Update release tag and fix R version in config.yml

idot · May 4, 2019 · 1d4b60e · 1d4b60e
1 parent 80647c3
commit 1d4b60e
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Showing 10 changed files with 18 additions and 18 deletions.
diff --git a/config.yml b/config.yml
@@ -1,12 +1,12 @@
 ---
 versions:
     release:
-        version_number: "3.8" # change this at release time
+        version_number: "3.9" # change this at release time
         r_url: "https://cran.rstudio.com/src/base/R-latest.tar.gz"
-        parent: "rocker/rstudio:3.5.3"
+        parent: "rocker/rstudio:3.6.0"
         use_r_devel: false # should always be false
     devel:
-        version_number: "3.9" # change this at release time
+        version_number: "3.10" # change this at release time
         ## IMPORTANT: Change r_url at release time if new bioc devel does(not) use R-devel
         #parent: "rocker/rstudio:3.5.1"
         parent: "rocker/rstudio:devel"

diff --git a/out/devel_base/install.R b/out/devel_base/install.R
@@ -9,8 +9,8 @@ install.packages("BiocManager", repos="https://cran.rstudio.com")
 #devtools::install_github("Bioconductor/BiocManager")
 library(BiocManager)
 
-if(BiocManager::version() != "3.9"){
-    BiocManager::install(version="3.9",
+if(BiocManager::version() != "3.10"){
+    BiocManager::install(version="3.10",
                          update=TRUE, ask=FALSE)
 }
 
@@ -19,5 +19,5 @@ builtins <- c("Matrix", "KernSmooth", "mgcv")
 for (builtin in builtins)
     if (!suppressWarnings(require(builtin, character.only=TRUE)))
         suppressWarnings(BiocManager::install(builtin,
-                                              version="3.9",
+                                              version="3.10",
                                               update=TRUE, ask=FALSE))
diff --git a/out/devel_metabolomics/install.R b/out/devel_metabolomics/install.R
@@ -8,7 +8,7 @@
 
 wantedBiocViews <- c("Metabolomics")
 
-url <- "https://www.bioconductor.org/packages/3.9/bioc/VIEWS"
+url <- "https://www.bioconductor.org/packages/3.10/bioc/VIEWS"
 
 t <- tempfile()
 download.file(url, t)

diff --git a/out/devel_proteomics/install.R b/out/devel_proteomics/install.R
@@ -9,10 +9,10 @@ wantedBiocViews <- c("Proteomics","MassSpectrometryData")
 install.packages("Cairo")
 
 ## software packages
-con1 <- url("https://www.bioconductor.org/packages/3.9/bioc/VIEWS")
+con1 <- url("https://www.bioconductor.org/packages/3.10/bioc/VIEWS")
 dcf1 <- as.data.frame(read.dcf(con1), stringsAsFactors=FALSE)
 ## data packages
-con2 <- url("https://www.bioconductor.org/packages/3.9/data/experiment/VIEWS")
+con2 <- url("https://www.bioconductor.org/packages/3.10/data/experiment/VIEWS")
 dcf2 <- as.data.frame(read.dcf(con2), stringsAsFactors=FALSE)
 
 dcf <- rbind(dcf1[, c("Package", "biocViews")],

diff --git a/out/devel_protmetcore/install.R b/out/devel_protmetcore/install.R
@@ -8,7 +8,7 @@
 
 wantedBiocViews <- c("Metabolomics","Proteomics")
 
-url <- "https://www.bioconductor.org/packages/3.9/bioc/VIEWS"
+url <- "https://www.bioconductor.org/packages/3.10/bioc/VIEWS"
 
 t <- tempfile()
 download.file(url, t)

diff --git a/out/release_base/Dockerfile b/out/release_base/Dockerfile
@@ -4,7 +4,7 @@
 
 # The suggested name for this image is: bioconductor/release_base.
 
-FROM rocker/rstudio:3.5.3
+FROM rocker/rstudio:3.6.0
 
 # FIXME? in release, default CRAN mirror is set to rstudio....should it be fhcrc?
 

diff --git a/out/release_base/install.R b/out/release_base/install.R
@@ -9,8 +9,8 @@ install.packages("BiocManager", repos="https://cran.rstudio.com")
 #devtools::install_github("Bioconductor/BiocManager")
 library(BiocManager)
 
-if(BiocManager::version() != "3.8"){
-    BiocManager::install(version="3.8",
+if(BiocManager::version() != "3.9"){
+    BiocManager::install(version="3.9",
                          update=TRUE, ask=FALSE)
 }
 
@@ -19,5 +19,5 @@ builtins <- c("Matrix", "KernSmooth", "mgcv")
 for (builtin in builtins)
     if (!suppressWarnings(require(builtin, character.only=TRUE)))
         suppressWarnings(BiocManager::install(builtin,
-                                              version="3.8",
+                                              version="3.9",
                                               update=TRUE, ask=FALSE))
diff --git a/out/release_metabolomics/install.R b/out/release_metabolomics/install.R
@@ -8,7 +8,7 @@
 
 wantedBiocViews <- c("Metabolomics")
 
-url <- "https://www.bioconductor.org/packages/3.8/bioc/VIEWS"
+url <- "https://www.bioconductor.org/packages/3.9/bioc/VIEWS"
 
 t <- tempfile()
 download.file(url, t)

diff --git a/out/release_proteomics/install.R b/out/release_proteomics/install.R
@@ -9,10 +9,10 @@ wantedBiocViews <- c("Proteomics","MassSpectrometryData")
 install.packages("Cairo")
 
 ## software packages
-con1 <- url("https://www.bioconductor.org/packages/3.8/bioc/VIEWS")
+con1 <- url("https://www.bioconductor.org/packages/3.9/bioc/VIEWS")
 dcf1 <- as.data.frame(read.dcf(con1), stringsAsFactors=FALSE)
 ## data packages
-con2 <- url("https://www.bioconductor.org/packages/3.8/data/experiment/VIEWS")
+con2 <- url("https://www.bioconductor.org/packages/3.9/data/experiment/VIEWS")
 dcf2 <- as.data.frame(read.dcf(con2), stringsAsFactors=FALSE)
 
 dcf <- rbind(dcf1[, c("Package", "biocViews")],

diff --git a/out/release_protmetcore/install.R b/out/release_protmetcore/install.R
@@ -8,7 +8,7 @@
 
 wantedBiocViews <- c("Metabolomics","Proteomics")
 
-url <- "https://www.bioconductor.org/packages/3.8/bioc/VIEWS"
+url <- "https://www.bioconductor.org/packages/3.9/bioc/VIEWS"
 
 t <- tempfile()
 download.file(url, t)