fix biocmanager package installation

Dockerfile

@@ -1,14 +1,20 @@
-# --platform=linux/amd64 to avoid 'no match for platform in the manifest' on M1
+# use --platform=linux/amd64 to avoid 'no match for platform in the manifest' on M1
 FROM rocker/tidyverse:4
 
 COPY . /cogaps
 WORKDIR /cogaps
 
 RUN sudo apt-get update -y && \
     apt-get upgrade -y && \
-    apt-get install libhdf5-dev build-essential patch cmake -y
+    apt-get install libhdf5-dev build-essential patch -y
 
-RUN Rscript -e 'devtools::install_deps()'
+#packages below didn't install with devtools::install_deps, needed BiocManager
+RUN Rscript -e 'install.packages("BiocManager");\
+                BiocManager::install(c("S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "rhdf5"))'
+
+#install all other dependencies
+RUN Rscript -e 'devtools::install_deps(".", dependencies=TRUE)'
+
+#need to restart R sometimes https://github.com/r-lib/devtools/issues/2395
+RUN Rscript -e 'devtools::install(".", dependencies=TRUE)'
 
-#https://github.com/r-lib/devtools/issues/2395
-RUN Rscript -e 'devtools::install()'