From 955833140a9f92f7e5e3b6f99c6aec2596ef65d5 Mon Sep 17 00:00:00 2001 From: Yann Richet Date: Wed, 20 Sep 2023 12:46:31 +0200 Subject: [PATCH 1/2] =?UTF-8?q?Cr=C3=A9=C3=A9=20avec=20Colaboratory?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- install_FunQuant.ipynb | 140 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 140 insertions(+) create mode 100644 install_FunQuant.ipynb diff --git a/install_FunQuant.ipynb b/install_FunQuant.ipynb new file mode 100644 index 0000000..08602f6 --- /dev/null +++ b/install_FunQuant.ipynb @@ -0,0 +1,140 @@ +{ + "nbformat": 4, + "nbformat_minor": 0, + "metadata": { + "colab": { + "provenance": [], + "authorship_tag": "ABX9TyOA86EWm6FsaLRDs5UbCvse", + "include_colab_link": true + }, + "kernelspec": { + "name": "ir", + "display_name": "R" + }, + "language_info": { + "name": "R" + } + }, + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "id": "view-in-github", + "colab_type": "text" + }, + "source": [ + "\"Open" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "fg8ZEhk9Lslv", + "outputId": "00224795-f4e8-4786-fe89-df20fdeaecaf" + }, + "outputs": [ + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Downloading GitHub repo CharlieSire/FunQuant@HEAD\n", + "\n" + ] + }, + { + "output_type": "stream", + "name": "stdout", + "text": [ + "GpOutput2D (NA -> 9f779d33f...) [GitHub]\n", + "rlibkriging (NA -> 59e87fd29...) [GitHub]\n", + "Rcpp (NA -> 1.0.11 ) [CRAN]\n", + "terra (NA -> 1.7-46 ) [CRAN]\n", + "sp (NA -> 2.0-0 ) [CRAN]\n", + "raster (NA -> 3.6-23 ) [CRAN]\n", + "iterators (NA -> 1.0.14 ) [CRAN]\n", + "RcppArmad... (NA -> 0.12.6.4.0 ) [CRAN]\n", + "DiceKriging (NA -> 1.6.0 ) [CRAN]\n", + "randomForest (NA -> 4.7-1.1 ) [CRAN]\n", + "dismo (NA -> 1.3-14 ) [CRAN]\n", + "foreach (NA -> 1.5.2 ) [CRAN]\n", + "waveslim (NA -> 1.8.4 ) [CRAN]\n", + "abind (NA -> 1.4-5 ) [CRAN]\n" + ] + }, + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Downloading GitHub repo tranvivielodie/GpOutput2D@HEAD\n", + "\n" + ] + }, + { + "output_type": "stream", + "name": "stdout", + "text": [ + "dotCall64 (NA -> 1.0-2 ) [CRAN]\n", + "iterators (NA -> 1.0.14 ) [CRAN]\n", + "parallelly (NA -> 1.36.0 ) [CRAN]\n", + "listenv (NA -> 0.9.0 ) [CRAN]\n", + "globals (NA -> 0.16.2 ) [CRAN]\n", + "future.apply (NA -> 1.11.0 ) [CRAN]\n", + "future (NA -> 1.33.0 ) [CRAN]\n", + "foreach (NA -> 1.5.2 ) [CRAN]\n", + "maps (NA -> 3.4.1 ) [CRAN]\n", + "spam (NA -> 2.9-1 ) [CRAN]\n", + "Rcpp (NA -> 1.0.11 ) [CRAN]\n", + "doFuture (NA -> 1.0.0 ) [CRAN]\n", + "doParallel (NA -> 1.0.17 ) [CRAN]\n", + "numDeriv (NA -> 2016.8-1.1) [CRAN]\n", + "nloptr (NA -> 2.0.3 ) [CRAN]\n", + "pracma (NA -> 2.4.2 ) [CRAN]\n", + "fields (NA -> 15.2 ) [CRAN]\n", + "DiceDesign (NA -> 1.9 ) [CRAN]\n", + "lhs (NA -> 1.1.6 ) [CRAN]\n", + "kergp (NA -> 0.5.5 ) [CRAN]\n", + "DiceKriging (NA -> 1.6.0 ) [CRAN]\n", + "orthogona... (NA -> 0.1.7 ) [CRAN]\n", + "waveslim (NA -> 1.8.4 ) [CRAN]\n" + ] + }, + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Installing 23 packages: dotCall64, iterators, parallelly, listenv, globals, future.apply, future, foreach, maps, spam, Rcpp, doFuture, doParallel, numDeriv, nloptr, pracma, fields, DiceDesign, lhs, kergp, DiceKriging, orthogonalsplinebasis, waveslim\n", + "\n", + "Installing packages into ‘/usr/local/lib/R/site-library’\n", + "(as ‘lib’ is unspecified)\n", + "\n" + ] + } + ], + "source": [ + "remotes::install_github(\"CharlieSire/FunQuant\") # when repo will becom public\n", + "#remotes::install_local(\"FunQuant-main.zip\") # once uploaded in colab path\n", + "#install.packages(\\\"remotes\\\") # when released on CRAN\n", + "\n", + "install.packages(\"randtoolbox\")\n", + "install.packages(\"evd\")\n", + "install.packages(\"ggplot2\")\n", + "install.packages(\"gridExtra\")" + ] + }, + { + "cell_type": "code", + "source": [ + "library(FunQuant)\n" + ], + "metadata": { + "id": "4fwm8jl3MCgD" + }, + "execution_count": null, + "outputs": [] + } + ] +} \ No newline at end of file From 0b6413f5cf4796911eb9c11a0947774f85559b92 