-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Switch installation to use pak::pkg_install
- Loading branch information
Showing
1 changed file
with
11 additions
and
4 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -12,7 +12,14 @@ LABEL maintainer="Steve Lianoglou ([email protected])" | |
# Newer versions of bioconductor_docker image sets options::repos to a | ||
# frozen RSPM date. This is good for reproducibility at large, but I like | ||
# to live on the edge/latest. | ||
RUN sudo echo 'options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/bionic/latest"))' >> /usr/local/lib/R/etc/Rprofile.site | ||
# Figure out the URL for the CRAN repository to use to install binary packages | ||
# using this tool: | ||
# https://packagemanager.posit.co/client/#/repos/cran/setup | ||
# RUN sudo echo 'options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/bionic/latest"))' >> /usr/local/lib/R/etc/Rprofile.site | ||
# RUN sudo echo 'options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest"))' >> /usr/local/lib/R/etc/Rprofile.site | ||
|
||
# Use pak? | ||
RUN Rscript -e "install.packages('pak')" | ||
|
||
# Required for textshaping library | ||
RUN sudo apt-get update -y | ||
|
@@ -34,7 +41,7 @@ ADD base-packages.txt /tmp/ | |
# and RSPM. | ||
# https://community.rstudio.com/t/package-manager-and-travis/73816 | ||
RUN Rscript -e "\ | ||
install.packages(c(\ | ||
pak::pkg_install(c(\ | ||
'RApiSerialize', \ | ||
'Rcpp', \ | ||
'cpp11', \ | ||
|
@@ -58,8 +65,8 @@ RUN R -f /tmp/base-packages-install.R | |
# every now and again without reinstalling all of them again, so we can | ||
# do that here. Run a no-op command to flip this on/of/rerun | ||
# RUN pwd | ||
RUN Rscript -e "options(repos = 'https://cran.rstudio.com/'); BiocManager::install(update = TRUE, ask = FALSE)" \ | ||
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds | ||
# RUN Rscript -e "options(repos = 'https://cran.rstudio.com/'); BiocManager::install(update = TRUE, ask = FALSE)" \ | ||
# && rm -rf /tmp/downloaded_packages/ /tmp/*.rds | ||
|
||
# Init command for s6-overlay | ||
CMD ["/init"] |