fix docker

Dockerfile

@@ -11,14 +11,16 @@ WORKDIR /home/rstudio
 COPY --chown=rstudio:rstudio . /home/rstudio/
 
 ## Install the required packages
-RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); \
-    BiocManager::install(c('RCurl', 'xcms', 'MsExperiment', 'SummarizedExperiment', \
-    'Spectra', 'MetaboCoreUtils', 'limma', 'matrixStats', \
-    'pander', 'RColorBrewer', 'pheatmap', 'vioplot', 'ggfortify', 'gridExtra', 'AnnotationHub', \
-    'CompoundDb', 'MetaboAnnotation', 'RforMassSpectrometry/MsIO', \
-    'RforMassSpectrometry/MsBackendMetaboLights'), ask = FALSE, dependencies = TRUE)"
-    BiocManager::install('RforMassSpectrometry/xcms', ref = 'phili')
+RUN Rscript -e "BiocManager::install(c('RCurl', 'xcms', 'MsExperiment', 'SummarizedExperiment', \
+    'Spectra', 'MetaboCoreUtils', 'limma', 'matrixStats', 'pander', 'RColorBrewer', \
+    'pheatmap', 'vioplot', 'ggfortify', 'gridExtra', 'AnnotationHub', 'CompoundDb', \
+    'MetaboAnnotation', 'RforMassSpectrometry/MsIO', 'RforMassSpectrometry/MsBackendMetaboLights'), \
+    ask = FALSE, dependencies = TRUE)" && \
+    Rscript -e "BiocManager::install('sneumann/xcms', ref = 'phili', ask = FALSE)"
 
-## Install the package from the current directory, build vignettes, and ensure dependencies
-RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); \
-    devtools::install('.', dependencies = TRUE, type = 'source', build_vignettes = TRUE, repos = BiocManager::repositories())"
+
+## Install the current package with vignettes
+RUN Rscript -e "devtools::install('.', dependencies = TRUE, type = 'source', build_vignettes = TRUE)"
+
+## Set the correct user for subsequent commands
+USER rstudio

_pkgdown.yml

@@ -1,8 +1,8 @@
-url: https://rformassspectrometry.github.io/metabonaut/
+url: "https://rformassspectrometry.github.io/metabonaut/"
 template:
   bootstrap: 5
   bootswatch: flatly
- light-switch: true
+  light-switch: true
 
 navbar:
   title: "Metabonaut"
@@ -17,8 +17,6 @@ navbar:
           href: articles/end-to-end-untargeted-metabolomics.html
         - text: "Seamless Alignment: Merging New data with Existing Preprocessed Datasets"
           href: articles/alignment-to-external-dataset.html
-  right:
-  - icon: fa-home
-    href: ../
-  - icon: fa-github
-    href: https://github.com/rformassspectrometry/metabonaut/
+
+structure:
+  right: [search, twitter, github, lightswitch]