Mon Sep 17 00:00:00 2001 From: Yann Richet Date: Wed, 20 Sep 2023 17:10:37 +0200 Subject: [PATCH 2/2] Created using Colaboratory --- install_FunQuant_n_deps.ipynb | 247 ++++++++++++++++++++++++++++++++++ 1 file changed, 247 insertions(+) create mode 100644 install_FunQuant_n_deps.ipynb diff --git a/install_FunQuant_n_deps.ipynb b/install_FunQuant_n_deps.ipynb new file mode 100644 index 0000000..7dbfbd3 --- /dev/null +++ b/install_FunQuant_n_deps.ipynb @@ -0,0 +1,247 @@ +{ + "nbformat": 4, + "nbformat_minor": 0, + "metadata": { + "colab": { + "provenance": [], + "authorship_tag": "ABX9TyP/gyzjalrw+Dev2Ktn6kRE", + "include_colab_link": true + }, + "kernelspec": { + "name": "ir", + "display_name": "R" + }, + "language_info": { + "name": "R" + } + }, + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "id": "view-in-github", + "colab_type": "text" + }, + "source": [ + "\"Open" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "tecQiUiZ6PVt", + "outputId": "78851d86-67dc-4036-f830-bb2ada46dfd1" + }, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "Get:1 https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ InRelease [3,626 B]\n", + "Hit:2 https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64 InRelease\n", + "Hit:3 http://archive.ubuntu.com/ubuntu jammy InRelease\n", + "Get:4 http://security.ubuntu.com/ubuntu jammy-security InRelease [110 kB]\n", + "Get:5 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [119 kB]\n", + "Get:6 http://archive.ubuntu.com/ubuntu jammy-backports InRelease [109 kB]\n", + "Hit:7 https://ppa.launchpadcontent.net/c2d4u.team/c2d4u4.0+/ubuntu jammy InRelease\n", + "Get:8 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 Packages [1,259 kB]\n", + "Get:9 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [1,282 kB]\n", + "Get:10 http://archive.ubuntu.com/ubuntu jammy-updates/restricted amd64 Packages [1,155 kB]\n", + "Get:11 http://security.ubuntu.com/ubuntu jammy-security/universe amd64 Packages [996 kB]\n", + "Hit:12 https://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu jammy InRelease\n", + "Hit:13 https://ppa.launchpadcontent.net/graphics-drivers/ppa/ubuntu jammy InRelease\n", + "Get:14 http://security.ubuntu.com/ubuntu jammy-security/main amd64 Packages [1,014 kB]\n", + "Get:15 http://security.ubuntu.com/ubuntu jammy-security/restricted amd64 Packages [1,134 kB]\n", + "Hit:16 https://ppa.launchpadcontent.net/ubuntugis/ppa/ubuntu jammy InRelease\n", + "Fetched 7,181 kB in 3s (2,846 kB/s)\n", + "Reading package lists...\n", + "Building dependency tree...\n", + "Reading state information...\n", + "19 packages can be upgraded. Run 'apt list --upgradable' to see them.\n", + "Reading package lists...\n", + "Building dependency tree...\n", + "Reading state information...\n", + "gfortran is already the newest version (4:11.2.0-1ubuntu1).\n", + "cmake is already the newest version (3.22.1-1ubuntu1.22.04.1).\n", + "0 upgraded, 0 newly installed, 0 to remove and 19 not upgraded." + ] + }, + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Installing package into ‘/usr/local/lib/R/site-library’\n", + "(as ‘lib’ is unspecified)\n", + "\n", + "'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n", + "'help(\"repositories\", package = \"BiocManager\")' for details.\n", + "Replacement repositories:\n", + " CRAN: https://cran.rstudio.com\n", + "\n", + "Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)\n", + "\n", + "Installing package(s) 'BiocVersion', 'Rhdf5lib'\n", + "\n", + "Old packages: 'bit', 'devtools', 'gargle', 'highr', 'isoband', 'knitr',\n", + " 'openssl', 'rmarkdown', 'roxygen2', 'whisker', 'boot', 'foreign', 'Matrix',\n", + " 'nlme'\n", + "\n", + "Installing package into ‘/usr/local/lib/R/site-library’\n", + "(as ‘lib’ is unspecified)\n", + "\n", + "also installing the dependencies ‘Rcpp’, ‘DiceKriging’, ‘RcppArmadillo’\n", + "\n", + "\n" + ] + } + ], + "source": [ + "# rlibkriging & dependencies (incl. HDF5 lib for save/load kriging objects)\n", + "shell_call <- function(command, ...) { # required for later call of shell...