From 5a7dd3ef30c1aad373836c1b48d1d4a21133070f Mon Sep 17 00:00:00 2001 From: Jerry Xiong Date: Mon, 26 Aug 2024 10:38:58 +1000 Subject: [PATCH 1/2] Update R version to 4.4.1, renv to 1.0.7 and renv dependencies. --- Dockerfile | 9 +- renv.lock | 447 +++++++++++++++++++++++++++++++---------------------- 2 files changed, 267 insertions(+), 189 deletions(-) diff --git a/Dockerfile b/Dockerfile index 093b659..5e4834d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM rocker/r-ver:4.1.2 +FROM rocker/r-ver:4.4.1 # DeGAUSS container metadata ENV degauss_name="geocoder" @@ -28,6 +28,7 @@ RUN apt-get update && apt-get install -y \ bison \ gnupg \ software-properties-common \ + pkg-config\ && apt-get clean RUN gem install sqlite3 json Text @@ -46,11 +47,11 @@ RUN make -f Makefile.ruby install \ WORKDIR /app # install required version of renv -RUN R --quiet -e "install.packages('remotes', repos = 'https://packagemanager.rstudio.com/all/__linux__/focal/latest')" -RUN R --quiet -e "remotes::install_github('rstudio/renv@0.15.4')" +RUN R --quiet -e "install.packages('remotes', repos = c(CRAN = 'https://packagemanager.posit.co/cran/latest'))" +RUN R --quiet -e "remotes::install_github('rstudio/renv@v1.0.7')" COPY renv.lock . -RUN R --quiet -e "renv::restore()" +RUN R --quiet -e "renv::restore(repos = c(CRAN = 'https://packagemanager.posit.co/cran/latest'))" COPY geocode.rb . COPY entrypoint.R . diff --git a/renv.lock b/renv.lock index 5b8214c..25c47f3 100644 --- a/renv.lock +++ b/renv.lock @@ -1,12 +1,7 @@ { "R": { - "Version": "4.2.2", - "Repositories": [ - { - "Name": "CRAN", - "URL": "https://cran.rstudio.com" - } - ] + "Version": "4.4.1", + "Repositories": [] }, "Packages": { "R6": { @@ -14,69 +9,88 @@ "Version": "2.5.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "470851b6d5d0ac559e9d01bb352b4021", - "Requirements": [] + "Requirements": [ + "R" + ], + "Hash": "470851b6d5d0ac559e9d01bb352b4021" }, "bit": { "Package": "bit", "Version": "4.0.5", "Source": "Repository", "Repository": "CRAN", - "Hash": "d242abec29412ce988848d0294b208fd", - "Requirements": [] + "Requirements": [ + "R" + ], + "Hash": "d242abec29412ce988848d0294b208fd" }, "bit64": { "Package": "bit64", "Version": "4.0.5", "Source": "Repository", "Repository": "CRAN", - "Hash": "9fe98599ca456d6552421db0d6772d8f", "Requirements": [ - "bit" - ] + "R", + "bit", + "methods", + "stats", + "utils" + ], + "Hash": "9fe98599ca456d6552421db0d6772d8f" }, "cachem": { "Package": "cachem", - "Version": "1.0.5", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "5346f76a33eb7417812c270b04a5581b", "Requirements": [ "fastmap", "rlang" - ] + ], + "Hash": "cd9a672193789068eb5a2aad65a0dedf" }, "cli": { "Package": "cli", - "Version": "3.5.0", + "Version": "3.6.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "eb9fc121ad9a1075c471107ef185be46", - "Requirements": [] + "Requirements": [ + "R", + "utils" + ], + "Hash": "b21916dd77a27642b447374a5d30ecf3" }, "clipr": { "Package": "clipr", "Version": "0.8.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "3f038e5ac7f41d4ac41ce658c85e3042", - "Requirements": [] + "Requirements": [ + "utils" + ], + "Hash": "3f038e5ac7f41d4ac41ce658c85e3042" }, "cpp11": { "Package": "cpp11", - "Version": "0.4.3", + "Version": "0.4.7", "Source": "Repository", "Repository": "CRAN", - "Hash": "ed588261931ee3be2c700d22e94a29ab", - "Requirements": [] + "Requirements": [ + "R" + ], + "Hash": "5a295d7d963cc5035284dcdbaf334f4e" }, "crayon": { "Package": "crayon", - "Version": "1.5.2", + "Version": "1.5.