diff --git a/r/Dockerfile b/r/Dockerfile index 9a4cffb..8f9879b 100644 --- a/r/Dockerfile +++ b/r/Dockerfile @@ -1,6 +1,7 @@ #syntax=docker/dockerfile:1.3 # FROM continuumio/miniconda3:4.12.0@sha256:58b1c7df8d69655ffec017ede784a075e3c2e9feff0fc50ef65300fc75aa45ae -FROM continuumio/miniconda3:24.9.2-0@sha256:39b820af05f0f9bb986ca145a0d077bbd3bd866256277dd869fefb93bd03cd21 +# 11/14/24: Use a miniconda image that's a bit older than the rstudio-server package; just in case +FROM continuumio/miniconda3:24.7.1-0@sha256:f37f8c7db26ae7ec0098df530e96c9cde139026b9faf3914800d1522c47a49b1 ENV NB_USER jovyan ENV NB_UID 1000 @@ -42,10 +43,6 @@ RUN --mount=type=cache,id=ohw_r_apt,target=/var/cache/apt \ sudo \ # 11/14/24: should this lib version be udpated? libapparmor1 \ - # 11/14/24: Neither libarchive-dev nor libarchive13 solved the error: - # Error while loading conda entry point: conda-libmamba-solver (libarchive.so.20: cannot open shared object file: No such file or directory) - # libarchive-dev \ - libarchive13 \ libfmt-dev \ # 11/14/24: should this lib version be udpated? libpq5 \ @@ -81,9 +78,11 @@ COPY ./conda-linux-64.lock /tmp/ RUN --mount=type=cache,id=ohw_r,target=${CONDA_DIR}/pkgs,uid=${NB_UID},gid=${NB_UID} \ # https://github.com/jupyterhub/jupyterhub-deploy-docker/issues/91#issuecomment-525563836 - conda update -n root conda && \ + # To avoid libmamba and libarchive channel conflicts, make sure conda-forge is the only channel + # https://github.com/conda/conda-libmamba-solver/issues/283#issuecomment-1949560105 + conda config --add channels conda-forge && \ + conda update --all && \ conda install --name ${CONDA_ENV} --file /tmp/conda-linux-64.lock && \ - # micromamba install --name ${CONDA_ENV} --file environment.yml && \ find -name '*.a' -delete && \ # rm -rf /opt/conda/conda-meta && \ rm -rf ${CONDA_DIR}/include && \ @@ -95,9 +94,10 @@ ARG MAMBA_DOCKERFILE_ACTIVATE=1 # 2024-10-10: Have there been improvements in install_cran and install_github such that # dependencies, upgrade_dependencies, upgrade could now be set to TRUE or the default? # RUN installGithub.R BigelowLab/rasf BigelowLab/ohwobpg # not working on GH but works locally :-/ -RUN Rscript -e "remotes::install_cran('assertthat', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \ - Rscript -e "remotes::install_cran('forecast', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \ - Rscript -e "remotes::install_cran('ggspatial', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \ +RUN \ + # -- Dependencies to the target packages, not already installed via the conda environment + Rscript -e "remotes::install_cran('PBSMapping', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \ + # -- Target packages Rscript -e "remotes::install_cran('plot.matrix', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \ Rscript -e "remotes::install_cran('isdparser', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \ Rscript -e "remotes::install_cran('geonames', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \ @@ -117,7 +117,6 @@ RUN Rscript -e "remotes::install_cran('assertthat', dependencies=FALSE, upgrade_ Rscript -e "remotes::install_github('hvillalo/echogram', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \ Rscript -e "remotes::install_github('hvillalo/periods', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \ Rscript -e "remotes::install_github('hvillalo/satin', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \ - Rscript -e "remotes::install_github('kwstat/pals', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \ Rscript -e "remotes::install_github('JorGarMol/VoCC', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" COPY CONDARC ./.condarc diff --git a/r/conda-linux-64.lock b/r/conda-linux-64.lock index d688fa2..6d5ae06 100644 --- a/r/conda-linux-64.lock +++ b/r/conda-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: e979ff969274903df954f836daa0bb0e0640b1358d951ab037805f47cc9258ca +# input_hash: b064f256a2e647aa5d9387adba87783c45f7ef10612be238e19dd2c1a4fd5838 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 @@ -20,12 +20,14 @@ https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766 https://conda.anaconda.org/conda-forge/linux-64/gh-2.61.0-h76a2195_0.conda#0a1f361c7570a47420effc1af30fe1c1 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda#048b02e3962f066da18efe3a21b77672 https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-14.2.0-h41c2201_101.conda#fb126e22f5350c15fec6ddbd062f4871 +https://conda.anaconda.org/conda-forge/linux-64/libglvnd-1.7.0-ha4b6fd6_2.conda#434ca7e50e40f4918ab701e3facd59a0 https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h77fa898_1.conda#cc3573974587f12dda90d96e3e55a702 https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-14.2.0-h41c2201_101.conda#60b9a16fd147f7184b5a964aa08f3b0f https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_18.conda#0ea96f90a10838f58412aa84fdd9df09 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-64-2.43-h4bf12b8_2.conda#cf0c5521ac2a20dfa6c662a4009eeef6 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab +https://conda.anaconda.org/conda-forge/linux-64/libegl-1.7.0-ha4b6fd6_2.conda#c151d5eb730e9b7480e6d48c0fc44048 https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda#3cb76c3f10d3bc7f1105b2fc9db984df https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.9.28-hb9d3cd8_0.conda#1b53af320b24547ce0fb8196d2604542 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.3-heb4867d_0.conda#09a6c610d002e54e18353c06ef61a253 @@ -49,6 +51,7 @@ https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.2.19-h756ea9 https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.1.19-h756ea98_3.conda#bfe6623096906d2502c78ccdbfc3bc7a https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.1.20-h756ea98_0.conda#ff7dbb319545f4bd1e5e0f8555cf9e7f https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.4-h5888daf_0.conda#1d6afef758879ef5ee78127eb4cd2c4a https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2#ac7bc6a654f8f41b352b38f4051135f8 https://conda.anaconda.org/conda-forge/linux-64/gflags-2.2.2-h5888daf_1005.conda#d411fc29e338efb48c5fd4576d71d881 https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda#3bf7b9fd5a7136126e0234db4b87c8b6 @@ -64,6 +67,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libgfortran-14.2.0-h69a702a_1.co https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libpciaccess-0.18-hd590300_0.conda#48f4330bfcd959c3cfb704d424903c82 https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.44-hadc24fc_0.conda#f4cc49d7aa68316213e4b12be35308d1 https://conda.anaconda.org/conda-forge/linux-64/libsanitizer-14.2.0-h2a3dede_1.conda#160623b9425f5c04941586da43bd1a9c https://conda.anaconda.org/conda-forge/linux-64/libsodium-1.0.20-h4ab18f5_0.conda#a587892d3c13b6621a6091be690dbca2 @@ -100,6 +104,7 @@ https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76 https://conda.anaconda.org/conda-forge/linux-64/libabseil-20240116.2-cxx17_he02047a_1.conda#c48fc56ec03229f294176923c3265c05 https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.3-h59595ed_0.conda#5e97e271911b8b2001a8b71860c32faa https://conda.anaconda.org/conda-forge/linux-64/libcrc32c-1.1.2-h9c3ff4c_0.tar.bz2#c965a5aa0d5c1c37ffc62dff36e28400 +https://conda.anaconda.org/conda-forge/linux-64/libdrm-2.4.123-hb9d3cd8_0.conda#ee605e794bdc14e2b7f84c4faa0d8c2c 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/libgfortran-ng-14.2.0-h69a702a_1.conda#0a7f4cd238267c88e5d69f7826a407eb https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.64.0-h161d5f1_0.conda#19e57602824042dfd0446292ef90488b @@ -130,6 +135,7 @@ https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f4 