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Merge branch 'main' of https://github.com/charliesire/FunQuant into main
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SIRE Charlie committed Sep 20, 2023
2 parents 8c62d3a + 0b6413f commit a3cf935
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140 changes: 140 additions & 0 deletions install_FunQuant.ipynb
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{
"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": [
"<a href=\"https://colab.research.google.com/github/charliesire/FunQuant/blob/main/install_FunQuant.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"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": []
}
]
}
247 changes: 247 additions & 0 deletions install_FunQuant_n_deps.ipynb
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{
"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": [
"<a href=\"https://colab.research.google.com/github/charliesire/FunQuant/blob/main/install_FunQuant_n_deps.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"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"
]
}
]
}
]
}

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