Merge pull request #68 from emiliom/r

R, add several CRAN and conda-forge packages
oceanhackweek · Feb 28, 2023 · 2b505d5 · 2b505d5
2 parents 5c98268 + 4c95a76
commit 2b505d5
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diff --git a/r/Dockerfile b/r/Dockerfile
@@ -76,6 +76,7 @@ ARG MAMBA_DOCKERFILE_ACTIVATE=1
 # Install BigelowLab dev R libs
 # 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)" && \
     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)" && \

diff --git 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: 41f13f8023818d09640051e295187db881ced875826f42751636ecd924dccc1a
+# input_hash: ba8b1ec3e3e44e77f5479070c79bdf80a9b33413085e90d0f53a32e0faacff13
 @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
@@ -104,7 +104,7 @@ https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-12.2.0-hcc96c0
 https://conda.anaconda.org/conda-forge/linux-64/hdf4-4.2.15-h9772cbc_5.tar.bz2#ee08782aff2ff9b3291c967fa6bc7336
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.20.1-h81ceb04_0.conda#89a41adce7106749573d883b2f657d78
 https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-16_linux64_openblas.tar.bz2#20bae26d0a1db73f758fc3754cab4719
-https://conda.anaconda.org/conda-forge/linux-64/libgit2-1.5.1-h1f77430_0.conda#16802fd0c80290248ea79a570bd83b95
+https://conda.anaconda.org/conda-forge/linux-64/libgit2-1.6.1-h1f77430_0.conda#678a120a7d1e1ea50d151b31047f0a28
 https://conda.anaconda.org/conda-forge/linux-64/libglib-2.74.1-h606061b_1.tar.bz2#ed5349aa96776e00b34eccecf4a948fe
 https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-16_linux64_openblas.tar.bz2#955d993f41f9354bf753d29864ea20ad
 https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.5.0-h6adf6a1_2.conda#2e648a34072eb39d7c4fc2a9981c5f0c
@@ -168,7 +168,7 @@ https://conda.anaconda.org/conda-forge/noarch/pycparser-2.21-pyhd8ed1ab_0.tar.bz
 https://conda.anaconda.org/conda-forge/noarch/pyjwt-2.6.0-pyhd8ed1ab_0.tar.bz2#56d08bbebf5b3719ca2b1688fcfd98a4
 https://conda.anaconda.org/conda-forge/linux-64/pyrsistent-0.19.3-py39h72bdee0_0.conda#659013ef00dcd1751bfd26d894f73857
 https://conda.anaconda.org/conda-forge/linux-64/pysocks-1.7.1-py39hf3d152e_5.tar.bz2#d34b97a2386932b97c7cb80916a673e7
-https://conda.anaconda.org/conda-forge/noarch/python-fastjsonschema-2.16.2-pyhd8ed1ab_0.tar.bz2#5fe4b6002f505336734ce92961b3e6a0
+https://conda.anaconda.org/conda-forge/noarch/python-fastjsonschema-2.16.3-pyhd8ed1ab_0.conda#7aa330a4d88b7ab891a42c39d5d2e742
 https://conda.anaconda.org/conda-forge/noarch/python-json-logger-2.0.7-pyhd8ed1ab_0.conda#a61bf9ec79426938ff785eb69dbb1960
 https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f59d49a7b464901cf714b9e7984d01a2
 https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0-py39hb9d737c_5.tar.bz2#ef9db3c38ae7275f6b14491cfe61a248
@@ -197,7 +197,7 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.co
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.10-h7f98852_1003.tar.bz2#f59c1242cc1dd93e72c2ee2b360979eb
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.2.1-h7f98852_2.tar.bz2#60d6eec5273f1c9af096c10c268912e3
 https://conda.anaconda.org/conda-forge/linux-64/y-py-0.5.9-py39h50f1755_0.conda#f9225a09f5cb046cfdecd2a54448d4c0
-https://conda.anaconda.org/conda-forge/noarch/zipp-3.14.0-pyhd8ed1ab_0.conda#01ea04980fa39d7b6dbdd6c67016d177
+https://conda.anaconda.org/conda-forge/noarch/zipp-3.15.0-pyhd8ed1ab_0.conda#13018819ca8f5b7cc675a8faf1f5fedf
 https://conda.anaconda.org/conda-forge/noarch/aiosignal-1.3.1-pyhd8ed1ab_0.tar.bz2#d1e1eb7e21a9e2c74279d87dafb68156