https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-25_linux64_openblas.conda#8ea26d42ca88ec5258802715fe1ee10b https://conda.anaconda.org/conda-forge/linux-64/libgit2-1.8.4-hd24f944_0.conda#94887b4deb460378a34e1533beaacfd5 https://conda.anaconda.org/conda-forge/linux-64/libglib-2.82.2-h2ff4ddf_0.conda#13e8e54035ddd2b91875ba399f0f7c04 +https://conda.anaconda.org/conda-forge/linux-64/libglx-1.7.0-ha4b6fd6_2.conda#c8013e438185f33b13814c5c488acd5c https://conda.anaconda.org/conda-forge/linux-64/libkml-1.3.0-hf539b9f_1021.conda#e8c7620cc49de0c6a2349b6dd6e39beb https://conda.anaconda.org/conda-forge/linux-64/libprotobuf-4.25.3-hd5b35b9_1.conda#06def97690ef90781a91b786cb48a0a9 https://conda.anaconda.org/conda-forge/linux-64/libre2-11-2023.09.01-h5a48ba9_2.conda#41c69fba59d495e8cf5ffda48a607e35 @@ -143,6 +149,7 @@ https://conda.anaconda.org/conda-forge/linux-64/spdlog-1.14.1-hed91bc2_1.conda#9 https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.47.0-h9eae976_1.conda#53abf1ef70b9ae213b22caa5350f97a9 https://conda.anaconda.org/conda-forge/linux-64/xerces-c-3.2.5-h988505b_2.conda#9dda9667feba914e0e80b95b82f7402b https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.6-hb9d3cd8_0.conda#febbab7d15033c913d53c7a2c102309d +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxfixes-6.0.1-hb9d3cd8_0.conda#4bdb303603e9821baf5fe5fdff1dc8f8 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.11-hb9d3cd8_1.conda#a7a49a8b85122b49214798321e2e96b4 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.0-hb9d3cd8_2.conda#d8602724ac0d276c380b97e9eb0f814b https://conda.anaconda.org/conda-forge/noarch/aiohappyeyeballs-2.4.3-pyhd8ed1ab_0.conda#ec763b0a58960558ca0ad7255a51a237 @@ -178,8 +185,9 @@ https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda#51bb https://conda.anaconda.org/conda-forge/linux-64/libarchive-3.7.4-hfca40fe_0.conda#32ddb97f897740641d8d46a829ce1704 https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-25_linux64_openblas.conda#5dbd1b0fc0d01ec5e0e1fbe667281a11 https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.10.1-hbbe4b11_0.conda#6e801c50a40301f6978c53976917b277 +https://conda.anaconda.org/conda-forge/linux-64/libgl-1.7.0-ha4b6fd6_2.conda#928b8be80851f5d8ffb016f9c81dae7a https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-25_linux64_openblas.conda#4dc03a53fc69371a6158d0ed37214cd3 -https://conda.anaconda.org/conda-forge/linux-64/libpq-16.4-h2d7952a_3.conda#50e2dddb3417a419cbc2388d0b1c06f7 +https://conda.anaconda.org/conda-forge/linux-64/libpq-16.5-h2d7952a_0.conda#3b863477ad017cfa8456a5aa0a17b950 https://conda.anaconda.org/conda-forge/noarch/locket-1.0.0-pyhd8ed1ab_0.tar.bz2#91e27ef3d05cc772ce627e51cff111c4 https://conda.anaconda.org/conda-forge/linux-64/lz4-4.3.3-py312hb3f7f12_1.conda#b99d90ef4e77acdab74828f79705a919 https://conda.anaconda.org/conda-forge/linux-64/markupsafe-3.0.2-py312h178313f_0.conda#a755704ea0e2503f8c227d84829a8e81 @@ -234,8 +242,10 @@ https://conda.anaconda.org/conda-forge/noarch/webcolors-24.8.0-pyhd8ed1ab_0.cond https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-pyhd8ed1ab_2.conda#daf5160ff9cde3a468556965329085b9 https://conda.anaconda.org/conda-forge/noarch/websocket-client-1.8.0-pyhd8ed1ab_0.conda#f372c576b8774922da83cda2b12f9d29 https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-4.0.13-pyhd8ed1ab_0.conda#6372cd99502721bd7499f8d16b56268d +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdamage-1.1.6-hb9d3cd8_0.conda#b5fcc7172d22516e1f965490e65e33a4 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxxf86vm-1.1.5-hb9d3cd8_4.conda#7da9007c0582712c4bad4131f89c8372 https://conda.anaconda.org/conda-forge/noarch/xyzservices-2024.9.0-pyhd8ed1ab_0.conda#156c91e778c1d4d57b709f8c5333fd06 -https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.5-h3b0a872_6.conda#113506c8d2d558e733f5c38f6bf08c50 +https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.5-h3b0a872_7.conda#3947a35e916fcc6b9825449affbf4214 https://conda.anaconda.org/conda-forge/noarch/zict-3.0.0-pyhd8ed1ab_0.conda#cf30c2c15b82aacb07f9c09e28ff2275 https://conda.anaconda.org/conda-forge/noarch/zipp-3.21.0-pyhd8ed1ab_0.conda#fee389bf8a4843bd7a2248ce11b7f188 https://conda.anaconda.org/conda-forge/noarch/aiosignal-1.3.1-pyhd8ed1ab_0.tar.bz2#d1e1eb7e21a9e2c74279d87dafb68156 @@ -264,6 +274,7 @@ https://conda.anaconda.org/conda-forge/noarch/jedi-0.19.2-pyhff2d567_0.conda#11e https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.4-pyhd8ed1ab_0.conda#7b86ecb7d3557821c649b3c31e3eb9f2 https://conda.anaconda.org/conda-forge/linux-64/jupyter_core-5.7.2-py312h7900ff3_0.conda#eee5a2e3465220ed87196bbb5665f420 https://conda.anaconda.org/conda-forge/noarch/jupyterlab_pygments-0.3.0-pyhd8ed1ab_1.conda#afcd1b53bcac8844540358e33f33d28f +https://conda.anaconda.org/conda-forge/linux-64/libglu-9.0.3-h03adeef_0.conda#b1df5affe904efe82ef890826b68881d https://conda.anaconda.org/conda-forge/linux-64/libgrpc-1.62.2-h15f2491_0.conda#8dabe607748cb3d7002ad73cd06f1325 https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.1.7-pyhd8ed1ab_0.conda#779345c95648be40d22aaa89de7d4254 https://conda.anaconda.org/conda-forge/linux-64/numpy-2.1.3-py312h58c1407_0.conda#dfdbc12e6d81889ba4c494a23f23eba8 @@ -272,7 +283,7 @@ https://conda.anaconda.org/conda-forge/noarch/partd-1.4.2-pyhd8ed1ab_0.conda#0ba https://conda.anaconda.org/conda-forge/noarch/pexpect-4.9.0-pyhd8ed1ab_0.conda#629f3203c99b32e0988910c93e77f3b6 https://conda.anaconda.org/conda-forge/linux-64/pillow-10.4.0-py312h56024de_1.conda#4bd6077376c7f9c1ce33fd8319069e5b https://conda.anaconda.org/conda-forge/linux-64/poppler-24.04.0-hb6cd0d7_0.conda#d19eed746748f1d44b575662f2bcfe95 -https://conda.anaconda.org/conda-forge/linux-64/postgresql-16.4-hb2eb5c0_3.conda#3ba28956641b0c59640bf2b124d2d731 +https://conda.anaconda.org/conda-forge/linux-64/postgresql-16.5-hb2eb5c0_0.conda#f0b1fc2c91661400dc7f516f96339e99 https://conda.anaconda.org/conda-forge/linux-64/proj-9.4.0-hb784bbd_2.conda#b0683c229de4c4c676450d24ff87538c https://conda.anaconda.org/conda-forge/noarch/prompt-toolkit-3.0.48-pyha770c72_0.conda#4c05134c48b6a74f33bbb9938e4a115e https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0-pyhd8ed1ab_0.conda#2cf4264fffb9e6eff6031c5b6884d61c @@ -340,6 +351,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-backports-1.5.0-r43hb1dbf0f_1. https://conda.anaconda.org/conda-forge/linux-64/r-base64enc-0.1_3-r43hb1dbf0f_1007.conda#3509080778587bf9d42eae11e0246633 https://conda.anaconda.org/conda-forge/linux-64/r-bit-4.5.0-r43h2b5f3a1_0.conda#c6852e3a0800b67e96827ebdaa756be5 https://conda.anaconda.org/conda-forge/linux-64/r-bitops-1.0_9-r43h2b5f3a1_0.conda#8643d84c1d28ea73e48db9deb9a2eff3 +https://conda.anaconda.org/conda-forge/noarch/r-boot-1.3_31-r43hc72bb7e_0.conda#3e3d3d9d6d06cd74b5574b01c7e65f1f https://conda.anaconda.org/conda-forge/noarch/r-brew-1.0_10-r43hc72bb7e_1.conda#043bab92bb313abd213f8bd083dff0f4 https://conda.anaconda.org/conda-forge/linux-64/r-brio-1.1.5-r43hb1dbf0f_1.conda#57032df549b16ca7bb49e961fc0cd8ee https://conda.anaconda.org/conda-forge/linux-64/r-cli-3.6.3-r43h0d4f4ea_1.conda#ba1f08e0eab53429d77026adb68960a5 @@ -357,6 +369,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-dbi-1.2.3-r43hc72bb7e_1.conda#6a https://conda.anaconda.org/conda-forge/linux-64/r-deldir-2.0_4-r43hbcb9c34_1.conda#074d8b42612f96699798bee86105009c https://conda.anaconda.org/conda-forge/noarch/r-dichromat-2.0_0.1-r43ha770c72_3.conda#40891660ade576876ce04578b0dc4170 https://conda.anaconda.org/conda-forge/linux-64/r-digest-0.6.37-r43h0d4f4ea_0.conda#edcd201672d47f522666954cc7b25e0d +https://conda.anaconda.org/conda-forge/linux-64/r-dotcall64-1.2-r43hb67ce94_0.conda#85aec1f86a06de00df5267c848d645f7 