Quick fix for current devel packages

Author: jorainer

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', ref = 'jomain')"
+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')); devtools::install('.', dependencies = TRUE, build_vignettes = TRUE, repos = BiocManager::repositories())"

vignettes/xcms-preprocessing.Rmd

@@ -2279,6 +2279,7 @@ Our data has two columns, one with *retention times* and one with
 data.
 
 ```{r peaks-plot, fig.width = 12, fig.height = 2.15}
+library(MSnbase)
 chr <- Chromatogram(rtime = cdata$rt, intensity = cdata$intensity)
 par(mar = c(2, 2, 0, 0))
 plot(chr)