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Expand Up @@ -218,7 +218,7 @@ <h1 class="title">Write, containerize and publish versioned Quarto books with Bi


</header><p><img src="inst/assets/cover.png" title="Write, containerize and publish versioned Quarto books with Bioconductor" class="quarto-cover-image img-fluid"></p>
<p><strong>Package:</strong> BiocBook<br><strong>Authors:</strong> Jacques Serizay [aut, cre]<br><strong>Compiled:</strong> 2023-08-10<br><strong>Package version:</strong> 0.99.0<br><strong>R version:</strong> <b style="color:red;">R version 4.3.1 (2023-06-16)</b><br><strong>BioC version:</strong> <b style="color:red;">3.18</b><br><strong>License:</strong> MIT + file LICENSE<br></p>
<p><strong>Package:</strong> BiocBook<br><strong>Authors:</strong> Jacques Serizay [aut, cre]<br><strong>Compiled:</strong> 2023-08-16<br><strong>Package version:</strong> 0.99.0<br><strong>R version:</strong> <b style="color:red;">R version 4.3.1 (2023-06-16)</b><br><strong>BioC version:</strong> <b style="color:red;">3.18</b><br><strong>License:</strong> MIT + file LICENSE<br></p>
<section id="what-are-biocbooks" class="level1 unnumbered"><h1 class="unnumbered">What are <code>BiocBook</code>s?</h1>
<p><code>BiocBook</code>s are <strong>package-based, versioned online books</strong> with a <strong>supporting <code>Docker</code> image</strong> for each book version.</p>
<p>A <code>BiocBook</code> can be created by authors (e.g.&nbsp;<code>R</code> developers, but also scientists, teachers, communicators, …) who wish to:</p>
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<span><span class="co">## collate en_US.UTF-8</span></span>
<span><span class="co">## ctype en_US.UTF-8</span></span>
<span><span class="co">## tz Etc/UTC</span></span>
<span><span class="co">## date 2023-08-10</span></span>
<span><span class="co">## date 2023-08-16</span></span>
<span><span class="co">## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)</span></span>
<span><span class="co">## </span></span>
<span><span class="co">## ─ Packages ────────────────────────────────────────────────────────────────</span></span>
<span><span class="co">## package * version date (UTC) lib source</span></span>
<span><span class="co">## askpass 1.1 2019-01-13 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## available 1.1.0 2022-07-10 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## base * 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## base * 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## BiocBook 0.99.0 2023-08-10 [1] local</span></span>
<span><span class="co">## BiocBook 0.99.0 2023-08-16 [1] local</span></span>
<span><span class="co">## BiocGenerics 0.47.0 2023-04-25 [1] Bioconductor</span></span>
<span><span class="co">## BiocManager 1.30.21.1 2023-07-18 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## BiocManager 1.30.22 2023-08-08 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## BiocVersion 3.18.0 2023-04-25 [1] Bioconductor</span></span>
<span><span class="co">## boot 1.3-28.1 2022-11-22 [2] CRAN (R 4.3.1)</span></span>
<span><span class="co">## brew 1.0-8 2022-09-29 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## brio 1.1.3 2021-11-30 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## bslib 0.5.0 2023-06-09 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## bslib 0.5.1 2023-08-11 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## class 7.3-22 2023-05-03 [2] CRAN (R 4.3.1)</span></span>
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<span><span class="co">## cluster 2.1.4 2022-08-22 [2] CRAN (R 4.3.1)</span></span>
<span><span class="co">## codetools 0.2-19 2023-02-01 [2] CRAN (R 4.3.1)</span></span>
<span><span class="co">## commonmark 1.9.0 2023-03-17 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## compiler 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## cpp11 0.4.5 2023-07-20 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## compiler 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## cpp11 0.4.6 2023-08-10 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## credentials 1.3.2 2021-11-29 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## curl 5.0.1 2023-06-07 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## datasets * 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## datasets * 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## desc 1.4.2 2022-09-08 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## diffobj 0.3.5 2021-10-05 [1] CRAN (R 4.3.1)</span></span>
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<span><span class="co">## foreign 0.8-84 2022-12-06 [2] CRAN (R 4.3.1)</span></span>
