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"CI" tag for system dependencies only #312
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,118 @@ | ||
| #!/bin/bash | ||
| set -e | ||
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| ## build ARGs | ||
| NCPUS=${NCPUS:--1} | ||
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| # always set this for scripts but don't declare as ENV.. | ||
| export DEBIAN_FRONTEND=noninteractive | ||
| export PATH=$PATH:/usr/local/texlive/bin/x86_64-linux/ | ||
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| apt-get update | ||
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| #----- SysDeps for Tidyverse----- | ||
| apt-get install -y --no-install-recommends \ | ||
| file \ | ||
| git \ | ||
| libapparmor1 \ | ||
| libgc1c2 \ | ||
| libclang-dev \ | ||
| libcurl4-openssl-dev \ | ||
| libedit2 \ | ||
| libobjc4 \ | ||
| libssl-dev \ | ||
| libpq5 \ | ||
| lsb-release \ | ||
| psmisc \ | ||
| procps \ | ||
| python-setuptools \ | ||
| pwgen \ | ||
| sudo \ | ||
| wget | ||
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| #----- SysDeps for Verse----- | ||
| apt-get install -y --no-install-recommends \ | ||
| cmake \ | ||
| default-jdk \ | ||
| fonts-roboto \ | ||
| ghostscript \ | ||
| hugo \ | ||
| less \ | ||
| libbz2-dev \ | ||
| libglpk-dev \ | ||
| libgmp3-dev \ | ||
| libfribidi-dev \ | ||
| libharfbuzz-dev \ | ||
| libhunspell-dev \ | ||
| libicu-dev \ | ||
| liblzma-dev \ | ||
| libmagick++-dev \ | ||
| libopenmpi-dev \ | ||
| libpcre2-dev \ | ||
| libv8-dev \ | ||
| libxml2-dev\ | ||
| libxslt1-dev \ | ||
| libzmq3-dev \ | ||
| qpdf \ | ||
| texinfo \ | ||
| software-properties-common \ | ||
| vim | ||
|
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| # librdf0-dev depends on libcurl4-gnutils-dev instead of libcurl4-openssl-dev... | ||
| # So: we can build the redland package bindings and then swap back to libcurl-openssl-dev... (ick) | ||
| # explicitly install runtime library sub-deps of librdf0-dev so they are not auto-removed. | ||
| apt-get install -y librdf0-dev | ||
| install2.r --error --skipinstalled -n $NCPUS redland | ||
| apt-get install -y \ | ||
| libcurl4-openssl-dev \ | ||
| libxslt-dev \ | ||
| librdf0 \ | ||
| redland-utils \ | ||
| rasqal-utils \ | ||
| raptor2-utils \ | ||
| && apt-get remove -y systemd \ | ||
| && apt-get -y autoremove | ||
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| apt-get install -y libgit2-dev libcurl4-openssl-dev | ||
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| ## Add LaTeX, rticles and bookdown support | ||
| wget "https://travis-bin.yihui.name/texlive-local.deb" \ | ||
| && dpkg -i texlive-local.deb \ | ||
| && rm texlive-local.deb | ||
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| ## Install texlive and pandoc | ||
| /rocker_scripts/install_texlive.sh | ||
| /rocker_scripts/install_pandoc.sh | ||
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| #----- SysDeps for Geospatial----- | ||
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| apt-get install -y --no-install-recommends \ | ||
| gdal-bin \ | ||
| lbzip2 \ | ||
| libfftw3-dev \ | ||
| libgdal-dev \ | ||
| libgeos-dev \ | ||
| libgsl0-dev \ | ||
| libgl1-mesa-dev \ | ||
| libglu1-mesa-dev \ | ||
| libhdf4-alt-dev \ | ||
| libhdf5-dev \ | ||
| libjq-dev \ | ||
| libpq-dev \ | ||
| libproj-dev \ | ||
| libprotobuf-dev \ | ||
| libnetcdf-dev \ | ||
| libsqlite3-dev \ | ||
| libudunits2-dev \ | ||
| lsb-release \ | ||
| netcdf-bin \ | ||
| postgis \ | ||
| protobuf-compiler \ | ||
| sqlite3 \ | ||
| tk-dev \ | ||
| unixodbc-dev | ||
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| #----- Cleanup ----- | ||
| rm -rf /var/lib/apt/lists/* | ||
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@cboettig Not sure what is needed in this section
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yeah, this is a bit of a mess. debian/ubuntu ship a few different versions of libcurl (specifically, gnutils vs openssl), which conflict. (Some packages can bind either one, but don't necessarily play nicely with both -- e.g. I believe
curlR package doesn't fail but does some unexpected things with the non-openssl version iirc?)The
redlandR package needslibrdf0-devwhich depends on gnutils, meaning that line 64 will uninstalls the openssl version and potentially breaks things. So if we're going to installlibrdf0-dev, I think it is necessary to reinstalllibcurl4-openssl-devafter we finish buildingredlandfrom source (maybe not necessary now that we can get binaries??)Anyway, long story short, I've always been very confused about the libcurl conflict. @eddelbuettel or @jeroen probably have a much better handle on this; maybe one of them could advise what's the best way to support both redland and curl R packages?
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Sorry, do not have a fix. There are alternative implementations, which in turn are use by different packages, so you could indeed end up with 'graph' with conflicts. Best solution might be to locally rebuild packages using, say, gnutls to use openssl. Not something I tried though.