https://conda.anaconda.org/conda-forge/noarch/r-evaluate-1.0.1-r43hc72bb7e_0.conda#8d25f602ce6b814cfae40fae50e0e806 https://conda.anaconda.org/conda-forge/linux-64/r-fansi-1.0.6-r43hb1dbf0f_1.conda#4c17a0f74a974316fdfafa5a9fe91b52 https://conda.anaconda.org/conda-forge/linux-64/r-farver-2.1.2-r43ha18555a_1.conda#85a82a5b78397daf57f002120aed9e3e @@ -388,6 +401,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-lpsolve-5.6.22-r43h2b5f3a1_0.c https://conda.anaconda.org/conda-forge/linux-64/r-magrittr-2.0.3-r43hb1dbf0f_3.conda#fc61bcf37e59037b486c8841a704e9da https://conda.anaconda.org/conda-forge/linux-64/r-maps-3.4.2.1-r43h2b5f3a1_0.conda#6f0792a8c58c6597b3334775ccd0bce5 https://conda.anaconda.org/conda-forge/linux-64/r-mass-7.3_60.0.1-r43hb1dbf0f_1.conda#c3c9184486ccabe19b86aba11351652e +https://conda.anaconda.org/conda-forge/linux-64/r-matrixstats-1.4.1-r43h2b5f3a1_0.conda#4e7f80d3e24e7dcc88fc6f3c3ce231b1 https://conda.anaconda.org/conda-forge/linux-64/r-mime-0.12-r43hb1dbf0f_3.conda#1e7d080b1e82a19e8a939c0e90405728 https://conda.anaconda.org/conda-forge/linux-64/r-ncdf4-1.23-r43ha053207_0.conda#4168416721cfdf4a140f31d0c23afe2a https://conda.anaconda.org/conda-forge/linux-64/r-nloptr-2.1.1-r43h9b87a3a_1.conda#cef47c6389cd73eb567d5474880f48e5 @@ -402,6 +416,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-pkgconfig-2.0.3-r43hc72bb7e_4.co https://conda.anaconda.org/conda-forge/noarch/r-plogr-0.2.0-r43hc72bb7e_1006.conda#75003e5611e863848d5c7b9d1544d11d https://conda.anaconda.org/conda-forge/noarch/r-plotrix-3.8_4-r43hc72bb7e_1.conda#1ccf6eb2982b8be2ff95a38f49aeffca https://conda.anaconda.org/conda-forge/linux-64/r-png-0.1_8-r43h21f035c_2.conda#bb38ba000f70e6776d546e1b41b8ce4c +https://conda.anaconda.org/conda-forge/noarch/r-pracma-2.4.4-r43hc72bb7e_1.conda#b01b8a12320a725816c72396eb6e0ad2 https://conda.anaconda.org/conda-forge/noarch/r-praise-1.0.0-r43hc72bb7e_1008.conda#73c82834d0920677d71a8a1bc0f624a9 https://conda.anaconda.org/conda-forge/noarch/r-presenceabsence-1.1.11-r43hc72bb7e_2.conda#eaba695a324a48db054af120823e4b48 https://conda.anaconda.org/conda-forge/linux-64/r-proxy-0.4_27-r43hb1dbf0f_3.conda#d7b831353a7bfbbe20980873e81fef97 @@ -418,6 +433,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-rcpp-1.0.13_1-r43h93ab643_0.co https://conda.anaconda.org/conda-forge/noarch/r-rcppprogress-0.4.2-r43hc72bb7e_4.conda#17f91f7813612e076b606b9a46b463a3 https://conda.anaconda.org/conda-forge/noarch/r-rematch-2.0.0-r43hc72bb7e_1.conda#3a0951ee971e0ecd8896771d8871cd73 https://conda.anaconda.org/conda-forge/noarch/r-remotes-2.5.0-r43hc72bb7e_1.conda#1b9d1d90de2bb174a8af58e402e1f74a +https://conda.anaconda.org/conda-forge/linux-64/r-rjson-0.2.23-r43h93ab643_0.conda#9b34770d3b82c2568e086b7772904c18 https://conda.anaconda.org/conda-forge/linux-64/r-rlang-1.1.4-r43ha18555a_1.conda#e9f6f76e66306bd6483935ad4c79ac28 https://conda.anaconda.org/conda-forge/linux-64/r-rpart-4.1.23-r43hb1dbf0f_1.conda#3a1bacb9094110d6c25c39daed36f3fc https://conda.anaconda.org/conda-forge/noarch/r-rprojroot-2.0.4-r43hc72bb7e_1.conda#f55d999288e1f7e5e5efb7042eba4f4d @@ -426,6 +442,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-rstudioapi-0.17.1-r43hc72bb7e_0. https://conda.anaconda.org/conda-forge/noarch/r-shape-1.4.6.1-r43ha770c72_1.conda#f3dc2930e4ff73b8913f773988fe47a9 https://conda.anaconda.org/conda-forge/linux-64/r-sourcetools-0.1.7_1-r43ha18555a_2.conda#ac984cdfeb93aecef6e2d5942a6d9ab3 https://conda.anaconda.org/conda-forge/noarch/r-squarem-2021.1-r43hc72bb7e_3.conda#7540130cd26e12a02742dac9ddc184d6 +https://conda.anaconda.org/conda-forge/linux-64/r-statmod-1.5.0-r43ha36c22a_2.conda#d1b3431cbf858fec53e7eb00f8b8cde0 https://conda.anaconda.org/conda-forge/linux-64/r-stringi-1.8.4-r43h33cde33_3.conda#827bd9c9e7a678acee9c6a2d5b0586a6 