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "e8a1e41acf02548751f45c718d55aa6a", - "Requirements": [] + "Requirements": [ + "grDevices", + "methods", + "utils" + ], + "Hash": "859d96e65ef198fd43e82b9628d593ef" }, "dht": { "Package": "dht", @@ -84,12 +98,12 @@ "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", - "RemoteRepo": "dht", "RemoteUsername": "degauss-org", - "RemoteRef": "HEAD", - "RemoteSha": "4d10437461416e688ea259a37c2ce3b5bae96238", - "Hash": "b16ae4484d2ef4a83738f6069c7868d3", + "RemoteRepo": "dht", + "RemoteRef": "master", + "RemoteSha": "f0b59bbb91697a55074d065642ed012b652e7d31", "Requirements": [ + "R", "cli", "dplyr", "fs", @@ -104,233 +118,245 @@ "tidyselect", "whisker", "withr" - ] + ], + "Hash": "05547abc78751624749fb01f2a2e49b9" }, "digest": { "Package": "digest", - "Version": "0.6.27", + "Version": "0.6.37", "Source": "Repository", "Repository": "CRAN", - "Hash": "a0cbe758a531d054b537d16dff4d58a1", - "Requirements": [] + "Requirements": [ + "R", + "utils" + ], + "Hash": "33698c4b3127fc9f506654607fb73676" }, "docopt": { "Package": "docopt", "Version": "0.7.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "e9eeef7931ee99ca0093f3f20b88e09b", - "Requirements": [] + "Requirements": [ + "methods" + ], + "Hash": "e9eeef7931ee99ca0093f3f20b88e09b" }, "dplyr": { "Package": "dplyr", - "Version": "1.0.10", + "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", - "Hash": "539412282059f7f0c07295723d23f987", "Requirements": [ + "R", "R6", + "cli", "generics", "glue", "lifecycle", "magrittr", + "methods", "pillar", "rlang", "tibble", "tidyselect", + "utils", "vctrs" - ] - }, - "ellipsis": { - "Package": "ellipsis", - "Version": "0.3.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077", - "Requirements": [ - "rlang" - ] + ], + "Hash": "fedd9d00c2944ff00a0e2696ccf048ec" }, "evaluate": { "Package": "evaluate", - "Version": "0.14", + "Version": "0.24.0", "Source": "Repository", "Repository": "CRAN", - 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"Version": "1.25.0", + "Version": "1.38.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "bc53006c11a08ba955ccbf85b586875f", - "Requirements": [] + "Requirements": [ + "parallel", + "tools", + "utils" + ], + "Hash": "6e8b139c1904f5e9e14c69db64453bbe" }, "pbmcapply": { "Package": "pbmcapply", - "Version": "1.5.0", + "Version": "1.5.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "4332529a23c4995d743ef489be54a839", - "Requirements": [] + "Requirements": [ + "parallel", + "utils" + ], + "Hash": "bf173fb42b60f8f404f7a9f9c3f95d0d" }, "pillar": { "Package": "pillar", - "Version": "1.8.1", + "Version": "1.9.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "f2316df30902c81729ae9de95ad5a608", "Requirements": [ "cli", "fansi", @@ -338,67 +364,78 @@ "lifecycle", "rlang", "utf8", + "utils", "vctrs" - ] + ], + "Hash": "15da5a8412f317beeee6175fbc76f4bb" }, "pkgconfig": { "Package": "pkgconfig", "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "01f28d4278f15c76cddbea05899c5d6f", - "Requirements": [] + "Requirements": [ + "utils" + ], + "Hash": "01f28d4278f15c76cddbea05899c5d6f" }, "prettyunits": { "Package": "prettyunits", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "95ef9167b75dde9d2ccc3c7528393e7e", - "Requirements": [] + "Requirements": [ + "R" + ], + "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7" }, "progress": { "Package": "progress", - "Version": "1.2.2", + "Version": "1.2.