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[r] test first-time R package installation (#687)
Adding a Dockerfile and script to test our instructions for installing `cellxgene.census` and `tiledbsoma`. For now it's to run manually. Co-authored-by: pablo-gar <[email protected]>
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FROM ubuntu:22.04 | ||
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \ | ||
automake \ | ||
build-essential \ | ||
cmake \ | ||
git \ | ||
libcurl4-openssl-dev \ | ||
libssl-dev \ | ||
libxml2-dev \ | ||
r-base \ | ||
zlib1g-dev | ||
ADD install.R /tmp | ||
RUN Rscript /tmp/install.R |
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This Dockerfile & script are used to test the installation instructions for our `cellxgene.census` R package in a clean environment (in contrast to developer machines which tend to have a lot of unrelated packages and other miscellaneous state). Simply: | ||
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``` | ||
docker build -t cellxgene_census_r_install_test api/r/cellxgene.census/tests/installation | ||
``` | ||
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And verify successful completion, which unfortunately may take 30+ minutes building all the dependencies. | ||
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The [install.R](install.R) script should be kept consistent with the user-facing installation instructions in the [package readme](../../README.md). |
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options(error = function() { | ||
q("no", status = 1, runLast = FALSE) | ||
}) | ||
Sys.setenv(MAKE = "make -j8") | ||
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####################################################################################### | ||
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install.packages( | ||
"tiledb", | ||
version = "0.20.3", | ||
repos = c("https://tiledb-inc.r-universe.dev", "https://cloud.r-project.org") | ||
) | ||
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install.packages( | ||
"cellxgene.census", | ||
repos = c("https://chanzuckerberg.r-universe.dev", "https://cloud.r-project.org") | ||
) | ||
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tiledbsoma::show_package_versions() | ||
print(as.data.frame( | ||
cellxgene.census::open_soma()$get("census_info")$get("summary")$read()$concat() | ||
)) |