https://conda.anaconda.org/conda-forge/linux-64/r-sys-3.4.3-r43h2b5f3a1_0.conda#b7ce9f99da446a47b97950ff9a9cbb60 https://conda.anaconda.org/conda-forge/noarch/r-teachingdemos-2.13-r43hc72bb7e_1.conda#d3ac5213e91502eb0587b664a8358905 @@ -454,6 +471,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-bit64-4.5.2-r43h2b5f3a1_0.cond https://conda.anaconda.org/conda-forge/linux-64/r-cachem-1.1.0-r43hb1dbf0f_1.conda#02b195910b59c2cfd1fb7159edbb047a https://conda.anaconda.org/conda-forge/linux-64/r-catools-1.18.3-r43h93ab643_0.conda#efba09c0ba682c357fe311aad5d0f6e4 https://conda.anaconda.org/conda-forge/linux-64/r-checkmate-2.3.2-r43hdb488b9_0.conda#3b649dfe3c1fe7d18d44ffb8a6bec909 +https://conda.anaconda.org/conda-forge/noarch/r-circstats-0.2_6-r43hd8ed1ab_1005.conda#c0e532091eae5524bd96ce69bcd72be3 https://conda.anaconda.org/conda-forge/linux-64/r-class-7.3_22-r43hb1dbf0f_2.conda#6ec44d3a4ccdf15b93feb5774a3de8a8 https://conda.anaconda.org/conda-forge/linux-64/r-colourvalues-0.3.9-r43h0d4f4ea_2.conda#6d0aaaecf8d3f1443dd926ca374589f3 https://conda.anaconda.org/conda-forge/noarch/r-desc-1.4.3-r43hc72bb7e_1.conda#fa71778594f1bfdca6c87079b5888ae0 @@ -466,7 +484,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-formula.tools-1.7.1-r43hc72bb7e_ https://conda.anaconda.org/conda-forge/linux-64/r-geometries-0.2.4-r43ha18555a_1.conda#d71de4e861ea25db1c621a432647cb45 https://conda.anaconda.org/conda-forge/noarch/r-globals-0.16.3-r43hc72bb7e_1.conda#7786db60901e0d45dbd08c29b9246ec6 https://conda.anaconda.org/conda-forge/linux-64/r-googlepolylines-0.8.5-r43h93ab643_0.conda#e03450d767bb83f51534b4e64e74df6c -https://conda.anaconda.org/conda-forge/linux-64/r-hexbin-1.28.4-r43hb67ce94_0.conda#4cf5cb3701d146d96b4ec3ee3b4c8164 +https://conda.anaconda.org/conda-forge/linux-64/r-hexbin-1.28.5-r43hb67ce94_0.conda#3e1e0a8fc7da252fc9e4f59f9820d7f9 https://conda.anaconda.org/conda-forge/noarch/r-highr-0.11-r43hc72bb7e_1.conda#23e4d2048f51cbe7c0fb8b9230edc701 https://conda.anaconda.org/conda-forge/noarch/r-hoardr-0.5.4-r43hc72bb7e_1.conda#9a61ff4fa89c4fbb0e63b93331b28546 https://conda.anaconda.org/conda-forge/linux-64/r-jsonify-1.2.2-r43ha18555a_2.conda#e814a4c331c8e097d2aaf81d27adf80a @@ -475,6 +493,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-lifecycle-1.0.4-r43hc72bb7e_1.co https://conda.anaconda.org/conda-forge/noarch/r-linprog-0.9_4-r43hc72bb7e_3.conda#195f15403db1cc2425ffac6f16200532 https://conda.anaconda.org/conda-forge/noarch/r-magic-1.6_1-r43hc72bb7e_2.conda#11695934cf382f3cdc6090e46579af03 https://conda.anaconda.org/conda-forge/linux-64/r-mapdata-2.3.1-r43hdb488b9_2.conda#4b1de1ea206065616b781a0f1864db05 +https://conda.anaconda.org/conda-forge/linux-64/r-mapproj-1.2.11-r43hb1dbf0f_2.conda#f3bb9617d392dcb442073071f6f417d5 https://conda.anaconda.org/conda-forge/noarch/r-markdown-1.13-r43hc72bb7e_1.conda#cb52c9f21c87a69826ca947a1cd9b92a https://conda.anaconda.org/conda-forge/linux-64/r-matrix-1.6_5-r43he966344_1.conda#df8a1175a62460e02dbf340966cbfeab https://conda.anaconda.org/conda-forge/linux-64/r-mmand-1.6.3-r43h0d4f4ea_2.conda#c2b47cd6bb154aff7444b116b9d17073 @@ -488,8 +507,10 @@ https://conda.anaconda.org/conda-forge/noarch/r-prettyunits-1.2.0-r43hc72bb7e_1. https://conda.anaconda.org/conda-forge/linux-64/r-processx-3.8.4-r43hb1dbf0f_1.conda#b9dcc14c0f4866d8593bb5fbd3f1c447 https://conda.anaconda.org/conda-forge/noarch/r-progressr-0.15.0-r43hc72bb7e_0.conda#3df99439f0242abfa0f76f582019b247 https://conda.anaconda.org/conda-forge/noarch/r-r.oo-1.27.0-r43hc72bb7e_0.conda#979441b68894f2f2a2505170d3117563 +https://conda.anaconda.org/conda-forge/linux-64/r-rcpparmadillo-14.0.2_1-r43hb79369c_0.conda#90307af4ac7cdce6409c98f28852d654 https://conda.anaconda.org/conda-forge/noarch/r-sessioninfo-1.2.2-r43hc72bb7e_3.conda#5e9865949e78fc703cc30b0644dd0ad5 