Allow config.guess code from configuremake.py to be used in rpackage.py

easybuild/easyblocks/generic/_config_guess.py

@@ -0,0 +1,119 @@
+# This file contains constants and functions required to find and update
+# config.guess files in a source tree.
+
+import os
+import re
+from datetime import datetime
+
+from easybuild.framework.easyblock import EasyBlock
+from easybuild.tools.config import source_paths
+from easybuild.tools.filetools import read_file, remove_file, verify_checksum
+from easybuild.easyblocks import VERSION as EASYBLOCKS_VERSION
+from easybuild.tools.filetools import CHECKSUM_TYPE_SHA256, adjust_permissions, compute_checksum, download_file
+
+# download location & SHA256 for config.guess script
+# note: if this is updated, don't forget to trash the cached download from generic/Configure/<eb_version>/!
+CONFIG_GUESS_VERSION = '2018-08-29'
+CONFIG_GUESS_URL_STUB = "https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb="
+CONFIG_GUESS_COMMIT_ID = "59e2ce0e6b46bb47ef81b68b600ed087e14fdaad"
+CONFIG_GUESS_SHA256 = "c02eb9cc55c86cfd1e9a794e548d25db5c9539e7b2154beb649bc6e2cbffc74c"
+
+class ConfigGuessUpdater(EasyBlock):
+    def __init__(self, *args, **kwargs):
+        """Initialize easyblock."""
+        super(ConfigGuessUpdater, self).__init__(*args, **kwargs)
+
+        self.config_guess = None
+
+    def fetch_step(self, *args, **kwargs):
+        """Custom fetch step for ConfigGuessUpdater so we use an updated config.guess."""
+        super(ConfigGuessUpdater, self).fetch_step(*args, **kwargs)
+
+        # Use an updated config.guess from a global location (if possible)
+        self.config_guess = self.obtain_config_guess()
+
+    def obtain_config_guess(self, download_source_path=None, search_source_paths=None):
+        """
+        Locate or download an up-to-date config.guess for use with ConfigureMake
+
+        :param download_source_path: Path to download config.guess to
+        :param search_source_paths: Paths to search for config.guess
+        :return: Path to config.guess or None
+        """
+        eb_source_paths = source_paths()
+        if download_source_path is None:
+            download_source_path = eb_source_paths[0]
+        if search_source_paths is None:
+            search_source_paths = eb_source_paths
+
+        config_guess = 'config.guess'
+        sourcepath_subdir = os.path.join('generic', 'eb_v%s' % EASYBLOCKS_VERSION, 'ConfigureMake')
+
+        config_guess_path = None
+
+        # check if config.guess has already been downloaded to source path
+        for path in eb_source_paths:
+            cand_config_guess_path = os.path.join(path, sourcepath_subdir, config_guess)
+            if os.path.isfile(cand_config_guess_path):
+                config_guess_path = cand_config_guess_path
+                self.log.info("Found recent %s at %s, using it if required", config_guess, config_guess_path)
+                break
+
+        # if not found, try to download it
+        if config_guess_path is None:
+            cand_config_guess_path = os.path.join(download_source_path, sourcepath_subdir, config_guess)
+            config_guess_url = CONFIG_GUESS_URL_STUB + CONFIG_GUESS_COMMIT_ID
+            downloaded_path = download_file(config_guess, config_guess_url, cand_config_guess_path)
+            if downloaded_path is not None:
+                # verify SHA256 checksum of download to avoid using a corrupted download
+                if verify_checksum(downloaded_path, CONFIG_GUESS_SHA256):
+                    config_guess_path = downloaded_path
+                    # add execute permissions
+                    adjust_permissions(downloaded_path, stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH, add=True)
+                    self.log.info("Downloaded recent %s to %s, using it if required", config_guess, config_guess_path)
+                else:
+                    self.log.warning("Checksum failed for downloaded file %s, not using it!", downloaded_path)
+                    remove_file(downloaded_path)
+            else:
+                self.log.warning("Failed to download recent %s to %s for use with ConfigureMake easyblock (if needed)",
+                                 config_guess, cand_config_guess_path)
+
+        return config_guess_path
+
+    def check_config_guess(self):
+        """
+        Check timestamp & SHA256 checksum of config.guess script.
+
+        Returns True if ok (or there is no config.guess for this package) and False if it's too old
+        or doesn't match the checksum.
+        """
+        # log version, timestamp & SHA256 checksum of config.guess that was found (if any)
+        if self.config_guess:
+            # config.guess includes a "timestamp='...'" indicating the version
+            config_guess_version = None
+            version_regex = re.compile("^timestamp='(.*)'", re.M)
+            res = version_regex.search(read_file(self.config_guess))
+            if res:
+                config_guess_version = res.group(1)
+
+            config_guess_checksum = compute_checksum(self.config_guess, checksum_type=CHECKSUM_TYPE_SHA256)
+            try:
+                config_guess_timestamp = datetime.fromtimestamp(os.stat(self.config_guess).st_mtime).isoformat()
+            except OSError as err:
+                self.log.warning("Failed to determine timestamp of %s: %s", self.config_guess, err)
+                config_guess_timestamp = None
+
+            self.log.info("config.guess version: %s (last updated: %s, SHA256 checksum: %s)",
+                          config_guess_version, config_guess_timestamp, config_guess_checksum)
+
+            if config_guess_version != CONFIG_GUESS_VERSION:
+                tup = (self.config_guess, config_guess_version, CONFIG_GUESS_VERSION)
+                self.log.warning("config.guess version at %s does not match expected version: %s vs %s" % tup)
+                return False
+
+            if config_guess_checksum != CONFIG_GUESS_SHA256:
+                tup = (self.config_guess, config_guess_checksum, CONFIG_GUESS_SHA256)
+                self.log.warning("SHA256 checksum of config.guess at %s does not match expected checksum: %s vs %s" % tup)
+                return False
+
+        return True