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061", "Requirements": [ + "R", "R6", "crayon", "hms", "prettyunits" - ] + ], + "Hash": "f4625e061cb2865f111b47ff163a5ca6" }, "ps": { "Package": "ps", - "Version": "1.7.2", + "Version": "1.7.7", "Source": "Repository", "Repository": "CRAN", - "Hash": "68dd03d98a5efd1eb3012436de45ba83", - "Requirements": [] + "Requirements": [ + "R", + "utils" + ], + "Hash": "878b467580097e9c383acbb16adab57a" }, "purrr": { "Package": "purrr", - "Version": "1.0.0", + "Version": "1.0.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "1ad491d27989ec6c26a2918ad6df116b", "Requirements": [ + "R", "cli", "lifecycle", "magrittr", "rlang", "vctrs" - ] + ], + "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc" }, "readr": { "Package": "readr", - "Version": "2.1.3", + "Version": "2.1.5", "Source": "Repository", "Repository": "CRAN", - "Hash": "2dfbfc673ccb3de3d8836b4b3bd23d14", "Requirements": [ + "R", "R6", "cli", "clipr", @@ -406,43 +443,61 @@ "crayon", "hms", "lifecycle", + "methods", "rlang", "tibble", "tzdb", + "utils", "vroom" - ] + ], + "Hash": "9de96463d2117f6ac49980577939dfb3" }, "renv": { "Package": "renv", - "Version": "0.15.4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "c1078316e1d4f70275fc1ea60c0bc431", - "Requirements": [] + "Version": "1.0.7", + "Source": "GitHub", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteRepo": "renv", + "RemoteUsername": "rstudio", + "RemoteRef": "v1.0.7", + "RemoteSha": "265a03869234f07c9171b6829d09427577e19baa", + "Requirements": [ + "utils" + ], + "Hash": "c9546c795efae077e4d11bce9eb9d059" }, "rlang": { "Package": "rlang", - "Version": "1.0.6", + "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", - "Hash": "4ed1f8336c8d52c3e750adcdc57228a7", - "Requirements": [] + "Requirements": [ + "R", + "utils" + ], + "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1" }, "stringi": { "Package": "stringi", - "Version": "1.7.8", + "Version": "1.8.4", "Source": "Repository", "Repository": "CRAN", - "Hash": "a68b980681bcbc84c7a67003fa796bfb", - "Requirements": [] + "Requirements": [ + "R", + "stats", + "tools", + "utils" + ], + "Hash": "39e1144fd75428983dc3f63aa53dfa91" }, "stringr": { "Package": "stringr", - "Version": "1.5.0", + "Version": "1.5.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8", "Requirements": [ + "R", "cli", "glue", "lifecycle", @@ -450,97 +505,109 @@ "rlang", "stringi", "vctrs" - ] + ], + "Hash": "960e2ae9e09656611e0b8214ad543207" }, "tibble": { "Package": "tibble", - "Version": "3.1.8", + "Version": "3.2.