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stonebig merged 1 commit into from
Jan 2, 2015
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r install by hand #14

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277 changes: 277 additions & 0 deletions examples/installing_R.ipynb
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"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Installating R on winpython (Version of October 2014 and after) \n",
"\n",
"#### This procedure applys for Winpython of October 2014 and after\n",
"###1 - Downloading and Installing R binary in the right place"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"import os\n",
"import sys\n",
"import io"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"os.environ[\"tmp_Rdirectory\"]= \"R\" \n",
"os.environ[\"R_HOME\"] = os.environ[\"WINPYDIR\"]+ \"\\\\..\\\\tools\\\\R\\\\\" \n",
"os.environ[\"R_HOMEbin\"]=os.environ[\"R_HOME\"] + \"bin\" \n",
"# for installation we need this\n",
"os.environ[\"tmp_Rbase\"]=os.path.join(os.path.split(os.environ[\"WINPYDIR\"])[0] , 'tools','R' ) "
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# downloading R-3.1.2 (55Mo, may take 2/3 minutes)\n",
"try:\n",
" import urllib.request as urllib2 # Python 3\n",
"except:\n",
" import urllib2 # Python 2\n",
"if 'amd64' in sys.version.lower():\n",
" r_comp ='/COMPONENTS=\"main,x64,translations'\n",
" r_binary=\"R-3.1.2-win.exe\"\n",
" r_url=\"http://cran.r-project.org/bin/windows/base/R-3.1.2-win.exe\"\n",
" hashes=(\"9e3c0cd6311355e0d5f8e1085b288361\", \"954499b243aef3856ca66132311dfd5e70d9f7e4\" )\n",
"else:\n",
" r_comp ='/COMPONENTS=\"main,i386,translations'\n",
" r_binary=\"R-3.1.2-win.exe\"\n",
" r_url=\"http://cran.r-project.org/bin/windows/base/R-3.1.2-win.exe\"\n",
" hashes=(\"9e3c0cd6311355e0d5f8e1085b288361\", \"954499b243aef3856ca66132311dfd5e70d9f7e4\" )\n",
" \n",
"r_installer=os.environ[\"WINPYDIR\"]+\"\\\\..\\\\tools\\\\\"+r_binary\n",
"os.environ[\"r_installer\"]=r_installer\n",
"g = urllib2.urlopen(r_url) \n",
"with io.open(r_installer, 'wb') as f:\n",
" f.write(g.read())\n",
"g.close\n",
"g = None"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 7
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#checking it's there\n",
"!dir %r_installer%"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" Le volume dans le lecteur D s'appelle DATA\n",
" Le num\u201aro de s\u201arie du volume est 10BD-2ADB\n",
"\n",
" R\u201apertoire de D:\\result_tests\\WinPython-64bit-3.3.5.4\\tools\n",
"\n",
"02/01/2015 14:16 56\u00ff930\u00ff149 R-3.1.2-win.exe\n",
" 1 fichier(s) 56\u00ff930\u00ff149 octets\n",
" 0 R\u201ap(s) 187\u00ff075\u00ff727\u00ff360 octets libres\n"
]
}
],
"prompt_number": 8
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# checking it's the official julia0.3 \n",
"import hashlib\n",
"def give_hash(of_file, with_this):\n",
" with io.open(r_installer, 'rb') as f:\n",
" return with_this(f.read()).hexdigest() \n",
"print (\" \"*12+\"MD5\"+\" \"*(32-12-3)+\" \"+\" \"*15+\"SHA-1\"+\" \"*(40-15-5)+\"\\n\"+\"-\"*32+\" \"+\"-\"*40)\n",
"\n",
"print (\"%s %s %s\" % (give_hash(r_installer, hashlib.md5) , give_hash(r_installer, hashlib.sha1),r_installer))\n",
"assert give_hash(r_installer, hashlib.md5) == hashes[0]\n",
"assert give_hash(r_installer, hashlib.sha1) == hashes[1]"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" MD5 SHA-1 \n",
"-------------------------------- ----------------------------------------\n",