 https://conda.anaconda.org/conda-forge/noarch/anyio-3.6.2-pyhd8ed1ab_0.tar.bz2#8ada050fa88f26916fc1e76e368a49fd
 https://conda.anaconda.org/conda-forge/noarch/asttokens-2.2.1-pyhd8ed1ab_0.conda#bf7f54dd0f25c3f06ecb82a07341841a
@@ -315,6 +315,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-fastmap-1.1.1-r42h38f115c_0.co
 https://conda.anaconda.org/conda-forge/linux-64/r-fnn-1.1.3.1-r42h7525677_1.tar.bz2#9844ae447dc2fa4888a3c42fbd87baee
 https://conda.anaconda.org/conda-forge/linux-64/r-foreign-0.8_84-r42h133d619_0.conda#76bc3df61cbef5f96593092371f69ad2
 https://conda.anaconda.org/conda-forge/noarch/r-formula-1.2_5-r42hc72bb7e_0.conda#c3b9ff74781091e91bce2d6ae260cac7
+https://conda.anaconda.org/conda-forge/linux-64/r-fracdiff-1.5_2-r42h64d53c3_0.tar.bz2#5ef3f26eebfc8ac63860c8d4cfd5a4d2
 https://conda.anaconda.org/conda-forge/linux-64/r-fs-1.6.1-r42h38f115c_0.conda#36adbeb6a2cee4773067a36c09dab95c
 https://conda.anaconda.org/conda-forge/noarch/r-generics-0.1.3-r42hc72bb7e_1.tar.bz2#d008373b48b8284492dfb2f81cdfaf82
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@@ -356,6 +357,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-praise-1.0.0-r42hc72bb7e_1006.ta
 https://conda.anaconda.org/conda-forge/noarch/r-presenceabsence-1.1.11-r42hc72bb7e_0.conda#e93fbffb6ecf670e1a9f5c117157f85d
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 https://conda.anaconda.org/conda-forge/linux-64/r-ps-1.7.2-r42h06615bd_0.tar.bz2#3ee92bed3751c1c81205fe8c08ac4dac
+https://conda.anaconda.org/conda-forge/linux-64/r-quadprog-1.5_8-r42hd009a43_4.tar.bz2#9edae583634924ce57d8f2b71c5d2e80
 https://conda.anaconda.org/conda-forge/noarch/r-r.methodss3-1.8.2-r42hc72bb7e_1.tar.bz2#7f771287adb5521c3cab7cd773dd6f10
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@@ -472,6 +474,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-here-1.0.1-r42hc72bb7e_1.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/r-htmltools-0.5.4-r42h38f115c_0.conda#f0ae9abca8407f43dff6498e236cf8f9
 https://conda.anaconda.org/conda-forge/linux-64/r-igraph-1.4.1-r42h65ed38e_0.conda#46feb8c1f008c187193e011667b25373
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+https://conda.anaconda.org/conda-forge/linux-64/r-lmtest-0.9_40-r42h8da6f51_1.tar.bz2#b1ece4db48ca0c34174b9ab82b7c23a7
 https://conda.anaconda.org/conda-forge/linux-64/r-lubridate-1.9.2-r42h133d619_1.conda#67abde15ac058f7b817635016d7867d6
 https://conda.anaconda.org/conda-forge/linux-64/r-maptools-1.1_6-r42h133d619_0.conda#bd8dbf7e9a4fc8d167b52f39449936b9
 https://conda.anaconda.org/conda-forge/linux-64/r-mda-0.5_3-r42h8da6f51_1.tar.bz2#d7960fee2dd2a60d04fa06792a455744
@@ -494,6 +497,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-sfheaders-0.4.0-r42h7525677_1.
 https://conda.anaconda.org/conda-forge/linux-64/r-survival-3.5_3-r42h133d619_0.conda#1569ea216ba2bbfa8c10e735c38a33e9
 https://conda.anaconda.org/conda-forge/linux-64/r-svglite-2.1.1-r42he8f5e61_0.conda#a1ba56a80e51973b7e3d65e8c4f2e903
 https://conda.anaconda.org/conda-forge/linux-64/r-textshaping-0.3.6-r42hbb20487_4.conda#7e4442f8d97d97532df643d67444c183
+https://conda.anaconda.org/conda-forge/linux-64/r-urca-1.3_3-r42h8da6f51_0.tar.bz2#706db7a400b33d6c45ebc7751789e56e
 https://conda.anaconda.org/conda-forge/noarch/r-urlchecker-1.0.1-r42hc72bb7e_1.tar.bz2#30c400f784e808557bdacfd12990f8e9
 https://conda.anaconda.org/conda-forge/linux-64/r-urltools-1.7.3-r42h7525677_3.tar.bz2#de791762c1eb42723d2314b2ba7fd318
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@@ -538,6 +542,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-satellite-1.0.4-r42h7525677_1.
