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import os
import sys
import io
# downloading R may takes a few minutes (80Mo)
try:
import urllib.request as urllib2 # Python 3
except:
import urllib2 # Python 2
# specify R binary and (md5, sha1) hash
# R-3.4.3:
r_url = "https://cran.r-project.org/bin/windows/base/old/3.5.0/R-3.5.0-win.exe"
hashes=("d3f579b3aacfdf45a008df3320cb3615","87cf0f72dcd91ff12627178e2438cb5a8d8a13c0")
# specify target location
# tweak change in recent winpython
tool_base_directory=os.environ["WINPYDIR"]+"\\..\\t\\"
if not os.path.isdir(tool_base_directory):
tool_base_directory=os.environ["WINPYDIR"]+"\\..\\tools\\"
r_installer = tool_base_directory+os.path.basename(r_url)
os.environ["r_installer"] = r_installer
# Download
g = urllib2.urlopen(r_url)
with io.open(r_installer, 'wb') as f:
f.write(g.read())
g.close
g = None
#checking it's there
!dir %r_installer%
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# checking it's the official R
import hashlib
def give_hash(of_file, with_this):
with io.open(r_installer, 'rb') as f:
return with_this(f.read()).hexdigest()
print (" "*12+"MD5"+" "*(32-12-3)+" "+" "*15+"SHA-1"+" "*(40-15-5)+"\n"+"-"*32+" "+"-"*40)
print ("%s %s %s" % (give_hash(r_installer, hashlib.md5) , give_hash(r_installer, hashlib.sha1),r_installer))
if give_hash(r_installer, hashlib.md5) == hashes[0] and give_hash(r_installer, hashlib.sha1) == hashes[1]:
print("looks good!")
else:
print("problem ! please check")
assert give_hash(r_installer, hashlib.md5) == hashes[0]
assert give_hash(r_installer, hashlib.sha1) == hashes[1]
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# preparing Dos variables
os.environ["R_HOME"] = tool_base_directory+ "R\\"
os.environ["R_HOMEbin"]=os.environ["R_HOME"] + "bin"
# for installation we need this
os.environ["tmp_Rbase"]=os.path.join(os.path.split(os.environ["WINPYDIR"])[0] , 't','R' )
if 'amd64' in sys.version.lower():
r_comp ='/COMPONENTS="main,x64,translations'
else:
r_comp ='/COMPONENTS="main,i386,translations'
os.environ["tmp_R_comp"]=r_comp
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# let's install it, if hashes do match
assert give_hash(r_installer, hashlib.md5) == hashes[0]
assert give_hash(r_installer, hashlib.sha1) == hashes[1]
# If you are "USB life style", or multi-winpython
# ==> CLICK the OPTION "Don't create a StartMenuFolder' <== (when it will show up)
!start cmd /C %r_installer% /DIR=%tmp_Rbase% %tmp_R_comp%
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import os
import sys
import io
# let's create a R launcher
r_launcher = r"""
@echo off
call %~dp0env.bat
rscript %*
"""
r_launcher_bat = os.environ["WINPYDIR"]+"\\..\\scripts\\R_launcher.bat"
# let's create a R init script
# in manual command line, you can use repos = c('http://irkernel.github.io/', getOption('repos'))
r_initialization = r"""
install.packages(c('repr', 'IRdisplay', 'stringr', 'crayon', 'pbdZMQ', 'devtools'), repos = c('http://cran.rstudio.com/', 'http://cran.rstudio.com/'))
devtools::install_github('IRkernel/IRkernel')
library('pbdZMQ')
library('repr')
library('IRkernel')
library('IRdisplay')
library('crayon')
library('stringr')
IRkernel::installspec()
"""
r_initialization_r = os.path.normpath(os.environ["WINPYDIR"]+"\\..\\scripts\\R_initialization.r")
for i in [(r_launcher,r_launcher_bat), (r_initialization, r_initialization_r)]:
with io.open(i[1], 'w', encoding = sys.getdefaultencoding() ) as f:
for line in i[0].splitlines():
f.write('%s\n' % line )
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#check what we are going to do
print ("!start cmd /C %WINPYDIR%\\..\\scripts\\R_launcher.bat --no-restore --no-save " + r_initialization_r)
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# Launch Rkernel setup
os.environ["r_initialization_r"] = r_initialization_r
!start cmd /C %WINPYDIR%\\..\\scripts\\R_launcher.bat --no-restore --no-save %r_initialization_r%
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# make RKernel a movable installation with the rest of WinPython
from winpython import utils
base_winpython = os.path.dirname(os.path.normpath(os.environ["WINPYDIR"]))
rkernel_json=(base_winpython+"\\settings\\kernels\\ir\\kernel.json")
# so we get "argv": ["{prefix}/../tools/R/bin/x64/R"
utils.patch_sourcefile(rkernel_json, base_winpython.replace("\\","/"), r'{prefix}/..', silent_mode=False)
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%load_ext rpy2.ipython
#vitals: 'dplyr', 'R.utils', 'nycflights13'
# installation takes 2 minutes
%R install.packages(c('dplyr','R.utils', 'nycflights13'), repos='http://cran.rstudio.com/')
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!echo %R_HOME%
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%load_ext rpy2.ipython
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# avoid some pandas deprecation warning
import warnings
warnings.filterwarnings("ignore", category=DeprecationWarning)
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%%R
library('dplyr')
library('nycflights13')
write.csv(flights, "flights.csv")
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%R head(flights)
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%R airports %>% mutate(dest = faa) %>% semi_join(flights) %>% head
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# essentials: 'tidyr', 'shiny', 'ggplot2', 'caret' , 'nnet'
# remaining of Hadley Wickahm "stack" (https://github.com/rstudio)
%R install.packages(c('tidyr', 'ggplot2', 'shiny','caret' , 'nnet'), repos='https://cran.rstudio.com/')
%R install.packages(c('knitr', 'purrr', 'readr', 'readxl'), repos='https://cran.rstudio.com/')
%R install.packages(c('rvest', 'lubridate', 'ggvis', 'readr','base64enc'), repos='https://cran.rstudio.com/')
# TRAINING = online training book http://r4ds.had.co.nz/ (or https://github.com/hadley/r4ds)
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