docker: install xcms from the jomain branch

Dockerfile

@@ -11,6 +11,6 @@ WORKDIR /home/rstudio
 COPY --chown=rstudio:rstudio . /home/rstudio/
 
 ## Install the xcmsTutorials package and additional required packages
-RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install(ask = FALSE); BiocManager::install('sneumann/xcms')"
+RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install(ask = FALSE); BiocManager::install('sneumann/xcms', ref = 'jomain')"
 
 RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); devtools::install('.', dependencies = TRUE, build_vignettes = TRUE, repos = BiocManager::repositories())"

vignettes/xcms-preprocessing.Rmd

@@ -46,7 +46,8 @@ which is followed by the description of a simple data centroiding approach and
 finally we present an *xcms*-based LC-MS data preprocessing that comprises
 chromatographic peak detection, alignment and correspondence. Data normalization
 procedures, compound identification and differential abundance analysis are not
-covered here. Particular emphasis is given on deriving and defining data set-dependent values for the most critical *xcms* preprocessing parameters.
+covered here. Particular emphasis is given on deriving and defining data
+set-dependent values for the most critical *xcms* preprocessing parameters.
 
 
 # Introduction