def test_package_repo(self):
"""
Test retrieving/setting the package repo
"""
self.assertEqual(RUtils.package_repo(), 'http://cran.at.r-project.org/')
ProcessingConfig.setSettingValue(RUtils.R_REPO, 'http://mirror.at.r-project.org/')
self.assertEqual(RUtils.package_repo(), 'http://mirror.at.r-project.org/')
ProcessingConfig.setSettingValue(RUtils.R_REPO, 'http://cran.at.r-project.org/')
self.assertEqual(RUtils.package_repo(), 'http://cran.at.r-project.org/')
def build_script_header_commands(self, _, __, ___):
"""
Builds the set of script startup commands for the algorithm
"""
commands = list()
# Just use main mirror
commands.append('options("repos"="{}")'.format(RUtils.package_repo()))
# Try to install packages if needed
if RUtils.use_user_library():
commands.append('.libPaths(\"' +
str(RUtils.r_library_folder()).replace('\\', '/') +
'\")')
packages = RUtils.get_required_packages(self.script)
packages.extend(['rgdal', 'raster'])
for p in packages:
commands.append('tryCatch(find.package("' + p +
'"), error=function(e) install.packages("' + p +
'", dependencies=TRUE))')
commands.append('library("raster")')
commands.append('library("rgdal")')
return commands
def build_script_header_commands(self, script) -> List[str]:
"""
Builds the set of script startup commands for the algorithm, based on necessary packages,
github_install parameter and script analysis.
:param script: variable self.script from RAlgorithm
:return: list of str (commands)
"""
commands = []
# Just use main mirror
commands.append(self.set_option_repos(RUtils.package_repo()))
# Try to install packages if needed
if RUtils.use_user_library():
path_to_use = str(RUtils.r_library_folder()).replace('\\', '/')
commands.append(self.change_libPath(path_to_use))
packages = self.get_necessary_packages()
for p in packages:
commands.append(self.check_package_availability(p))
commands.append(self.load_package(p))
if self.install_github:
for dependency in self.github_dependencies:
commands.append(self.install_package_github(dependency))
packages_script = RUtils.get_required_packages(script)
for p in packages_script:
commands.append(self.check_package_availability(p))
commands.append(self.load_package(p))
return commands
