Bug#661287: patches
Julian Taylor
jtaylor.debian at googlemail.com
Sat Mar 3 19:22:00 UTC 2012
tags 661287 + patch
thanks
for the record, attached the patches ubuntu applied to fix the issue.
I tested them on armel, armhf, sparc and mipsel, the rdep pandas also
works with it.
For hurd and kfreebsd need additional fixes which are available in the
debian package git.
The patch to skip the blosc tests needs some adaption for arches != arm
and please also read the header for issues with it.
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diff -Nru pytables-2.3.1/debian/control pytables-2.3.1/debian/control
--- pytables-2.3.1/debian/control 2012-01-28 12:50:35.000000000 +0100
+++ pytables-2.3.1/debian/control 2012-03-03 12:26:47.000000000 +0100
@@ -1,13 +1,14 @@
Source: pytables
Section: python
Priority: optional
-Maintainer: Debian Science Maintainers <debian-science-maintainers at lists.alioth.debian.org>
+Maintainer: Ubuntu Developers <ubuntu-devel-discuss at lists.ubuntu.com>
+XSBC-Original-Maintainer: Debian Science Maintainers <debian-science-maintainers at lists.alioth.debian.org>
Uploaders: Antonio Valentino <antonio.valentino at tiscali.it>, Yaroslav Halchenko <debian at onerussian.com>
DM-Upload-Allowed: yes
Homepage: http://www.pytables.org
Standards-Version: 3.9.2
X-Python-Version: >= 2.4
-Build-Depends: debhelper (>= 8.1.0), libhdf5-dev (>= 1.6.5),
+Build-Depends: debhelper (>= 8.1.0), libhdf5-serial-dev (>= 1.6.5),
python-all-dev (>= 2.6.6-3~), python-numpy (>= 1:1.4.1-4~),
python-numexpr (>= 1.4.1), cython (>= 0.13),
zlib1g-dev, liblzo2-dev, libbz2-dev, python-sphinx (>= 1.0.7+dfsg),
diff -Nru pytables-2.3.1/debian/patches/disable_blosc.patch pytables-2.3.1/debian/patches/disable_blosc.patch
--- pytables-2.3.1/debian/patches/disable_blosc.patch 1970-01-01 01:00:00.000000000 +0100
+++ pytables-2.3.1/debian/patches/disable_blosc.patch 2012-03-03 12:26:47.000000000 +0100
@@ -0,0 +1,65 @@
+Description: disable blosc on arm
+ blosc compression is not functional due to the reliance on unaligned
+ memory access. This patch replaces all blosc write functionality with
+ zlib (default fallback) and disables a test reading blosc compressed data.
+ One could also disable reading by removing it from all_complibs in
+ tables/filters.py but that would require fixing up all tests to expect
+ exceptions.
+Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=661286
+Bug: https://github.com/FrancescAlted/blosc/issues/3
+Author: Julian Taylor <jtaylor at ubuntu.com>
+--- a/tables/utilsExtension.pyx
++++ b/tables/utilsExtension.pyx
+@@ -14,6 +14,7 @@
+
+ import sys
+ import warnings
++import platform
+
+ try:
+ import zlib
+@@ -376,7 +377,8 @@
+ (bzip2_version_string, bzip2_version_date) = bzip2_version
+ return (bzip2_version, bzip2_version_string, bzip2_version_date)
+ elif strcmp(name, "blosc") == 0:
+- return (blosc_version, blosc_version_string, blosc_version_date)
++ if "arm" not in platform.machine().lower():
++ return (blosc_version, blosc_version_string, blosc_version_date)
+ else:
+ raise ValueError("""\
+ asked version of unsupported library ``%s``; \
+--- a/tables/tests/test_all.py
++++ b/tables/tests/test_all.py
+@@ -14,6 +14,7 @@
+ from tables.req_versions import *
+ from tables.tests import common
+ from tables.utils import detectNumberOfCores
++import platform
+
+
+
+@@ -133,9 +134,10 @@
+ if tinfo is not None:
+ print "BZIP2 version: %s (%s)" % (tinfo[1], tinfo[2])
+ tinfo = tables.whichLibVersion("blosc")
+- blosc_date = tinfo[2].split()[1]
+- if tinfo is not None:
+- print "Blosc version: %s (%s)" % (tinfo[1], blosc_date)
++ if "arm" not in platform.machine().lower():
++ blosc_date = tinfo[2].split()[1]