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "56b6934ef0f8c68225949a8672fe1a8f", "Requirements": [ + "R", "fansi", "lifecycle", "magrittr", + "methods", "pillar", "pkgconfig", "rlang", + "utils", "vctrs" - ] + ], + "Hash": "a84e2cc86d07289b3b6f5069df7a004c" }, "tidyr": { "Package": "tidyr", - "Version": "1.2.1", + "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "cdb403db0de33ccd1b6f53b83736efa8", "Requirements": [ + "R", + "cli", "cpp11", "dplyr", - "ellipsis", "glue", "lifecycle", "magrittr", "purrr", "rlang", + "stringr", "tibble", "tidyselect", + "utils", "vctrs" - ] + ], + "Hash": "915fb7ce036c22a6a33b5a8adb712eb1" }, "tidyselect": { "Package": "tidyselect", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "79540e5fcd9e0435af547d885f184fd5", "Requirements": [ + "R", "cli", "glue", "lifecycle", "rlang", "vctrs", "withr" - ] + ], + "Hash": "829f27b9c4919c16b593794a6344d6c0" }, "tzdb": { "Package": "tzdb", - "Version": "0.3.0", + "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "b2e1cbce7c903eaf23ec05c58e59fb5e", "Requirements": [ + "R", "cpp11" - ] + ], + "Hash": "f561504ec2897f4d46f0c7657e488ae1" }, "utf8": { "Package": "utf8", - "Version": "1.2.2", + "Version": "1.2.4", "Source": "Repository", "Repository": "CRAN", - "Hash": "c9c462b759a5cc844ae25b5942654d13", - "Requirements": [] + "Requirements": [ + "R" + ], + "Hash": "62b65c52671e6665f803ff02954446e9" }, "vctrs": { "Package": "vctrs", - "Version": "0.5.1", + "Version": "0.6.5", "Source": "Repository", "Repository": "CRAN", - "Hash": "970324f6572b4fd81db507b5d4062cb0", "Requirements": [ + "R", "cli", "glue", "lifecycle", "rlang" - ] + ], + "Hash": "c03fa420630029418f7e6da3667aac4a" }, "vroom": { "Package": "vroom", - "Version": "1.6.0", + "Version": "1.6.5", "Source": "Repository", "Repository": "CRAN", - "Hash": "64f81fdead6e0d250fb041e175d123ab", "Requirements": [ + "R", "bit64", "cli", "cpp11", @@ -548,46 +615,56 @@ "glue", "hms", "lifecycle", + "methods", "progress", "rlang", + "stats", "tibble", "tidyselect", "tzdb", "vctrs", "withr" - ] + ], + "Hash": "390f9315bc0025be03012054103d227c" }, "whisker": { "Package": "whisker", "Version": "0.4.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "c6abfa47a46d281a7d5159d0a8891e88", - "Requirements": [] + "Hash": "c6abfa47a46d281a7d5159d0a8891e88" }, "withr": { "Package": "withr", - "Version": "2.5.0", + "Version": "3.0.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "c0e49a9760983e81e55cdd9be92e7182", - "Requirements": [] + "Requirements": [ + "R", + "grDevices", + "graphics" + ], + "Hash": "07909200e8bbe90426fbfeb73e1e27aa" }, "xfun": { "Package": "xfun", - "Version": "0.23", + "Version": "0.47", "Source": "Repository", "Repository": "CRAN", - "Hash": "791a57f43c887111490851dcd166d344", - "Requirements": [] + "Requirements": [ + "R", + "grDevices", + "stats", + "tools" + ], + "Hash": "36ab21660e2d095fef0d83f689e0477c" }, "yaml": { "Package": "yaml", - "Version": "2.2.1", + "Version": "2.3.10", "Source": "Repository", "Repository": "CRAN", - "Hash": "2826c5d9efb0a88f657c7a679c7106db", - "Requirements": [] + "Hash": "51dab85c6c98e50a18d7551e9d49f76c" } } } From ab687f9aa59f37015bb4fa21dfa7fe8f897d2996 Mon Sep 17 00:00:00 2001 From: Cole Brokamp Date: Mon, 26 Aug 2024 08:34:40 -0400 Subject: [PATCH 2/2] upgrade degauss version --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 5e4834d..5cced36 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,7 +2,7 @@ FROM rocker/r-ver:4.4.1 # DeGAUSS container metadata ENV degauss_name="geocoder" -ENV degauss_version="3.3.0" +ENV degauss_version="3.4.0" ENV degauss_description="geocodes" ENV degauss_argument="valid_geocode_score_threshold [default: 0.5]"