<span><span class="co">## fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## gert 1.9.2 2022-12-05 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## gert 1.9.3 2023-08-07 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## gh 1.4.0 2023-02-22 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## gitcreds 0.1.2 2022-09-08 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## graphics * 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## grDevices * 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## grid 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## graphics * 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## grDevices * 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## grid 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## highr 0.10 2022-12-22 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## htmltools 0.5.6 2023-08-10 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## httpuv 1.6.11 2023-05-11 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## httr 1.4.6 2023-05-08 [1] CRAN (R 4.3.1)</span></span>
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<span><span class="co">## MASS 7.3-60 2023-05-04 [2] CRAN (R 4.3.1)</span></span>
<span><span class="co">## Matrix 1.6-0 2023-07-08 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## methods * 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## methods * 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## mgcv 1.9-0 2023-07-11 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## mime 0.12 2021-09-28 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## nlme 3.1-162 2023-01-31 [2] CRAN (R 4.3.1)</span></span>
<span><span class="co">## nlme 3.1-163 2023-08-09 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## nnet 7.3-19 2023-05-03 [2] CRAN (R 4.3.1)</span></span>
<span><span class="co">## openssl 2.1.0 2023-07-15 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## packrat 0.9.1 2023-02-27 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## pak 0.5.1.9000 2023-08-02 [1] local</span></span>
<span><span class="co">## parallel 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## parallel 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## pkgbuild 1.4.2 2023-06-26 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.1)</span></span>
Expand All @@ -435,9 +435,9 @@ <h1 class="title">Write, containerize and publish versioned Quarto books with Bi
<span><span class="co">## prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## processx 3.8.2 2023-06-30 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## ps 1.7.5 2023-04-18 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## purrr 1.0.1 2023-01-10 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## quarto 1.2 2022-07-06 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## ragg 1.2.5 2023-01-12 [1] CRAN (R 4.3.1)</span></span>
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<span><span class="co">## Rcpp 1.0.11 2023-07-06 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## renv 1.0.1 2023-08-10 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## renv 1.0.2 2023-08-15 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## rmarkdown 2.23 2023-07-01 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## roxygen2 7.2.3 2022-12-08 [1] CRAN (R 4.3.1)</span></span>
Expand All @@ -461,33 +461,33 @@ <h1 class="title">Write, containerize and publish versioned Quarto books with Bi
<span><span class="co">## SnowballC 0.7.1 2023-04-25 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## sourcetools 0.1.7-1 2023-02-01 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## spatial 7.3-17 2023-07-20 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## splines 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## stats * 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## stats4 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## splines 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## stats * 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## stats4 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## stringdist 0.9.10 2022-11-07 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## stringi 1.7.12 2023-01-11 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## stringr 1.5.0 2022-12-02 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## survival 3.5-5 2023-03-12 [2] CRAN (R 4.3.1)</span></span>
<span><span class="co">## sys 3.4.2 2023-05-23 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## systemfonts 1.0.4 2022-02-11 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## tcltk 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## tcltk 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## testthat 3.1.10 2023-07-06 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## textshaping 0.3.6 2021-10-13 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## tidytext 0.4.1 2023-01-07 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## tinytex 0.45 2023-04-18 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## tinytex 0.46 2023-08-09 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## tokenizers 0.3.0 2022-12-22 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## tools 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## tools 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## usethis 2.2.2 2023-07-06 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## utf8 1.2.3 2023-01-31 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## utils * 4.3.1 2023-08-03 [2] local</span></span>