++ if tinfo is not None:
++ print "Blosc version: %s (%s)" % (tinfo[1], blosc_date)
+ try:
+ from Cython.Compiler.Main import Version as Cython_Version
+ print 'Cython version: %s' % Cython_Version.version
+--- a/tables/tests/test_basics.py
++++ b/tables/tests/test_basics.py
+@@ -2338,7 +2338,7 @@
+ theSuite.addTest(unittest.makeSuite(PythonAttrsTestCase))
+ theSuite.addTest(unittest.makeSuite(StateTestCase))
+ theSuite.addTest(unittest.makeSuite(FlavorTestCase))
+- theSuite.addTest(unittest.makeSuite(BloscBigEndian))
++ #theSuite.addTest(unittest.makeSuite(BloscBigEndian))
+ theSuite.addTest(unittest.makeSuite(BloscSubprocess))
+
+ return theSuite
diff -Nru pytables-2.3.1/debian/patches/fix_alignment.patch pytables-2.3.1/debian/patches/fix_alignment.patch
--- pytables-2.3.1/debian/patches/fix_alignment.patch 1970-01-01 01:00:00.000000000 +0100
+++ pytables-2.3.1/debian/patches/fix_alignment.patch 2012-03-03 12:26:47.000000000 +0100
@@ -0,0 +1,32 @@
+Description: remove unaligned memory accesses
+Bug: https://github.com/PyTables/PyTables/issues/134
+Author: Julian Taylor <jtaylor at ubuntu.com
+--- a/src/typeconv.c
++++ b/src/typeconv.c
+@@ -66,18 +66,21 @@
+
+ for (record = 0; record < nrecords; record++) {
+ for (element = 0; element < nelements; element++) {
++ double fb;
++ memcpy(&fb, fieldbase, sizeof(fb));
+ if (sense == 0) {
+ /* Convert from float64 to timeval32. */
+- tv.i64 = (((PY_LONG_LONG)(*fieldbase) << 32)
+- | (lround((*fieldbase - (int)(*fieldbase)) * 1e+6)
++ tv.i64 = (((PY_LONG_LONG)(fb) << 32)
++ | (lround((fb - (int)(fb)) * 1e+6)
+ & 0x0ffffffff));
+- *fieldbase = tv.f64;
++ fb = tv.f64;
+ } else {
+ /* Convert from timeval32 to float64. */
+- tv.f64 = *fieldbase;
++ tv.f64 = fb;
+ /* the next computation is 64 bit-platforms aware */
+- *fieldbase = 1e-6 * (int)tv.i64 + (tv.i64 >> 32);
++ fb = 1e-6 * (int)tv.i64 + (tv.i64 >> 32);
+ }
++ memcpy(fieldbase, &fb, sizeof(fb));
+ fieldbase++;
+ }
+
diff -Nru pytables-2.3.1/debian/patches/fix_library_detection.patch pytables-2.3.1/debian/patches/fix_library_detection.patch
--- pytables-2.3.1/debian/patches/fix_library_detection.patch 1970-01-01 01:00:00.000000000 +0100
+++ pytables-2.3.1/debian/patches/fix_library_detection.patch 2012-03-03 12:26:47.000000000 +0100
@@ -0,0 +1,118 @@
+From b26297256ed94ee34b65429520fb9adf1686fc04 Mon Sep 17 00:00:00 2001
+From: Antonio Valentino <antonio.valentino at tiscali.it>
+Date: Sun, 19 Feb 2012 18:26:25 +0100
+Subject: Fix the detection of multiarched libraries
+
+Bug: https://github.com/PyTables/PyTables/issues/124
+Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=657789
+Forwarded: yes
+
+---
+ setup.py | 37 ++++++++++++++++++++++++++++---------
+ 1 file changed, 28 insertions(+), 9 deletions(-)
+
+--- a/setup.py
++++ b/setup.py
+@@ -21,6 +21,7 @@
+ from distutils.core import Extension
+ from distutils.dep_util import newer
+ from distutils.util import convert_path
++from distutils.ccompiler import new_compiler
+
+ # The minimum required versions
+ # (keep these in sync with tables.req_versions and user's guide and README)
+@@ -241,12 +242,14 @@
+
+ _component_dirs = ['include', 'lib']
+
+- def __init__(self, name, tag, header_name, library_name):
++ def __init__(self, name, tag, header_name, library_name,
++ target_function=None):
+ self.name = name
+ self.tag = tag
+ self.header_name = header_name
+ self.library_name = library_name
+ self.runtime_name = library_name
++ self.target_function = target_function
+
+ class WindowsPackage(Package):
+ _library_prefixes = ['']
+@@ -257,12 +260,14 @@
+ # lookup in '.' seems necessary for LZO2
+ _component_dirs = ['include', 'lib', 'dll', '.']
