Updated to R version 4.0.1; fixed missing packages error.

AG-Boerries · Jun 22, 2020 · a1940ff · a1940ff
1 parent 56dbb66
commit a1940ff
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Showing 3 changed files with 19 additions and 6 deletions.
diff --git a/RScripts/cnv_ana_tools.R b/RScripts/cnv_ana_tools.R
@@ -22,7 +22,7 @@ assess_significance <- function(ratio_file, cnvs_file, outfile){
   ratio.bed = GRanges(ratio$Chromosome, IRanges(ratio$Start, ratio$Start),
                       score=ratio$Ratio)
   overlaps <- subsetByOverlaps(ratio.bed, cnvs.bed)
-  normals <- setdiff(ratio.bed, cnvs.bed)
+  normals <- GenomicRanges::setdiff(ratio.bed, cnvs.bed)
   normals <- subsetByOverlaps(ratio.bed, normals)
   numberOfCol=length(cnvs)
   for (i in c(1:length(cnvs[,1]))) {

diff --git a/RScripts/install_packages.R b/RScripts/install_packages.R
@@ -9,9 +9,13 @@ options(repos=structure(c(CRAN="http://cloud.r-project.org")))
 
 if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
-BiocManager::install(version = "3.8")
-
-# TODO package install in a more efficient way
+BiocManager::install("Biobase")
+#BiocManager::install(version = "3.8")
+#BiocManager::install(pkgs = "devtools", update  = TRUE, ask = FALSE)
+#url_1 <- "https://cran.rstudio.com/src/contrib/GetoptLong_1.0.0.tar.gz"
+#devtools::install_url(url_1)
+# package install in a more efficient way
+#install.packages("GetoptLong", type = "source", repos=NULL)
 packages <- c("foreach", "doMC", "openxlsx", "circlize", "knitr", "kableExtra", "OmicCircos", "rtracklayer", "org.Hs.eg.db",
               "Homo.sapiens", "RMySQL", "biomaRt", "Rsamtools", "gtrellis", "ComplexHeatmap",
               "VariantAnnotation", "BSgenome.Hsapiens.UCSC.hg19", "devtools",
@@ -26,4 +30,4 @@ url <- "https://cran.r-project.org/src/contrib/Archive/lsei/lsei_1.2-0.1.tar.gz"
 #unlink(pkgFile)
 
 devtools::install_url(url)
-BiocManager::install(c("YAPSA", "SomaticSignatures"), update  = TRUE, ask = FALSE)
+BiocManager::install(c("YAPSA", "SomaticSignatures"), update  = FALSE, ask = FALSE)
diff --git a/debian/setup.sh b/debian/setup.sh
@@ -38,6 +38,14 @@ function install_texlive()
     preprint
   tlmgr init-usertree
 }
+
+function install_R()
+{
+  echo "deb http://cloud.r-project.org/bin/linux/debian buster-cran40/" >> /etc/apt/sources.list && \
+  apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF'
+  apt-get update && apt-get install -y -t buster-cran40 r-base
+}
+
 # update packages
 apt-get update
 
@@ -49,11 +57,11 @@ apt-get install -y build-essential gcc-multilib libc-dev git-core cmake patch cm
   default-jre \
   ant \
   perl-base \
-  r-base-core r-recommended r-cran-latticeextra r-cran-hmisc r-cran-rmysql \
   python3 python3-pysam python3-pip python3-numpy python3-scipy python3-matplotlib python3-reportlab python3-pandas python3-biopython python3-pyfaidx python3-pyvcf cython \
   cnvkit \
   libsnappy-java && \
   install_java8 && \
+  install_R && \
   apt-get -y purge  default-jre default-jdk-headless \
                     openjdk-11-jdk openjdk-11-jdk-headless \
                     openjdk-11-jre openjdk-11-jre-headless && \
@@ -62,3 +70,4 @@ apt-get install -y build-essential gcc-multilib libc-dev git-core cmake patch cm
   #apt-get purge -y python3-pip && \
   apt-get -y autoremove
   #update-alternatives --set java /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java 
+#r-base-core r-recommended r-cran-latticeextra r-cran-hmisc r-cran-rmysql \