<span><span class="co">## utils * 4.3.1 2023-08-10 [2] local</span></span>
<span><span class="co">## vctrs 0.6.3 2023-06-14 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## waldo 0.5.1 2023-05-08 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## whisker 0.4.1 2022-12-05 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## withr 2.5.0 2022-03-03 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## xfun 0.39 2023-04-20 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## xfun 0.40 2023-08-09 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## xml2 1.3.5 2023-07-06 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## xopen 1.0.0 2018-09-17 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.1)</span></span>
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Expand Up @@ -349,7 +349,7 @@ <h1 class="title">
</section><section id="so-what-packages-can-i-use" class="level2" data-number="1.4"><h2 data-number="1.4" class="anchored" data-anchor-id="so-what-packages-can-i-use">
<span class="header-section-number">1.4</span> So what packages can I use?</h2>
<p>Any package that has been released in the Bioconductor version you are using (in this book version, this is 3.18).</p>
<p>The <code>HiContacts</code> package is available in Bioconductor since <code>3.16</code>, while the <code>HiCExperiment</code> package was only made available in <code>3.17</code>. <code>MICSQTL</code> has recently been accepted in <code>3.18</code> (current <code>devel</code>, on Thu Aug 10 18:04:54 2023). Let’s check this!</p>
<p>The <code>HiContacts</code> package is available in Bioconductor since <code>3.16</code>, while the <code>HiCExperiment</code> package was only made available in <code>3.17</code>. <code>MICSQTL</code> has recently been accepted in <code>3.18</code> (current <code>devel</code>, on Wed Aug 16 07:47:54 2023). Let’s check this!</p>
<div class="cell" data-layout-align="center">
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html">Sys.getenv</a></span><span class="op">(</span><span class="st">"R_BIOC_VERSION"</span><span class="op">)</span></span>
<span><span class="co">## [1] "3.18"</span></span>
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"href": "pages/Chapter-1.html#so-what-packages-can-i-use",
"title": "\n1  BiocBook versioning system\n",
"section": "\n1.4 So what packages can I use?",
"text": "1.4 So what packages can I use?\nAny package that has been released in the Bioconductor version you are using (in this book version, this is 3.18).\nThe HiContacts package is available in Bioconductor since 3.16, while the HiCExperiment package was only made available in 3.17. MICSQTL has recently been accepted in 3.18 (current devel, on Thu Aug 10 18:04:54 2023). Let’s check this!\n\nSys.getenv(\"R_BIOC_VERSION\")\n## [1] \"3.18\"\nBiocManager::available(\"HiContacts\")\n## 'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n## 'help(\"repositories\", package = \"BiocManager\")' for details.\n## Replacement repositories:\n## CRAN: https://cloud.r-project.org\n## [1] \"HiContacts\" \"HiContactsData\"\nBiocManager::available(\"HiCExperiment\")\n## 'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n## 'help(\"repositories\", package = \"BiocManager\")' for details.\n## Replacement repositories:\n## CRAN: https://cloud.r-project.org\n## [1] \"HiCExperiment\"\nBiocManager::available(\"MICSQTL\")\n## 'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n## 'help(\"repositories\", package = \"BiocManager\")' for details.\n## Replacement repositories:\n## CRAN: https://cloud.r-project.org\n## [1] \"MICSQTL\""
"text": "1.4 So what packages can I use?\nAny package that has been released in the Bioconductor version you are using (in this book version, this is 3.18).\nThe HiContacts package is available in Bioconductor since 3.16, while the HiCExperiment package was only made available in 3.17. MICSQTL has recently been accepted in 3.18 (current devel, on Wed Aug 16 07:47:54 2023). Let’s check this!\n\nSys.getenv(\"R_BIOC_VERSION\")\n## [1] \"3.18\"\nBiocManager::available(\"HiContacts\")\n## 'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n## 'help(\"repositories\", package = \"BiocManager\")' for details.\n## Replacement repositories:\n## CRAN: https://cloud.r-project.org\n## [1] \"HiContacts\" \"HiContactsData\"\nBiocManager::available(\"HiCExperiment\")\n## 'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n## 'help(\"repositories\", package = \"BiocManager\")' for details.\n## Replacement repositories:\n## CRAN: https://cloud.r-project.org\n## [1] \"HiCExperiment\"\nBiocManager::available(\"MICSQTL\")\n## 'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n## 'help(\"repositories\", package = \"BiocManager\")' for details.\n## Replacement repositories:\n## CRAN: https://cloud.r-project.org\n## [1] \"MICSQTL\""
},
{
"objectID": "pages/Chapter-2.html#register-a-github-account-in-r",
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