Remove renv dependencies from conda env

This simplifies the dependencies in the main
conda environment.

This required then to rewrite the tests to use
a separate conda environment with renv installed
in order to build and restore the renv.

Author: Vito Zanotelli

utils/quarto/environment.linux-64.pin.txt

@@ -16,41 +16,32 @@ https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7
 https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-13.2.0-hdb50d1a_111.conda#43178c27fac2dcd495bd9e58e18272d9
 https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-13.2.0-hdb50d1a_111.conda#4ffa92ea4ba6555dee156ce3d0ae7a9b
 https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.1.11.1-ha770c72_0.conda#0e2f14aff42adf4675bcd5335d644a5f
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29
 https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_11.conda#8c462ced2af33648195dc9459f331f31
 https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_17.conda#595db67e32b276298ff3d94d07d47fbf
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
 https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-ha1999f0_7.conda#3f840c7ed70a96b5ebde8044b2f36f32
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
-https://conda.anaconda.org/conda-forge/linux-64/binutils-2.40-h4852527_7.conda#df53aa8418f8c289ae9b9665986034f8
-https://conda.anaconda.org/conda-forge/linux-64/binutils_linux-64-2.40-hb3c18ed_7.conda#ca84cd2dcc3d3e200f8e9aff105cbcb3
 https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_11.conda#0b3b218a596bb4c3854cc9ee799f94e5
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
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-https://conda.anaconda.org/conda-forge/linux-64/gettext-tools-0.22.5-h59595ed_2.conda#985f2f453fb72408d6b6f1be0f324033
 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
 https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79
 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
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-https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-0.22.5-h59595ed_2.conda#172bcc51059416e7ce99e7b528cede83
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-https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7
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-https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814
-https://conda.anaconda.org/conda-forge/linux-64/m4-1.4.18-h516909a_1001.tar.bz2#4abb931c0d08a41583fc637c663e45e2
 https://conda.anaconda.org/conda-forge/linux-64/make-4.3-hd18ef5c_1.tar.bz2#4049ebfd3190b580dffe76daed26155a
 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
 https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_0.conda#a41fa0e391cc9e0d6b78ac69ca047a6c
-https://conda.anaconda.org/conda-forge/linux-64/pkg-config-0.29.2-h36c2ea0_1008.tar.bz2#fbef41ff6a4c8140c30057466a1cdd47
 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036
 https://conda.anaconda.org/conda-forge/linux-64/sed-4.8-he412f7d_0.tar.bz2#7362f0042e95681f5d371c46c83ebd08
 https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2#4b230e8381279d76131116660f5a241a
@@ -63,69 +54,44 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/deno-dom-0.1.35-hd9586b0_1.conda#263ee0870b18b013d9ec8539113ac69f
 https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53fb86322bdb89496d7579fe3f02fd61
-https://conda.anaconda.org/conda-forge/linux-64/gmp-6.3.0-h59595ed_1.conda#e358c7c5f6824c272b5034b3816438a7
 https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c
 https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff
 https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f
-https://conda.anaconda.org/conda-forge/linux-64/libasprintf-0.22.5-h661eb56_2.conda#dd197c968bf9760bba0031888d431ede
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-devel-0.22.5-h59595ed_2.conda#b63d9b6da3653179a278077f0de20014
 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_11.conda#4c3e460d6acf8e43e4ce8bf405187eb7
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 https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.44-h0f59acf_0.conda#3914f7ac1761dce57102c72ca7c35d01
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utils/quarto/environment.yaml

@@ -2,34 +2,4 @@ channels:
     - conda-forge
     - nodefaults
 dependencies:
-    - r-base
-    - r-renv
-    - r-quarto
-    # This lists fairly excessive
-    # dependencies that may be used to build
-    # R packages from source within this environment.
-    - binutils
-    - glib
-    - gettext
-    - gxx_linux-64
-    - gcc_linux-64
-    - make
-    - pkg-config
-    - libgomp
-    - zlib
-    - libblas
-    - liblapack
-    - autoconf
-    - glpk
-    - gmp
-    # r xml2: https://github.com/r-lib/xml2/issues/418
-    - libxml2==2.11.6
-    - gfortran
-    - openmp
-    - gettext-tools
-    - libiconv
-    - pcre2
-    - libint
-    - packaging
-    - setuptools
-    - cxx-compiler
+    - r-quarto

utils/quarto/test/Snakefile

@@ -87,32 +87,26 @@ wildcard_constraints:
 # The `renv_lock` on renv rules is an artificial resource to prevent multiple
 # renv operations at the same time, which may cause issues..
 # In such cases restrict it via the
-# resources CLI flag: --resources renv_lock=1
+# resources CLI flag: --resources renv_lock=1 --set-resource-scopes renv_lock=global
 
 
 rule renv_example_init:
     conda:
-        "../environment.yaml"
+        "env/renv.yaml"
+    input:
+        lockfile="env/renv_dt.lock",
     output:
         rprofile="{renv_dir}/.Rprofile",
         lockfile="{renv_dir}/renv.lock",
-    params:
-        dependencies="'quarto','data.table'",
     resources:
         renv_lock=1,
     log:
         "logs/renv/{renv_dir}_init.log",
     shell:
         """
-        DIRNAME="{wildcards.renv_dir}"
-        mkdir -p $DIRNAME
-        cd $DIRNAME
-        Rscript -e "renv::init();"
-        # somehow the lockfile needs to be removed
-        # otherwise renv::install wont work with `Error: package 'data.table' is not available'
-        rm $(basename {output.lockfile})
-        Rscript -e "renv::install(c('data.table', 'quarto'));\
-        renv::snapshot(type='all')"
+        Rscript -e "renv::init(project='{wildcards.renv_dir}', bare=T); \
+                    renv::restore(project='{wildcards.renv_dir}', lockfile='$(realpath {input.lockfile})');\
+                    renv::snapshot(type='all')"
         """