https://conda.anaconda.org/conda-forge/linux-64/r-sp-2.1_4-r43hdb488b9_1.conda#82384c0769c1a041e839872db20e8c7a +https://conda.anaconda.org/conda-forge/linux-64/r-spam-2.11_0-r43h773be8d_0.conda#286c9e930feb482530af05993b59cbc9 https://conda.anaconda.org/conda-forge/linux-64/r-timechange-0.3.0-r43ha18555a_1.conda#da155dc726414cca04cdc76a297c4463 https://conda.anaconda.org/conda-forge/noarch/r-tinytex-0.54-r43hc72bb7e_0.conda#76667bd83c417143366999534a0d4b09 https://conda.anaconda.org/conda-forge/linux-64/r-triebeard-0.4.1-r43ha18555a_2.conda#e0284c04dd2ea2bec947b3645bb6db61 @@ -536,6 +557,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-rversions-2.1.2-r43hc72bb7e_3.co https://conda.anaconda.org/conda-forge/linux-64/r-s2-1.1.7-r43h4b309dc_0.conda#494a6872ae3a6fda1cf4f80d5e0a6d7c https://conda.anaconda.org/conda-forge/noarch/r-scales-1.3.0-r43hc72bb7e_1.conda#119d9c10dc652ac1492fc49951d86860 https://conda.anaconda.org/conda-forge/linux-64/r-sfheaders-0.4.4-r43h0d4f4ea_1.conda#086d408c7f91bfed730310eb8b6d8916 +https://conda.anaconda.org/conda-forge/linux-64/r-splancs-2.01_45-r43hc4980d5_1.conda#88479d8305b21700aac81e569daed16e https://conda.anaconda.org/conda-forge/linux-64/r-survival-3.7_0-r43hdb488b9_1.conda#06d0a4ee19176ea1a9a0ec1f767dd2ae https://conda.anaconda.org/conda-forge/linux-64/r-systemfonts-1.1.0-r43h38d38ca_1.conda#03e51a887e5284ddae8ea6983e682e76 https://conda.anaconda.org/conda-forge/linux-64/r-terra-1.7_78-r43h4d71811_0.conda#11ec920ee1e4963ccc7099fd59b988c1 @@ -613,6 +635,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-satellite-1.0.5-r43ha503ecb_0. https://conda.anaconda.org/conda-forge/noarch/r-selectr-0.4_2-r43hc72bb7e_4.conda#08ede6e9829e45bdc8ff712f3b56eb22 https://conda.anaconda.org/conda-forge/noarch/r-servr-0.32-r43hc72bb7e_0.conda#eb62e31f6b7ec661800b94ee6adcdd8a https://conda.anaconda.org/conda-forge/linux-64/r-sf-1.0_16-r43hce28180_2.conda#075f0502c30e1623158f697d419d83f1 +https://conda.anaconda.org/conda-forge/noarch/r-texreg-1.39.4-r43hc72bb7e_0.conda#07f98cffe3868dfdbf34f801171e02a6 https://conda.anaconda.org/conda-forge/linux-64/r-tibble-3.2.1-r43hdb488b9_3.conda#3e78c6ee2205ef56c165cbf2c166fdf6 https://conda.anaconda.org/conda-forge/noarch/jupyter-rsession-proxy-2.2.1-pyhd8ed1ab_0.conda#0e677523a7ff94dac839437c07606dd0 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.2.4-pyhd8ed1ab_0.conda#28f3334e97c39de2b7ac15743b041784 @@ -646,6 +669,7 @@ https://conda.anaconda.org/conda-forge/noarch/pyarrow-hotfix-0.6-pyhd8ed1ab_0.co https://conda.anaconda.org/conda-forge/noarch/r-biomod2-4.2_5_2-r43hc72bb7e_0.conda#b1138b631593384a65e3fb1f60488dcc https://conda.anaconda.org/conda-forge/noarch/r-cowplot-1.1.3-r43hc72bb7e_1.conda#2f20d2368e1258a42227b1af7b1f7270 https://conda.anaconda.org/conda-forge/noarch/r-dtplyr-1.3.1-r43hc72bb7e_2.conda#1de89f4b9a7560db5ed812ee4e92879b +https://conda.anaconda.org/conda-forge/linux-64/r-forecast-8.23.0-r43h4387864_1.conda#f54a822075fba859b660774c705df008 https://conda.anaconda.org/conda-forge/noarch/r-googlesheets4-1.1.1-r43h785f33e_2.conda#332576dbba1cf5eea98ade568264a297 https://conda.anaconda.org/conda-forge/noarch/r-htmlwidgets-1.6.4-r43h785f33e_3.conda#70fe86ab3d54f9a4daf938aedf2d1734 https://conda.anaconda.org/conda-forge/linux-64/r-ipred-0.9_15-r43hdb488b9_1.conda#45bd44a48d22dfdbcf353801002c34ce @@ -671,6 +695,8 @@ https://conda.anaconda.org/conda-forge/noarch/nb_conda_kernels-2.5.1-pyh707e725_ https://conda.anaconda.org/conda-forge/noarch/nbgitpuller-1.2.1-pyhd8ed1ab_0.conda#73abf90c19790f8d6c600b0aa152c932 https://conda.anaconda.org/conda-forge/noarch/r-broom-1.0.7-r43hc72bb7e_0.conda#e9bcdc8ab599d045b1d7ef7aede49bdc https://conda.anaconda.org/conda-forge/noarch/r-dbplyr-2.5.0-r43hc72bb7e_1.conda#73cd48c8632ca1a98381cc0f1ebed3d4 +https://conda.anaconda.org/conda-forge/linux-64/r-fields-16.3-r43hb67ce94_0.conda#f6f67009590986fd3dfb3645c33d206d +https://conda.anaconda.org/conda-forge/noarch/r-ggspatial-1.1.9-r43hc72bb7e_1.conda#3d4ac40fcf1e987b2d2b0cca525413e0 https://conda.anaconda.org/conda-forge/linux-64/r-gstat-2.1_2-r43h2b5f3a1_1.conda#9b644d426a1a10daadde2772dd7fa490 https://conda.anaconda.org/conda-forge/linux-64/r-haven-2.5.4-r43h0d4f4ea_1.conda#5ea73f6c0626a144907ac2748d19050e https://conda.anaconda.org/conda-forge/noarch/r-leaflet-2.2.2-r43hc72bb7e_1.conda#1b0076ea8c42c9ec3343992aa72cc05f @@ -679,6 +705,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-mapdeck-0.3.5-r43h0d4f4ea_1.co https://conda.anaconda.org/conda-forge/noarch/r-plotly-4.10.4-r43hc72bb7e_1.conda#030d74ad170584977b14cc6f5dea4fe6 https://conda.anaconda.org/conda-forge/linux-64/r-profvis-0.4.0-r43h2b5f3a1_0.conda#e8ec5ac1f8db7e075826f3f747ae9226 https://conda.anaconda.org/conda-forge/noarch/r-recipes-1.1.0-r43hc72bb7e_1.conda#3c6b8915c6a6823420943fc2d3acd4a1 +https://conda.anaconda.org/conda-forge/linux-64/r-rgl-1.3.1-r43h2184249_2.conda#00d31401fb6988cd0a90283dba95a7fb https://conda.anaconda.org/conda-forge/linux-64/r-testthat-3.2.1.1-r43h0d4f4ea_1.conda#31050a5b39d5c4e957574cc5ced41f43 https://conda.anaconda.org/conda-forge/linux-64/r-tidygraph-1.3.0-r43h0d4f4ea_1.conda#400b5dba377dd045557ac58be08f9073 https://conda.anaconda.org/conda-forge/noarch/r-tmaptools-3.1_1-r43hc72bb7e_3.conda#d3fbb7956853285d5d190b4f7a7be1e7 @@ -694,6 +721,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-leafsync-0.1.0-r43hc72bb7e_4.con https://conda.anaconda.org/conda-forge/noarch/r-modelr-0.1.11-r43hc72bb7e_2.conda#2cdd8c74b0c949695af0debfd3a44974 https://conda.anaconda.org/conda-forge/linux-64/r-oce-1.8_3-r43h41dd86c_0.conda#39ef10ff4d17144e6bc8abaa2afdecc9 https://conda.anaconda.org/conda-forge/linux-64/r-ocedata-0.2.2-r43hc72bb7e_3.conda#2b854e3973fd60c27a81d7ed59069bf2 +https://conda.anaconda.org/conda-forge/noarch/r-pals-1.9-r43hc72bb7e_1.conda#1967ee8728c12b508935843ec9d9996e https://conda.anaconda.org/conda-forge/noarch/pangeo-dask-2024.08.07-hd8ed1ab_0.conda#dcf89dec3b5d48a0678bb083fbbbcf2c https://conda.anaconda.org/conda-forge/noarch/r-mapview-2.11.2-r43hc72bb7e_0.conda#21d49cc1e6ee48f0593e1c644f5b81c5 https://conda.anaconda.org/conda-forge/noarch/r-tidyverse-2.0.0-r43h785f33e_2.conda#02a988567686de86cc822fb4e33b14ad diff --git a/r/environment.yml b/r/environment.yml index 076a081..2b8f79f 100644 --- a/r/environment.yml +++ b/r/environment.yml @@ -1,9 +1,12 @@ name: OHW-r channels: - conda-forge + - nodefaults dependencies: # base - python=3.12 + # - mamba + # - libarchive - pangeo-notebook=2024.08.07 - nb_conda_kernels - jupyter-rsession-proxy @@ -22,12 +25,14 @@ dependencies: - r-abind - r-akima - r-ape + - r-assertthat - r-automap - r-biomod2 - r-bitops - r-caret - r-catools - r-checkmate + - r-circstats - r-commonmark - r-cowplot - r-crul @@ -39,13 +44,16 @@ dependencies: - r-dplyr - r-earth - r-rerddap + - r-fields - r-foreach + - r-forecast - r-foreign - r-fracdiff - r-gbm >=2.1.3 - r-geometry - r-geosphere - r-ggplot2 + - r-ggspatial - r-glmnet - r-gridextra - r-gsw @@ -68,11 +76,13 @@ dependencies: - r-mmand - r-mapdata - r-mapedit + - r-mapproj - r-maps - r-maptools - r-marmap - r-markdown - r-mass + - r-matrixstats - r-mda - r-metr - r-ncdf4 @@ -80,12 +90,13 @@ dependencies: - r-nloptr - r-oce - r-ocedata - - r-rosm - r-palmerpenguins + - r-pals - r-patchwork - r-PCICt - r-plotly - r-proc >=1.15.0 + - r-pracma - r-ps>=1.3.4 - r-purrr - r-r.utils @@ -98,11 +109,13 @@ dependencies: - r-reshape - r-rgdal >=1.5 - r-rgeos + - r-rjson - r-rlang - r-rmarkdown - r-rnaturalearth - r-rnaturalearthdata - r-robis + - r-rosm - r-rpart - r-rsqlite - r-rstackdeque @@ -111,8 +124,11 @@ dependencies: - r-scales - r-sf >=0.9_5 - r-sp + - r-splancs - r-stars + - r-statmod - r-terra + - r-texreg - r-tibble - r-tidyr - r-tidygraph