easybuild/easyblocks/generic/configuremake.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2020 Ghent University
+# Copyright 2009-2019 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -36,38 +36,26 @@
 @author: Alan O'Cais (Juelich Supercomputing Centre)
 """
 import os
-import re
 import stat
-from datetime import datetime
 
-from easybuild.easyblocks import VERSION as EASYBLOCKS_VERSION
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import print_warning
-from easybuild.tools.config import source_paths
-from easybuild.tools.filetools import CHECKSUM_TYPE_SHA256, adjust_permissions, compute_checksum, download_file
-from easybuild.tools.filetools import read_file, remove_file, verify_checksum
+from easybuild.tools.filetools import read_file
 from easybuild.tools.run import run_cmd
+from easybuild.easyblocks.generic._config_guess import ConfigGuessUpdater
 
 # string that indicates that a configure script was generated by Autoconf
 # note: bytes string since this constant is used to check the contents of 'configure' which is read as bytes
 # (mainly important when EasyBuild is using Python 3)
 AUTOCONF_GENERATED_MSG = b"Generated by GNU Autoconf"
 
-# download location & SHA256 for config.guess script
-# note: if this is updated, don't forget to trash the cached download from generic/Configure/<eb_version>/!
-CONFIG_GUESS_VERSION = '2018-08-29'
-CONFIG_GUESS_URL_STUB = "https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb="
-CONFIG_GUESS_COMMIT_ID = "59e2ce0e6b46bb47ef81b68b600ed087e14fdaad"
-CONFIG_GUESS_SHA256 = "c02eb9cc55c86cfd1e9a794e548d25db5c9539e7b2154beb649bc6e2cbffc74c"
-
-
 DEFAULT_CONFIGURE_CMD = './configure'
 DEFAULT_BUILD_CMD = 'make'
 DEFAULT_INSTALL_CMD = 'make install'
 
 
-class ConfigureMake(EasyBlock):
+class ConfigureMake(ConfigGuessUpdater):
     """
     Support for building and installing applications with configure/make/make install
     """
@@ -92,96 +80,6 @@ def extra_options(extra_vars=None):
         })
         return extra_vars
 
