def _gnur_install_test(forwarded_args, pkgs, gnur_libinstall,
gnur_install_tmp):
'''
Install/test with GNU R exactly those packages that installed correctly with FastR.
N.B. That means that regardless of how the packages were specified to pkgtest
we always use a --pkg-filelist' arg to GNU R
'''
gnur_packages = join(get_fastr_repo_dir(), 'gnur.packages')
with open(gnur_packages, 'w') as f:
for pkg in pkgs:
f.write(pkg)
f.write('\n')
env = os.environ.copy()
env["TMPDIR"] = gnur_install_tmp
env['R_LIBS_USER'] = gnur_libinstall
env["TZDIR"] = "/usr/share/zoneinfo/"
# forward any explicit args to pkgtest
args = [_installpkgs_script()]
args += forwarded_args
args += ['--pkg-filelist', gnur_packages]
args += ['--run-tests']
args += ['--ignore-blacklist']
args += ['--testdir', get_opts().gnur_testdir]
log_step('BEGIN', 'install/test', 'GnuR')
_ensure_R_on_PATH(env, os.path.dirname(get_gnur_rscript()))
cmd_line = [get_gnur_rscript()] + args
logging.debug("Running GnuR with cmd line: " + str(cmd_line))
pkgtest_run(cmd_line, env=env)
log_step('END', 'install/test', 'GnuR')
def commit_fastr_builtins():
'''
There are some FastR builtins which we also want to use in GnuR (i.e. 'install.fastr.packages').
This function deparses these functions and writes them into a file which is then loaded by GnuR.
'''
dest_file = join(_packages_test_project_dir(), 'r', 'fastr.functions.rdx')
cmd_line = [
get_fastr_rscript(), "--silent", "-e",
'{ fastrRepoPath <- NULL; save(fastrRepoPath, install.fastr.packages, file="%s") }'
% dest_file
]
logging.debug("Generating fastr.functions.R: " + str(cmd_line))
return pkgtest_run(cmd_line)
def _installpkgs(args, **kwargs):
'''
Runs the R script that does package/installation and testing.
'''
if kwargs.has_key('env'):
env = kwargs['env']
else:
env = os.environ.copy()
kwargs['env'] = env
out = kwargs.get('out', None)
err = kwargs.get('err', None)
if "FASTR_WORKING_DIR" in os.environ:
env["TMPDIR"] = os.environ["FASTR_WORKING_DIR"]
_ensure_R_on_PATH(env, os.path.dirname(get_fastr_rscript()))
cmd_line = [get_fastr_rscript(), _installpkgs_script()] + args
logging.debug("Running FastR with cmd line: " + str(cmd_line))
return pkgtest_run(cmd_line, out=out, err=err, env=env)