archive-packages-for-ssh.ipynb

archive-packages-for-ssh.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "archive-packages-for-ssh.ipynb",
      "provenance": [],
      "collapsed_sections": [],
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/gist/paithiov909/6327d6c3cf09c613e51d4659b08b0d48/archive-packages-for-ssh.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "JWA4ZM2jC6QS"
      },
      "source": [
        "# Archive R packages for Colaboratory\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "6AP6nYBZU1Pe"
      },
      "source": [
        "## セッション切れの防止\n"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "xs1n3ccvUzDX",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 17
        },
        "outputId": "47fe9643-b881-4356-dd97-e854bd70892f"
      },
      "source": [
        "%%javascript\n",
        "function ClickConnect(){\n",
        "  console.log(\"Working\");\n",
        "  document.querySelector(\"colab-toolbar-button#connect\").click()\n",
        "}\n",
        "/**\n",
        " * 必要な場合、setIntevalをコメントアウト\n",
        "*/\n",
        "// setInterval(ClickConnect,60000)"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "application/javascript": [
              "function ClickConnect(){\n",
              "  console.log(\"Working\");\n",
              "  document.querySelector(\"colab-toolbar-button#connect\").click()\n",
              "}\n",
              "/**\n",
              " * 必要な場合、setIntevalをコメントアウト\n",
              "*/\n",
              "// setInterval(ClickConnect,60000)"
            ],
            "text/plain": [
              "<IPython.core.display.Javascript object>"
            ]
          },
          "metadata": {}
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "5teOmxdrvMjr"
      },
      "source": [
        "## 依存パッケージなどのインストール\n",
        "\n",
        "System RequirementsがあるRパッケージは先に必要なものをインストールしておく必要がある。"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "HUXd49yW34Mp"
      },
      "source": [
        "!sudo add-apt-repository \"deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/\"\n",
        "!sudo apt -yqq update\n",
        "\n",
        "## 要るもの\n",
        "# !sudo apt -qq -y install default-jdk default-jre\n",
        "!sudo apt install -yqq --no-install-recommends software-properties-common dirmngr\n",
        "!sudo apt install -yqq libprotobuf-dev libxml2 libjq-dev libmecab-dev"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "3v0rkNrPvlmX"
      },
      "source": [
        "## Rパッケージのインストール\n",
        "\n",
        "1. renvでプロジェクトを切る\n",
        "2. `renv::isolate`でプロジェクトを固定する\n",
        "3. プロジェクトディレクトリごと圧縮してZIPファイルに固める"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "-yw_QN_V4ThY"
      },
      "source": [
        "## rJavaのインストール用のスニペット\n",
        "import os\n",
        "os.environ[\"JAVA_HOME\"] = \"/usr/lib/jvm/java-11-openjdk-amd64\"\n",
        "!R CMD javareconf\n",
        "\n",
        "## 新しくディレクトリをつくる\n",
        "!mkdir workspace\n",
        "\n",
        "%load_ext rpy2.ipython"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "QjO5nxLpnlh1"
      },
      "source": [
        "%%writefile workspace/pkgs.R\n",
        "\n",
        "## ここにCRANから入れたいパッケージを書く\n",
        "## https://rstudio.github.io/renv/reference/dependencies.html\n",
        "require(languageserver)\n",
        "require(httpgd)\n",
        "require(usethis)\n",
        "require(devtools)\n",
        "require(styler)\n",
        "require(rJava)\n",
        "require(reticulate)\n",
        "require(tidyverse)\n",
        "# require(tidymodels)\n",
        "# require(ggpubr)\n",
        "# require(ggcharts)\n",
        "# require(DataExplorer)"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "lDB_s1kHXwbV"
      },
      "source": [
        "%%R\n",
        "## See https://uribo.hatenablog.com/entry/2019/01/11/082000\n",
        "# Sys.setenv(GITHUB_PAT = \"\")\n",
        "\n",
        "install.packages(\"renv\", quiet = TRUE)\n",
        "\n",
        "if (requireNamespace(\"renv\", quietly = TRUE)) {\n",
        "\n",
        "  setwd(\"./workspace\")\n",
        "\n",
        "  renv::init(bare = TRUE)\n",
        "  renv::hydrate()\n",
        "\n",
        "  ## `renv::dependencies`で拾えないGitHubなどのパッケージは、ここで個別に指定する\n",
        "  ## See https://rstudio.github.io/renv/reference/install.html\n",
        "  renv::install(\"uribo/zipangu\")\n",
        "  renv::install(\"paithiov909/rjavacmecab\")\n",
        "  # renv::install(\"paithiov909/RcppMeCab@release\")\n",
        "  # renv::install(\"bioc::BiocVersion\")\n",
        "\n",
        "  renv::snapshot(prompt = FALSE)\n",
        "\n",
        "  ## パッケージをキャッシュからプロジェクト内にコピーする\n",
        "  ## See https://rstudio.github.io/renv/reference/isolate.html\n",
        "  renv::isolate()\n",
        "\n",
        "  setwd(\"../\")\n",
        "}"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "0dyqkqNFwDiz",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "c7ac8d08-e318-4a17-c777-42496bd32048"
      },
      "source": [
        "!zip -r workspace workspace > /dev/null\n",
        "print(os.path.getsize('workspace.zip'))"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "236505648\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "084M0VP-M2Cj"
      },
      "source": [
        "## ファイルアップロード"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "SRGbR8XBL-Ih"
      },
      "source": [
        "# Import PyDrive and associated libraries.\n",
        "# This only needs to be done once in a notebook.\n",
        "from pydrive.auth import GoogleAuth\n",
        "from pydrive.drive import GoogleDrive\n",
        "from google.colab import auth\n",
        "from oauth2client.client import GoogleCredentials\n",
        "\n",
        "# Authenticate and create the PyDrive client.\n",
        "# This only needs to be done once in a notebook.\n",
        "auth.authenticate_user()\n",
        "gauth = GoogleAuth()\n",
        "gauth.credentials = GoogleCredentials.get_application_default()\n",
        "drive = GoogleDrive(gauth)\n",
        "\n",
        "# Create & upload the zip file.\n",
        "uploaded = drive.CreateFile({ 'title': 'workspace.zip' })\n",
        "uploaded.SetContentFile('workspace.zip')\n",
        "uploaded.Upload()\n",
        "print('Uploaded file with ID {}'.format(uploaded.get('id')))"
      ],
      "execution_count": null,
      "outputs": []
    }
  ]
}