-    def __init__(self, *args, **kwargs):
-        """Initialize easyblock."""
-        super(ConfigureMake, self).__init__(*args, **kwargs)
-
-        self.config_guess = None
-
-    def obtain_config_guess(self, download_source_path=None, search_source_paths=None):
-        """
-        Locate or download an up-to-date config.guess for use with ConfigureMake
-
-        :param download_source_path: Path to download config.guess to
-        :param search_source_paths: Paths to search for config.guess
-        :return: Path to config.guess or None
-        """
-        eb_source_paths = source_paths()
-        if download_source_path is None:
-            download_source_path = eb_source_paths[0]
-        if search_source_paths is None:
-            search_source_paths = eb_source_paths
-
-        config_guess = 'config.guess'
-        sourcepath_subdir = os.path.join('generic', 'eb_v%s' % EASYBLOCKS_VERSION, 'ConfigureMake')
-
-        config_guess_path = None
-
-        # check if config.guess has already been downloaded to source path
-        for path in eb_source_paths:
-            cand_config_guess_path = os.path.join(path, sourcepath_subdir, config_guess)
-            if os.path.isfile(cand_config_guess_path):
-                config_guess_path = cand_config_guess_path
-                self.log.info("Found recent %s at %s, using it if required", config_guess, config_guess_path)
-                break
-
-        # if not found, try to download it
-        if config_guess_path is None:
-            cand_config_guess_path = os.path.join(download_source_path, sourcepath_subdir, config_guess)
-            config_guess_url = CONFIG_GUESS_URL_STUB + CONFIG_GUESS_COMMIT_ID
-            downloaded_path = download_file(config_guess, config_guess_url, cand_config_guess_path)
-            if downloaded_path is not None:
-                # verify SHA256 checksum of download to avoid using a corrupted download
-                if verify_checksum(downloaded_path, CONFIG_GUESS_SHA256):
-                    config_guess_path = downloaded_path
-                    # add execute permissions
-                    adjust_permissions(downloaded_path, stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH, add=True)
-                    self.log.info("Downloaded recent %s to %s, using it if required", config_guess, config_guess_path)
-                else:
-                    self.log.warning("Checksum failed for downloaded file %s, not using it!", downloaded_path)
-                    remove_file(downloaded_path)
-            else:
-                self.log.warning("Failed to download recent %s to %s for use with ConfigureMake easyblock (if needed)",
-                                 config_guess, cand_config_guess_path)
-
-        return config_guess_path
-
-    def check_config_guess(self):
-        """Check timestamp & SHA256 checksum of config.guess script."""
-        # log version, timestamp & SHA256 checksum of config.guess that was found (if any)
-        if self.config_guess:
-            # config.guess includes a "timestamp='...'" indicating the version
-            config_guess_version = None
-            version_regex = re.compile("^timestamp='(.*)'", re.M)
-            res = version_regex.search(read_file(self.config_guess))
-            if res:
-                config_guess_version = res.group(1)
-
-            config_guess_checksum = compute_checksum(self.config_guess, checksum_type=CHECKSUM_TYPE_SHA256)
-            try:
-                config_guess_timestamp = datetime.fromtimestamp(os.stat(self.config_guess).st_mtime).isoformat()
-            except OSError as err:
-                self.log.warning("Failed to determine timestamp of %s: %s", self.config_guess, err)
-                config_guess_timestamp = None
-
-            self.log.info("config.guess version: %s (last updated: %s, SHA256 checksum: %s)",
-                          config_guess_version, config_guess_timestamp, config_guess_checksum)
-
-            if config_guess_version != CONFIG_GUESS_VERSION:
-                tup = (self.config_guess, config_guess_version, CONFIG_GUESS_VERSION)
-                print_warning("config.guess version at %s does not match expected version: %s vs %s" % tup)
-
-            if config_guess_checksum != CONFIG_GUESS_SHA256:
-                tup = (self.config_guess, config_guess_checksum, CONFIG_GUESS_SHA256)
-                print_warning("SHA256 checksum of config.guess at %s does not match expected checksum: %s vs %s" % tup)
-
-    def fetch_step(self, *args, **kwargs):
-        """Custom fetch step for ConfigureMake so we use an updated config.guess."""
-        super(ConfigureMake, self).fetch_step(*args, **kwargs)
-
-        # Use an updated config.guess from a global location (if possible)
-        self.config_guess = self.obtain_config_guess()
-
     def configure_step(self, cmd_prefix=''):
         """
         Configure step
@@ -229,7 +127,7 @@ def configure_step(self, cmd_prefix=''):
 
             if build_type is None or host_type is None:
 
-                # config.guess script may not be obtained yet despite the call in fetch_step,
+                # config.guess script may not be obtained yet despite the call in fetch_step in ConfigGuessUpdater,
                 # for example when installing a Bundle component with ConfigureMake
                 if self.config_guess is None:
                     self.config_guess = self.obtain_config_guess()

easybuild/easyblocks/generic/rpackage.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2020 Ghent University
+# Copyright 2009-2019 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -39,8 +39,9 @@
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.framework.extensioneasyblock import ExtensionEasyBlock
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import mkdir
+from easybuild.tools.filetools import mkdir, copy_file
 from easybuild.tools.run import run_cmd, parse_log_for_error
+from easybuild.easyblocks.generic._config_guess import ConfigGuessUpdater
 
 
 def make_R_install_option(opt, values, cmdline=False):
@@ -74,12 +75,12 @@ def extra_options(extra_vars=None):
         extra_vars.update({
             'exts_subdir': ['', "Subdirectory where R extensions should be installed info", CUSTOM],
             'unpack_sources': [False, "Unpack sources before installation", CUSTOM],
+            'update_config_guess': [False, "Update the config.guess file(s) in this package", CUSTOM],
         })
         return extra_vars
 
     def __init__(self, *args, **kwargs):
         """Initliaze RPackage-specific class variables."""
-
         super(RPackage, self).__init__(*args, **kwargs)
 
         self.configurevars = []
@@ -215,10 +216,21 @@ def run(self):
             lib_install_prefix = os.path.join(self.installdir, self.cfg['exts_subdir'])
             mkdir(lib_install_prefix, parents=True)
 
-        if self.patches:
+        if self.patches or self.cfg['update_config_guess']:
             super(RPackage, self).run(unpack_src=True)
         else:
             super(RPackage, self).run()
+
+        if self.cfg['update_config_guess']:
+            cgu = ConfigGuessUpdater(self.cfg)
+            for root, dirs, files in os.walk(self.builddir):
+                for name in files:
+                    if name == 'config.guess':
+                        cgu.config_guess = os.path.join(root, name)
+                        if not cgu.check_config_guess():
+                            updated = cgu.obtain_config_guess()
+                            self.log.warning("Using updated config.guess for %s", cgu.config_guess)
+                            copy_file(updated, cgu.config_guess)
 
         if self.src:
             self.ext_src = self.src