diff options
Diffstat (limited to 'gnu/packages/patches')
| -rw-r--r-- | gnu/packages/patches/hmmer-remove-cpu-specificity.patch | 22 | ||||
| -rw-r--r-- | gnu/packages/patches/python-pandas-skip-failing-tests.patch | 44 | ||||
| -rw-r--r-- | gnu/packages/patches/wget-CVE-2017-6508.patch | 45 |
3 files changed, 84 insertions, 27 deletions
diff --git a/gnu/packages/patches/hmmer-remove-cpu-specificity.patch b/gnu/packages/patches/hmmer-remove-cpu-specificity.patch new file mode 100644 index 0000000000..ba98db4d0e --- /dev/null +++ b/gnu/packages/patches/hmmer-remove-cpu-specificity.patch @@ -0,0 +1,22 @@ +This patch removes compilation flags which make the build for the machine +where compilation takes place, rendering the build not reproducible. + +diff --git a/configure b/configure +index 8b6aaef..49a6afc 100755 +--- a/configure ++++ b/configure +@@ -6125,14 +6125,6 @@ fi # guess arch + + if test "x$ax_gcc_arch" != x -a "x$ax_gcc_arch" != xno; then + for arch in $ax_gcc_arch; do +- if test "x$acx_maxopt_portable" = xyes; then # if we require portable code +- flags="-mtune=$arch" +- # -mcpu=$arch and m$arch generate nonportable code on every arch except +- # x86. And some other arches (e.g. Alpha) don't accept -mtune. Grrr. +- case $host_cpu in i*86|x86_64*) flags="$flags -mcpu=$arch -m$arch";; esac +- else +- flags="-march=$arch -mcpu=$arch -m$arch" +- fi + for flag in $flags; do + as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$flag" | $as_tr_sh` + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts $flag" >&5 diff --git a/gnu/packages/patches/python-pandas-skip-failing-tests.patch b/gnu/packages/patches/python-pandas-skip-failing-tests.patch index 31fc912d00..8ac330c18f 100644 --- a/gnu/packages/patches/python-pandas-skip-failing-tests.patch +++ b/gnu/packages/patches/python-pandas-skip-failing-tests.patch @@ -2,39 +2,29 @@ These tests fail on 32bit architectures. Upstream bug URL: https://github.com/pandas-dev/pandas/issues/14866 ---- a/pandas/tests/test_base.py 2017-03-08 17:49:44.422282717 +0100 -+++ b/pandas/tests/test_base.py 2017-03-08 17:50:59.476701799 +0100 -@@ -363,30 +363,6 @@ - self.assertFalse(result.iat[0]) - self.assertFalse(result.iat[1]) +--- a/pandas/tests/indexes/common.py 2017-03-09 00:10:26.063996176 +0100 ++++ b/pandas/tests/indexes/common.py 2017-03-09 00:10:53.152844191 +0100 +@@ -119,20 +119,6 @@ + with tm.assertRaisesRegexp(ValueError, 'Invalid fill method'): + idx.get_indexer(idx, method='invalid') - def test_ndarray_compat_properties(self): - -- for o in self.objs: +- idx = self.create_index() +- self.assertTrue(idx.T.equals(idx)) +- self.assertTrue(idx.transpose().equals(idx)) - -- # check that we work -- for p in ['shape', 'dtype', 'flags', 'T', 'strides', 'itemsize', -- 'nbytes']: -- self.assertIsNotNone(getattr(o, p, None)) -- self.assertTrue(hasattr(o, 'base')) +- values = idx.values +- for prop in self._compat_props: +- self.assertEqual(getattr(idx, prop), getattr(values, prop)) - -- # if we have a datetimelike dtype then needs a view to work -- # but the user is responsible for that -- try: -- self.assertIsNotNone(o.data) -- except ValueError: -- pass +- # test for validity +- idx.nbytes +- idx.values.nbytes - -- self.assertRaises(ValueError, o.item) # len > 1 -- self.assertEqual(o.ndim, 1) -- self.assertEqual(o.size, len(o)) -- -- self.assertEqual(Index([1]).item(), 1) -- self.assertEqual(Series([1]).item(), 1) -- - def test_ops(self): - for op in ['max', 'min']: - for o in self.objs: + def test_repr_roundtrip(self): + + idx = self.create_index() --- a/pandas/tools/tests/test_tile.py 2017-03-08 17:47:39.762261841 +0100 +++ b/pandas/tools/tests/test_tile.py 2017-03-08 17:48:26.831780495 +0100 @@ -271,19 +271,6 @@ diff --git a/gnu/packages/patches/wget-CVE-2017-6508.patch b/gnu/packages/patches/wget-CVE-2017-6508.patch new file mode 100644 index 0000000000..0218fceaad --- /dev/null +++ b/gnu/packages/patches/wget-CVE-2017-6508.patch @@ -0,0 +1,45 @@ +Fix CVE-2017-6508: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-6508 + +Patch copied from upstream source repository: + +https://git.savannah.gnu.org/cgit/wget.git/commit/?id=4d729e322fae359a1aefaafec1144764a54e8ad4 + +From 4d729e322fae359a1aefaafec1144764a54e8ad4 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Tim=20R=C3=BChsen?= <tim.ruehsen@gmx.de> +Date: Mon, 6 Mar 2017 10:04:22 +0100 +Subject: [PATCH] Fix CRLF injection in Wget host part + +* src/url.c (url_parse): Reject control characters in host part of URL + +Reported-by: Orange Tsai +--- + src/url.c | 11 +++++++++++ + 1 file changed, 11 insertions(+) + +diff --git a/src/url.c b/src/url.c +index 8f8ff0b8..7d36b27d 100644 +--- a/src/url.c ++++ b/src/url.c +@@ -925,6 +925,17 @@ url_parse (const char *url, int *error, struct iri *iri, bool percent_encode) + url_unescape (u->host); + host_modified = true; + ++ /* check for invalid control characters in host name */ ++ for (p = u->host; *p; p++) ++ { ++ if (c_iscntrl(*p)) ++ { ++ url_free(u); ++ error_code = PE_INVALID_HOST_NAME; ++ goto error; ++ } ++ } ++ + /* Apply IDNA regardless of iri->utf8_encode status */ + if (opt.enable_iri && iri) + { +-- +2.12.0 + |