM",
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@@ -1277,7 +1280,7 @@
         "cpp11",
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-      "Hash": "1ab6223d3670fac7143202cb6a2d43d5"
+      "Hash": "997aac9ad649e0ef3b97f96cddd5622b"
     },
     "tibble": {
       "Package": "tibble",
@@ -1390,13 +1393,13 @@
     },
     "tinytex": {
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-      "Version": "0.46",
+      "Version": "0.48",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "xfun"
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-      "Hash": "0c41a73214d982f539c56a7773c7afa5"
+      "Hash": "8f96d229b7311beb32b94cf413b13f84"
     },
     "tzdb": {
       "Package": "tzdb",
@@ -1411,13 +1414,13 @@
     },
     "utf8": {
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-      "Version": "1.2.3",
+      "Version": "1.2.4",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R"
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-      "Hash": "1fe17157424bb09c48a8b3b550c753bc"
+      "Hash": "62b65c52671e6665f803ff02954446e9"
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     "uuid": {
       "Package": "uuid",
@@ -1431,7 +1434,7 @@
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+      "Version": "0.6.4",
       "Source": "Repository",
       "Repository": "CRAN",
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@@ -1441,7 +1444,7 @@
         "lifecycle",
         "rlang"
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-      "Hash": "d0ef2856b83dc33ea6e255caf6229ee2"
+      "Hash": "266c1ca411266ba8f365fcc726444b87"
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     "viridisLite": {
       "Package": "viridisLite",
@@ -1455,7 +1458,7 @@
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+      "Version": "1.6.4",
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@@ -1477,31 +1480,31 @@
         "vctrs",
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-      "Hash": "8318e64ffb3a70e652494017ec455561"
+      "Hash": "9db52c1656cf19c124f93124ea57f0fd"
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     "withr": {
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+      "Version": "2.5.2",
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-      "Repository": "RSPM",
+      "Repository": "CRAN",
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         "graphics",
         "stats"
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-      "Hash": "c0e49a9760983e81e55cdd9be92e7182"
+      "Hash": "4b25e70111b7d644322e9513f403a272"
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     "xfun": {
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+      "Version": "0.41",
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       "Requirements": [
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         "tools"
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-      "Hash": "be07d23211245fc7d4209f54c4e4ffc8"
+      "Hash": "460a5e0fe46a80ef87424ad216028014"
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     "xml2": {
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