early Sept packages

comorment · Oct 15, 2024 · 6391375 · 6391375
1 parent ce5c5ba
commit 6391375
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Showing 4 changed files with 7 additions and 9 deletions.
diff --git a/docker/dockerfiles/r/Dockerfile b/docker/dockerfiles/r/Dockerfile
@@ -35,7 +35,7 @@ RUN bash /tmp/gcta/install_gcta.sh && \
 # R packages.
 # CRAN packages
 WORKDIR /tmp/
-RUN R -e "install.packages('devtools', repos='https://packagemanager.posit.co/cran/__linux__/jammy/2024-10-01', dependencies=c('Depends', 'Imports', 'LinkingTo'))"
+RUN R -e "install.packages('devtools', repos='https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-01', dependencies=c('Depends', 'Imports', 'LinkingTo'))"
 COPY /scripts/R/cran.R .
 RUN Rscript cran.R
 

diff --git a/docker/scripts/R/bioconductor.R b/docker/scripts/R/bioconductor.R
@@ -2,13 +2,13 @@
 dependencies <- c('Depends', 'Imports', 'LinkingTo')
 upgrade <- 'default'
 
-url = "https://packagemanager.posit.co/bioconductor/__linux__/jammy/2024-10-01"
+url = "https://packagemanager.posit.co/bioconductor/__linux__/jammy/2024-09-02"
 # Configure BioCManager to use Posit Package Manager:
-options(BioC_mirror = "https://packagemanager.posit.co/bioconductor/2024-10-01")
-options(BIOCONDUCTOR_CONFIG_FILE = "https://packagemanager.posit.co/bioconductor/2024-10-01/config.yaml")
+options(BioC_mirror = "https://packagemanager.posit.co/bioconductor/2024-09-02")
+options(BIOCONDUCTOR_CONFIG_FILE = "https://packagemanager.posit.co/bioconductor/2024-09-02/config.yaml")
 
 # Configure a CRAN snapshot compatible with Bioconductor 3.19:
-options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/2024-10-01"))
+options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-01"))
 
 # Bioconductor packages
 packages <- c(
@@ -32,7 +32,6 @@ library(devtools)
 for (package in packages) {
     tryCatch(
     {
-        # devtools::install_bioc(package, mirror=url, dependencies=dependencies, upgrade=upgrade)
         BiocManager::install(package, version='3.19')
     },
     error = function(e) {

diff --git a/docker/scripts/R/cran.R b/docker/scripts/R/cran.R
@@ -1,5 +1,5 @@
 require(devtools)
-url <- "https://packagemanager.posit.co/cran/__linux__/jammy/2024-10-01"
+url <- "https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-01"
 dependencies <- c('Depends', 'Imports', 'LinkingTo')
 upgrade <- 'default'
 
@@ -103,7 +103,6 @@ for (package in packages) {
     tryCatch(
     {
         devtools::install_cran(package, dependencies=dependencies, upgrade=upgrade)
-        # devtools::install_version(package, version=version, repos=url, dependencies=dependencies, upgrade=upgrade)
     },
     error = function(e) {
         cat("Error occurred during package installation:\n")

diff --git a/docker/scripts/R/github.R b/docker/scripts/R/github.R
@@ -1,4 +1,4 @@
-url <- "https://packagemanager.posit.co/cran/__linux__/jammy/2024-10-01"
+url <- "https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-01"
 dependencies <- c('Depends', 'Imports', 'LinkingTo')
 upgrade <- 'default'
 auth_token <- Sys.getenv("github_pat")