def install_R_package(self, cmd, inp=None):
"""Install R package as specified, and check for errors."""
cmdttdouterr, _ = run_cmd(cmd,
log_all=True,
simple=False,
inp=inp,
regexp=False)
cmderrors = parse_log_for_error(cmdttdouterr, regExp="^ERROR:")
if cmderrors:
cmd = "R -q --no-save"
stdin = """
remove.library(%s)
""" % self.name
# remove package if errors were detected
# it's possible that some of the dependencies failed, but the package itself was installed
run_cmd(cmd,
log_all=False,
log_ok=False,
simple=False,
inp=stdin,
regexp=False)
self.log.error(
"Errors detected during installation of R package %s!" %
self.name)
else:
self.log.debug("R package %s installed succesfully" % self.name)
def sanity_check_step(self, *args, **kwargs):
"""
Custom sanity check for Julia packages
"""
#NOTE: we don't use Pkg.status with arguments as only supported for Julia >=v1.1
cmd = "unset EBJULIA_USER_DEPOT_PATH && export EBJULIA_ADMIN_DEPOT_PATH=%s && export JULIA_DEPOT_PATH=%s && export JULIA_PROJECT=%s && julia --eval 'using Pkg; Pkg.status()'" % (self.depot, self.depot, self.projectdir)
cmdttdouterr, _ = run_cmd(cmd, log_all=True, simple=False, regexp=False)
self.log.error("Julia package %s sanity returned %s" % (self.name, cmdttdouterr))
return len(parse_log_for_error(cmdttdouterr, regExp="%s\s+v%s" % (self.package_name, self.version))) != 0
def install_step(self):
"""Install procedure for Julia packages."""
cmd = self.make_julia_cmd(remove=False)
cmdttdouterr, _ = run_cmd(cmd, log_all=True, simple=False, regexp=False)
cmderrors = parse_log_for_error(cmdttdouterr, regExp="^ERROR:")
if cmderrors:
cmd = self.make_julia_cmd(remove=True)
run_cmd(cmd, log_all=False, log_ok=False, simple=False, inp=stdin, regexp=False)
raise EasyBuildError("Errors detected during installation of Julia package %s!", self.name)
else:
self.log.info("Julia package %s installed succesfully" % self.name)
def install_R_package(self, cmd, inp=None):
"""Install R package as specified, and check for errors."""
cmdttdouterr, _ = run_cmd(cmd, log_all=True, simple=False, inp=inp, regexp=False)
cmderrors = parse_log_for_error(cmdttdouterr, regExp="^ERROR:")
if cmderrors:
cmd = "R -q --no-save"
stdin = """
remove.library(%s)
""" % self.name
# remove package if errors were detected
# it's possible that some of the dependencies failed, but the package itself was installed
run_cmd(cmd, log_all=False, log_ok=False, simple=False, inp=stdin, regexp=False)
raise EasyBuildError("Errors detected during installation of R package %s!", self.name)
else:
self.log.debug("R package %s installed succesfully" % self.name)
def check_install_output(self, output):
"""
Check output of installation command, and clean up installation if needed.
"""
errors = parse_log_for_error(output, regExp="^ERROR:")
if errors:
self.handle_installation_errors()
cmd = "R -q --no-save"
stdin = """
remove.library(%s)
""" % self.name
# remove package if errors were detected
# it's possible that some of the dependencies failed, but the package itself was installed
run_cmd(cmd,
log_all=False,
log_ok=False,
simple=False,
inp=stdin,
regexp=False)
raise EasyBuildError(
"Errors detected during installation of R package %s!",
self.name)
else:
self.log.debug("R package %s installed succesfully", self.name)
def test_parse_log_error(self):
"""Test basic parse_log_for_error functionality."""
errors = parse_log_for_error("error failed", True)
self.assertEqual(len(errors), 1)
def parse_log_for_error(txt, regExp=None, stdout=True, msg=None):
"""Legacy wrapper/placeholder for run.parse_log_for_error"""
return run.parse_log_for_error(txt, regExp=regExp, stdout=stdout, msg=msg)
def test_parse_log_error(self):
"""Test basic parse_log_for_error functionality."""
errors = parse_log_for_error("error failed", True)
self.assertEqual(len(errors), 1)
def parse_log_for_error(txt, regExp=None, stdout=True, msg=None):
"""Legacy wrapper/placeholder for run.parse_log_for_error"""
_log.deprecated("parse_log_for_error was moved from tools.filetools to tools.run", '2.0')
return run.parse_log_for_error(txt, regExp=regExp, stdout=stdout, msg=msg)
def parse_log_for_error(txt, regExp=None, stdout=True, msg=None):
"""Legacy wrapper/placeholder for run.parse_log_for_error"""
return run.parse_log_for_error(txt, regExp=regExp, stdout=stdout, msg=msg)