\n", + " result <- system(command, intern = TRUE, ...)\n", + " cat(paste0(result, collapse = \"\\n\"))\n", + "}\n", + "shell_call('apt update && apt install cmake gfortran')\n", + "\n", + "install.packages('BiocManager',repos='https://cloud.r-project.org')\n", + "BiocManager::install('Rhdf5lib')\n", + "\n", + "install.packages('rlibkriging')" + ] + }, + { + "cell_type": "code", + "source": [ + "# GPOutput2D dependency\n", + "remotes::install_github(\"tranvivielodie/GpOutput2D/GpOutput2D\")\n", + "#install.packages('https://github.com/tranvivielodie/GpOutput2D/raw/main/GpOutput2D_0.1.0.tar.gz',repos=NULL)" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "_cCwhvFx6SIB", + "outputId": "4c0e5e97-44a5-44ef-d28c-b18e4129238c" + }, + "execution_count": 4, + "outputs": [ + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Downloading GitHub repo tranvivielodie/GpOutput2D@HEAD\n", + "\n" + ] + }, + { + "output_type": "stream", + "name": "stdout", + "text": [ + "lhs (NA -> 1.1.6) [CRAN]\n" + ] + }, + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Installing 1 packages: lhs\n", + "\n", + "Installing package into ‘/usr/local/lib/R/site-library’\n", + "(as ‘lib’ is unspecified)\n", + "\n" + ] + }, + { + "output_type": "stream", + "name": "stdout", + "text": [ + "\u001b[36m──\u001b[39m \u001b[36mR CMD build\u001b[39m \u001b[36m─────────────────────────────────────────────────────────────────\u001b[39m\n", + "* checking for file ‘/tmp/RtmpO9sJ4u/remotes6a211dc46418/tranvivielodie-GpOutput2D-9f779d3/GpOutput2D/DESCRIPTION’ ... OK\n", + "* preparing ‘GpOutput2D’:\n", + "* checking DESCRIPTION meta-information ... OK\n", + "* checking for LF line-endings in source and make files and shell scripts\n", + "* checking for empty or unneeded directories\n", + "Omitted ‘LazyData’ from DESCRIPTION\n", + "* building ‘GpOutput2D_0.1.0.tar.gz’\n", + "\n" + ] + }, + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Installing package into ‘/usr/local/lib/R/site-library’\n", + "(as ‘lib’ is unspecified)\n", + "\n" + ] + } + ] + }, + { + "cell_type": "code", + "source": [ + "#remotes::install_local(\"FunQuant-main.zip\") # from upload in colab path\n", + "remotes::install_github(\"CharlieSire/FunQuant\", upgrade=\"never\") # from public github repo\n", + "#install.packages(\"FunQuant\") # from CRAN (when released)\n", + "\n", + "library(FunQuant)" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "eXBqaMVd-dfN", + "outputId": "baf0816c-16b3-4af1-8c32-48e66b22dae5" + }, + "execution_count": 1, + "outputs": [ + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Downloading GitHub repo CharlieSire/FunQuant@HEAD\n", + "\n", + "Installing 5 packages: terra, sp, raster, randomForest, dismo\n", + "\n", + "Installing packages into ‘/usr/local/lib/R/site-library’\n", + "(as ‘lib’ is unspecified)\n", + "\n" + ] + }, + { + "output_type": "stream", + "name": "stdout", + "text": [ + "\u001b[36m──\u001b[39m \u001b[36mR CMD build\u001b[39m \u001b[36m─────────────────────────────────────────────────────────────────\u001b[39m\n", + "* checking for file ‘/tmp/Rtmp51d5zv/remotes965744b9270b/charliesire-FunQuant-9558331/DESCRIPTION’ ... OK\n", + "* preparing ‘FunQuant’:\n", + "* checking DESCRIPTION meta-information ... OK\n", + "* checking for LF line-endings in source and make files and shell scripts\n", + "* checking for empty or unneeded directories\n", + "Omitted ‘LazyData’ from DESCRIPTION\n", + " NB: this package now depends on R (>= 3.5.0)\n", + " WARNING: Added dependency on R >= 3.5.0 because serialized objects in\n", + " serialize/load version 3 cannot be read in older versions of R.\n", + " File(s) containing such objects:\n", + " ‘FunQuant/ip.RData’\n", + "* building ‘FunQuant_0.1.1.tar.gz’\n", + "\n" + ] + }, + { + "output_type": "stream", + "name": "stderr", + "text": [ + "Installing package into ‘/usr/local/lib/R/site-library’\n", + "(as ‘lib’ is unspecified)\n", + "\n" + ] + } + ] + } + ] +} \ No newline at end of file