Force commit: pkgdown documentation was old because vignettes were ol…

…d. Fixed it

DESCRIPTION

@@ -8,6 +8,7 @@ Maintainer: Thomas Rauter <[email protected]>
 Description: Timeseries analysis of omics data can be carried out by fitting spline curves to the data and using limma for hypothesis testing. For this, the right spline freedom and further hyperparameters must be identified, and the obtained hits clustered based on the spline shape.The R package splinetime streamlines this whole process and generates reports.
 Depends: R (>= 4.3.0)
 License: MIT + file LICENSE
+URL: https://csbg.github.io/SplineOmics
 Imports:
     ComplexHeatmap(>= 2.18.0),
     base64enc(>= 0.1-3),

README.Rmd

@@ -210,18 +210,7 @@ An explanation of the three different `limma` results is [here](https://csbg.git
 
 #### RNA-seq data
 
-Transcriptomics data must be preprocessed for `limma`. You need to provide an
-appropriate object, such as a `voom` object, in the `rna_seq_data` argument of
-the `SplineOmics` object (see 
-[documentation](https://csbg.github.io/SplineOmics/reference/create_splineomics.html)). 
-Along with this, the normalized matrix 
-(e.g., the `$E` slot of the `voom` object) must be passed to the `data`
-argument. This allows flexibility in preprocessing; you can use any method
-you prefer as long as the final object and matrix are compatible with limma.
-One way to preprocess your RNA-seq data is by using the `preprocess_rna_seq_data()`
-function included in the `SplineOmics` package 
-(see [documentation](https://csbg.github.io/SplineOmics/reference/preprocess_rna_seq_data.html)).
-
+Transcriptomics data must be preprocessed for `limma`. You need to provide an appropriate object, such as a `voom` object, in the `rna_seq_data` argument of the `SplineOmics` object (see [documentation](https://csbg.github.io/SplineOmics/reference/create_splineomics.html)). Along with this, the normalized matrix (e.g., the `$E` slot of the `voom` object) must be passed to the `data` argument. This allows flexibility in preprocessing; you can use any method you prefer as long as the final object and matrix are compatible with limma. One way to preprocess your RNA-seq data is by using the `preprocess_rna_seq_data()` function included in the `SplineOmics` package (see [documentation](https://csbg.github.io/SplineOmics/reference/preprocess_rna_seq_data.html)).
 
 #### Glycan fractional abundance data
 

doc/Docker_permission_denied.Rmd

@@ -1,10 +1,10 @@
 ---
-title: "Docker permission denied"
+title: "Docker_permission_denied"
 author: "Thomas Rauter"
 date: "10 June, 2024"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Docker-permission-denied}
+  %\VignetteIndexEntry{Docker_permission_denied}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -18,23 +18,23 @@ knitr::opts_chunk$set(
 
 If you face 'permission denied' issues, you might need to add your user to the Docker group. Follow these steps:
 
-**1.  Create the Docker Group (if it doesn't already exist):**
+**1. Create the Docker Group (if it doesn't already exist):**
 
 ``` sh
 sudo groupadd docker
 ```
 
 This command creates a Docker group if it does not already exist on your system.
 
-**2.  Add Your User to the Docker Group:**
+**2. Add Your User to the Docker Group:**
 
 ``` sh
 sudo usermod -aG docker $USER
 ```
 
 This command adds your user to the Docker group, which allows you to run Docker commands without sudo.
 
-**3.  Log Out and Log Back In:**
+**3. Log Out and Log Back In:**
 
 This step is necessary to apply the group membership changes. After logging back in, you should be able to run Docker commands without sudo.
 
@@ -44,7 +44,7 @@ Alternatively, you can use the following command to apply the group changes imme
 newgrp docker
 ```
 
-**4.  Verify Docker Permissions:**
+**4. Verify Docker Permissions:**
 
 To check if the permission issue is resolved, run a simple Docker command:
 
@@ -54,7 +54,7 @@ docker run hello-world
 
 If the command runs successfully, you have configured Docker correctly.
 
-**5.  Ensure Docker Service is Running:**
+**5. Ensure Docker Service is Running:**
 
 If you still encounter issues, ensure that the Docker service is running:
 

doc/Docker_permission_denied.html

@@ -13,7 +13,7 @@
 <meta name="author" content="Thomas Rauter" />
 
 
-<title>Docker permission denied</title>
+<title>Docker_permission_denied</title>
 
 <script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
 // be compatible with the behavior of Pandoc < 2.8).
@@ -337,7 +337,7 @@
 
 
 
-<h1 class="title toc-ignore">Docker permission denied</h1>
+<h1 class="title toc-ignore">Docker_permission_denied</h1>
 <h4 class="author">Thomas Rauter</h4>
 <h4 class="date">10 June, 2024</h4>