 https://conda.anaconda.org/conda-forge/noarch/r-spacetime-1.2_8-r42hc72bb7e_1.tar.bz2#3e5cf89e5cb506dc136b973191bdda20
 https://conda.anaconda.org/conda-forge/noarch/r-stringr-1.5.0-r42h785f33e_0.conda#5eaeafbfe340886a30863322edf82b5c
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+https://conda.anaconda.org/conda-forge/linux-64/r-ttr-0.24.3-r42h06615bd_1.tar.bz2#ee04695dcc8b39927c90d63308f1b28d
 https://conda.anaconda.org/conda-forge/linux-64/r-vegan-2.6_4-r42hb20cf53_0.conda#b2aa6a3daeee9a238704e482a5110f06
 https://conda.anaconda.org/conda-forge/noarch/r-webshot-0.5.4-r42hc72bb7e_1.tar.bz2#5de5ff6bc25704fde50b1b4b89fc229b
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@@ -546,14 +551,15 @@ https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.5.2-pyhd8ed1ab_0.conda
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-https://conda.anaconda.org/conda-forge/linux-64/r-gert-1.9.2-r42hf3f2ec2_0.conda#b1e418a5e9d0efe79e8b4de086f5c191
+https://conda.anaconda.org/conda-forge/linux-64/r-gert-1.9.2-r42h492061e_1.conda#721bc4e39978d75923c5911c3d4bb01d
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 https://conda.anaconda.org/conda-forge/noarch/r-prettymapr-0.2.4-r42hc72bb7e_1.tar.bz2#b08d9d6fb70c6b6ba10b0004afa64707
 https://conda.anaconda.org/conda-forge/noarch/r-progress-1.2.2-r42hc72bb7e_3.tar.bz2#d56bcec1d57443abfede702c22067855
+https://conda.anaconda.org/conda-forge/noarch/r-quantmod-0.4.20-r42hc72bb7e_1.tar.bz2#76d21956de647c0ef364aa4cebd2c98f
 https://conda.anaconda.org/conda-forge/noarch/r-rcmdcheck-1.4.0-r42h785f33e_1.tar.bz2#a5c0bdb67cc09209c59b48eec1acf290
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@@ -585,14 +591,14 @@ https://conda.anaconda.org/conda-forge/noarch/r-rvest-1.0.3-r42hc72bb7e_1.tar.bz
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+https://conda.anaconda.org/conda-forge/linux-64/r-tseries-0.10_53-r42h0b340dd_0.conda#b0507013392f42cae47241455276f8b1
 https://conda.anaconda.org/conda-forge/noarch/r-usethis-2.1.6-r42hc72bb7e_1.tar.bz2#5358b89d0ca17581a3fc1098c208984f
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 https://conda.anaconda.org/conda-forge/noarch/r-cowplot-1.1.1-r42hc72bb7e_1.tar.bz2#aeff9827393b7225a5f688f489341840
-https://conda.anaconda.org/conda-forge/noarch/r-dbplyr-2.3.0-r42hc72bb7e_0.conda#c51795b067c1cd13c32b512eb1b13711
 https://conda.anaconda.org/conda-forge/noarch/r-dtplyr-1.3.0-r42hc72bb7e_0.conda#bf7ffecd43a402b6f2e013884328caaa
 https://conda.anaconda.org/conda-forge/noarch/r-googlesheets4-1.0.1-r42h785f33e_1.tar.bz2#d10dcdb6b3c2797b7f44b948dbb9e820
 https://conda.anaconda.org/conda-forge/noarch/r-htmlwidgets-1.6.1-r42hc72bb7e_0.conda#0aec2cc4c41792604194d4545ff1315b
@@ -617,6 +623,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-xaringan-0.28-r42hc72bb7e_0.cond
 https://conda.anaconda.org/conda-forge/noarch/dask-labextension-6.0.0-pyhd8ed1ab_0.tar.bz2#32a0ba2d4b9ed598d90463d0032aace3
 https://conda.anaconda.org/conda-forge/noarch/jupyterhub-singleuser-3.1.1-pyh2a2186d_0.conda#6d0a3394efe9ff7c0ad1ed03a6ca3720
 https://conda.anaconda.org/conda-forge/noarch/r-broom-1.0.3-r42hc72bb7e_0.conda#d7d739609a1aca2256b5d648d831e384
+https://conda.anaconda.org/conda-forge/noarch/r-dbplyr-2.3.1-r42hc72bb7e_0.conda#c5477ab0dd1b1c8f4c14468e320b896e
 https://conda.anaconda.org/conda-forge/linux-64/r-fields-14.1-r42hac0b197_1.conda#2a4b23e5e1a3bc4b280101a32c13ebbb
 https://conda.anaconda.org/conda-forge/linux-64/r-gstat-2.1_0-r42h06615bd_0.tar.bz2#40b07615a3406fe0895983fd7c5b809b
 https://conda.anaconda.org/conda-forge/linux-64/r-haven-2.5.1-r42h7525677_0.tar.bz2#e4f07a451fcbf395759390452d24c7c2

diff --git a/r/environment.yml b/r/environment.yml
@@ -41,6 +41,7 @@ dependencies:
   - r-rerddap
   - r-foreach
   - r-foreign
+  - r-fracdiff
   - r-gbm >=2.1.3
   - r-geometry
   - r-geosphere
@@ -59,6 +60,7 @@ dependencies:
   - r-lattice
   - r-leaflet
   - r-littler
+  - r-lmtest
   - r-lpsolve
   - r-lubridate
   - r-mmand
@@ -115,9 +117,11 @@ dependencies:
   - r-tiff
   - r-tmap
   - r-tmaptools
+  - r-tseries
   - r-tsibble
   - r-tzdb
   - r-udunits2
+  - r-urca
   - r-vegan
   - r-viridis
   - r-vroom