+
+- def __init__(self, name, tag, header_name, library_name, runtime_name):
++ def __init__(self, name, tag, header_name, library_name, runtime_name,
++ target_function=None):
+ self.name = name
+ self.tag = tag
+ self.header_name = header_name
+ self.library_name = library_name
+ self.runtime_name = runtime_name
++ self.target_function = target_function
+
+ def find_runtime_path(self, locations=default_runtime_dirs):
+ # An explicit path can not be provided for runtime libraries.
+@@ -319,10 +324,14 @@
+ if '--debug' in sys.argv:
+ _platdep['HDF5'] = ['hdf5ddll', 'hdf5ddll']
+
+-hdf5_package = _Package("HDF5", 'HDF5', 'H5public', *_platdep['HDF5'])
+-lzo2_package = _Package("LZO 2", 'LZO2', _cp('lzo/lzo1x'), *_platdep['LZO2'])
+-lzo1_package = _Package("LZO 1", 'LZO', 'lzo1x', *_platdep['LZO'])
+-bzip2_package = _Package("bzip2", 'BZ2', 'bzlib', *_platdep['BZ2'])
++hdf5_package = _Package("HDF5", 'HDF5', 'H5public', *_platdep['HDF5'],
++ target_function='H5close')
++lzo2_package = _Package("LZO 2", 'LZO2', _cp('lzo/lzo1x'), *_platdep['LZO2'],
++ target_function='lzo_version_date')
++lzo1_package = _Package("LZO 1", 'LZO', 'lzo1x', *_platdep['LZO'],
++ target_function='lzo_version_date')
++bzip2_package = _Package("bzip2", 'BZ2', 'bzlib', *_platdep['BZ2'],
++ target_function='BZ2_bzlibVersion')
+
+
+ #-----------------------------------------------------------------
+@@ -383,6 +392,7 @@
+
+ # Try to locate the compulsory and optional libraries.
+ lzo2_enabled = False
++c = new_compiler()
+ for (package, location) in [
+ (hdf5_package, HDF5_DIR),
+ (lzo2_package, LZO_DIR),
+@@ -397,6 +407,11 @@
+
+ (hdrdir, libdir, rundir) = package.find_directories(location)
+
++ # check if the library is in the standard compiler paths
++ if not libdir:
++ libdir = c.has_function(package.target_function,
++ libraries=(package.library_name,))
++
+ if not (hdrdir and libdir):
+ if package.tag in ['HDF5']: # these are compulsory!
+ pname, ptag = package.name, package.tag
+@@ -411,8 +426,12 @@
+ "disabling support for it." % package.name)
+ continue # look for the next library
+
+- print ( "* Found %s headers at ``%s``, library at ``%s``."
+- % (package.name, hdrdir, libdir) )
++ if libdir in ("", True):
++ print ( "* Found %s headers at ``%s``, the library is located in the "
++ "standard system search dirs." % (package.name, hdrdir) )
++ else:
++ print ( "* Found %s headers at ``%s``, library at ``%s``."
++ % (package.name, hdrdir, libdir) )
+
+ if package.tag in ['HDF5']:
+ hdf5_header = os.path.join(hdrdir, "H5public.h")
+@@ -423,7 +442,7 @@
+
+ if hdrdir not in default_header_dirs:
+ inc_dirs.append(hdrdir) # save header directory if needed
+- if libdir not in default_library_dirs:
++ if libdir not in default_library_dirs and libdir not in ("", True):
+ # save library directory if needed
+ if os.name == "nt":
+ # Important to quote the libdir for Windows (Vista) systems
diff -Nru pytables-2.3.1/debian/patches/series pytables-2.3.1/debian/patches/series
--- pytables-2.3.1/debian/patches/series 1970-01-01 01:00:00.000000000 +0100
+++ pytables-2.3.1/debian/patches/series 2012-03-03 12:26:47.000000000 +0100
@@ -0,0 +1,3 @@
+fix_library_detection.patch
+disable_blosc.patch
+fix_alignment.patch
diff -Nru pytables-2.3.1/debian/rules pytables-2.3.1/debian/rules
--- pytables-2.3.1/debian/rules 2012-01-28 12:50:35.000000000 +0100
+++ pytables-2.3.1/debian/rules 2012-03-03 12:26:47.000000000 +0100
@@ -43,7 +43,7 @@
set -e; \
for v in $(PYVERS); do \
cd "$(CURDIR)/debian/tmp/usr/lib/python$$v/dist-packages/"; \
- env PYTHONPATH=. python$$v tables/tests/test_all.py; \
+ env PYTHONPATH=. python$$v tables/tests/test_all.py -vvv; \
done
endif
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