Implementation of a singularity definition file to contain R with affymetrix package

R_4.4.0_affymetrix.def

+BootStrap: docker
+From: ubuntu:22.04
+
+%help 
+This is a singularity container packing R version 4.4.0 and all the dependencies necessary to run the affy package from affymetrix, in order to process .cel transcriptomics files
+run the command 'apptainer test <image_name>.sif' to see the actual versions of R and "affy" package installed
+built-in R packages should be located in /usr/lib/R/library
+other R packages should be located in /usr/local/lib/R/site-library
+Authors : valentin.vautrot@u-bourgogne.fr
+
+%post
+
+# export R_VERSION=4.3.3
+# echo "export R_VERSION=${R_VERSION}" >> $SINGULARITY_ENVIRONMENT
+export DEBIAN_FRONTEND=noninteractive
+
+apt-get update
+apt-get install -y --no-install-recommends apt-utils
+apt-get install -y --no-install-recommends locales language-pack-fr software-properties-common dirmngr wget
+
+wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/"
+
+apt-get install -y --no-upgrade --no-install-recommends -t jammy-cran40 r-base-core=4.4.0-1.2204.0 r-base=4.4.0-1.2204.0 r-recommended=4.4.0-1.2204.0 r-base-dev=4.4.0-1.2204.0
+
+apt-get install -y --no-upgrade --no-install-recommends build-essential libcurl4-openssl-dev zlib1g-dev libxml2-dev libssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libbz2-dev gfortran
+
+echo "installed R version :"
+R --version
+
+# # install R packages :
+# Rscript -e 'install.packages("devtools")'
+Rscript -e 'install.packages("BiocManager", dependencies=TRUE)'
+Rscript -e 'BiocManager::install("Biobase", version = "3.19")'
+Rscript -e 'BiocManager::install("affy", version = "3.19")'
+
+# Clean up
+rm -rf /var/lib/apt/lists/*
+
+%environment
+export LANGUAGE=fr_FR.UTF-8
+export LC_ALL=fr_FR.UTF-8
+export LANG=fr_FR.UTF-8
+export LC_CTYPE=fr_FR.UTF-8
+
+%test
+echo "installed R version :"
+R --version
+echo "installed affy package version :"
+Rscript -e 'packageVersion("affy")'
+
+%labels 
+Auhtors valentin.vautrot@u-bourgogne.fr
+Contained_OS_version Ubuntu_22.04_LTS_JammyJellyfish
+Contained_R_version 4.4.0
+Contained_FRASER_version 1.14.1
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