"9e3c0cd6311355e0d5f8e1085b288361 954499b243aef3856ca66132311dfd5e70d9f7e4 D:\\result_tests\\WinPython-64bit-3.3.5.4\\python-3.3.5.amd64\\..\\tools\\R-3.1.2-win.exe"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n"
]
}
],
"prompt_number": 9
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# let's install it \n",
"# If you are \"USB life style\", or multi-winpython\n",
"# ==> CLICK the OPTION \"Don't create a StartMenuFolder' <== (when it will show up)\n",
"os.environ[\"tmp_R_comp\"]=r_comp\n",
"!start cmd /C %r_installer% /DIR=%tmp_Rbase% %tmp_R_comp%\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 10
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<img src=\"https://raw.githubusercontent.com/stonebig/winpython_afterdoc/master/examples/images/r_setup_unclick_shortcut.GIF\">"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"###2 - create Ipython with Rmagic .bat launcher (needed for Winpython < 2014-12-29th)"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# let's create a Ipython with \"%load_ext rmagic\" launcher \n",
"bat_text = r\"\"\"\n",
"@echo off\n",
"call %~dp0env.bat\n",
"set R_HOME=%WINPYDIR%\\..\\tools\\R\\\n",
"set R_HOMEbin=%WINPYDIR%\\..\\tools\\R\\bin\n",
"set PATH=%PATH%;%R_HOMEbin%\n",
"\n",
"Ipython notebook --matplotlib=inline\n",
"\"\"\"\n",
"ipython_with_R_launcher_bat=os.environ[\"WINPYDIR\"]+\"\\\\..\\\\scripts\\\\ipython_with_R_launcher.bat\"\n",
"if sys.version_info[0] == 3:\n",
" with io.open(ipython_with_R_launcher_bat, 'w', encoding = sys.getdefaultencoding() ) as f:\n",
" for line in bat_text.splitlines():\n",
" f.write('%s\\n' % line )\n",
"else:\n",
" with io.open(ipython_with_R_launcher_bat, 'wb' ) as f:\n",
" for line in bat_text.splitlines():\n",
" f.write('%s\\r\\n' % line.encode(sys.getdefaultencoding()) )\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 5
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"###3 - Launching Ipython with R \n",
"\n",
"#### if you have a winpython release after 2014-12-29 version:\n",
" Click on your usual \"ipython notebook icon\" \n",
"\n",
"#### if you have a winpython release before 2014-12-29 version:\n",
" Click on the.bat you have just created winpython-*\\scripts\\ipython_with_R_launcher.bat \n",
" \n",
" or launch the option below which will start a new Ipython Notebook server"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Nota : this not needed for winpython versions after 2014-12-29 !\n",
"!start cmd /C %WINPYDIR%\\\\..\\\\scripts\\\\ipython_with_R_launcher.bat"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 7
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"And now, you should see a IPython notebook starting next to this IPython Notebook\n",
"\n",
"Check the start of this example http://nbviewer.ipython.org/github/winpython/winpython_afterdoc/blob/master/docs/FlavorR/dplyr_pandas.ipynb \n",
"\n",
"or below 2 lines\n",
"\n",
"---------------\n",
"\n",
"%load_ext rpy2.ipython\n",
"\n",
"%R install.packages('dplyr') \n",
"\n",
"---------------\n",
"\n",
"<img src=\"https://raw.githubusercontent.com/stonebig/winpython_afterdoc/master/examples/images/r_basic_example.GIF\">"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"###4 - To Un-install / Re-install R (or other trouble-shooting)\n",
"\n",
"- launch winpython**\\tools\\R\\unins000.exe\n",
"\n",
"- delete the directory winpython**\\tools\\R\n",
"\n",
"- re-install\n"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": []
}
],
"metadata": {}
}
]
}