Source code for dclab.lme4.rsetup

import logging
import os
import subprocess as sp

from .rlibs import (
    RUnavailableError, rpy2, rpy2_is_version_3, import_r_submodules)

# Disable rpy2 logger because of unnecessary prints to stdout
logging.getLogger("rpy2.rinterface_lib.callbacks").disabled = True

[docs]class RNotFoundError(BaseException): pass
[docs]class AutoRConsole(object): """Helper class for catching R console output""" lock = False perform_lock = rpy2_is_version_3 def __init__(self): """ By default, this console always returns "yes" when asked a question. If you need something different, you can subclass and override `consoleread` fucntion. The console stream is recorded in ``. """ = [["init", "Starting RConsole class\n"]] if AutoRConsole.perform_lock: if AutoRConsole.lock: raise ValueError("Only one RConsole instance allowed!") AutoRConsole.lock = True self.original_funcs = { "consoleread": rpy2.rinterface_lib.callbacks.consoleread, "consolewrite_print": rpy2.rinterface_lib.callbacks.consolewrite_print, "consolewrite_warnerror": rpy2.rinterface_lib.callbacks.consolewrite_warnerror, } rpy2.rinterface_lib.callbacks.consoleread = self.consoleread rpy2.rinterface_lib.callbacks.consolewrite_print = \ self.consolewrite_print rpy2.rinterface_lib.callbacks.showmessage = \ self.consolewrite_print rpy2.rinterface_lib.callbacks.consolewrite_warnerror = \ self.consolewrite_warnerror # Set locale (to get always English messages) rpy2.robjects.r('Sys.setlocale("LC_MESSAGES", "C")') rpy2.robjects.r('Sys.setlocale("LC_CTYPE", "C")') def __enter__(self): return self def __exit__(self, *args): if AutoRConsole.perform_lock: AutoRConsole.lock = False rpy2.rinterface_lib.callbacks.consoleread = \ self.original_funcs["consoleread"] rpy2.rinterface_lib.callbacks.consolewrite_print = \ self.original_funcs["consolewrite_print"] rpy2.rinterface_lib.callbacks.consolewrite_warnerror = \ self.original_funcs["consolewrite_warnerror"]
[docs] def close(self): """Remove the rpy2 monkeypatches""" self.__exit__()
[docs] def consoleread(self, prompt): """Read user input, returns "yes" by default""" self.write_to_stream("consoleread", prompt + "YES") return "yes"
[docs] def consolewrite_print(self, s): self.write_to_stream("consolewrite_print", s)
[docs] def consolewrite_warnerror(self, s): self.write_to_stream("consolewrite_warnerror", s)
[docs] def write_to_stream(self, topic, s): prev_topic =[-1][0] same_topic = prev_topic == topic unfinished_line =[-1][1][-1] not in ["\n", "\r"] if same_topic and unfinished_line: # append to previous line[-1][1] += s else:[topic, s])
[docs] def get_prints(self): prints = [] for line in if line[0] == "consolewrite_print": prints.append(line[1].strip()) return prints
[docs] def get_warnerrors(self): warnerrors = [] for line in if line[0] == "consolewrite_warnerror": warnerrors.append(line[1].strip()) return warnerrors
[docs]def check_r(): """Make sure R is installed an R HOME is set""" if not has_r(): raise RNotFoundError("Cannot find R, please set its path with the " + "`set_r_path` function.")
[docs]def get_r_path(): """Get the path of the R executable/binary from rpy2""" r_home = rpy2.situation.get_r_home() return rpy2.situation.get_r_exec(r_home)
[docs]def get_r_version(): check_r() ver_string = rpy2.situation.r_version_from_subprocess().strip() if ver_string: # get the actual version string if ver_string.startswith("R version "): ver_string = ver_string.split(" ")[2] return ver_string
[docs]def has_lme4(): """Return True if the lme4 package is installed""" check_r() lme4_there = rpy2.robjects.packages.isinstalled("lme4") statmod_there = rpy2.robjects.packages.isinstalled("statmod") nloptr_there = rpy2.robjects.packages.isinstalled("nloptr") return lme4_there and statmod_there and nloptr_there
[docs]def has_r(): """Return True if R is available""" try: hasr = rpy2.situation.get_r_home() is not None except RUnavailableError: hasr = False return hasr
[docs]def import_lme4(): check_r() if has_lme4(): lme4pkg = rpy2.robjects.packages.importr("lme4") else: raise ValueError( "The R package 'lme4' is not installed, please install it via " + "`dclab.lme4.rsetup.install_lme4()` or by executing " + "in a shell: R -e " + '"install.packages(' + "'lme4', " + "repos='')" + '"') return lme4pkg
[docs]def install_lme4(): """Install the lme4 package (if not already installed) The packages are installed to the user data directory given in :const:`lib_path`. """ check_r() if not has_lme4(): # import R's utility package utils = rpy2.robjects.packages.importr('utils') # select the first mirror in the list utils.chooseCRANmirror(ind=1) # install lme4 to user data directory (say yes to user dir install) with AutoRConsole() as rc: # install statmod and nloptr first # (Doesn't R have package dependencies?!) utils.install_packages( rpy2.robjects.vectors.StrVector(["statmod", "nloptr", "lme4"])) return rc
[docs]def set_r_path(r_path): """Set the path of the R executable/binary for rpy2""" tmp = sp.check_output((r_path, 'RHOME'), universal_newlines=True) r_home = tmp.split(os.linesep) if r_home[0].startswith('WARNING'): res = r_home[1] else: res = r_home[0].strip() os.environ["R_HOME"] = res import_r_submodules()