Fix implicits and array out of bounds

Package-Manager: portage-2.2.0_alpha75/cvs/Linux x86_64

diff --git a/sci-libs/hdf5/ChangeLog b/sci-libs/hdf5/ChangeLog
index 115613f1a475bdbcc3451230d78d3ed06d0181cc..68ec612baf02b69bca2b0c6ce18602b7e36aafe5 100644 (file)
--- a/sci-libs/hdf5/ChangeLog
+++ b/sci-libs/hdf5/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-libs/hdf5
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/ChangeLog,v 1.76 2011/11/17 12:19:37 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/ChangeLog,v 1.77 2011/11/21 17:33:09 xarthisius Exp $
+
+  21 Nov 2011; Kacper Kowalik <xarthisius@gentoo.org>
+  +files/hdf5-1.8.8-array_bounds.patch, +files/hdf5-1.8.8-implicits.patch,
+  hdf5-1.8.8.ebuild:
+  Fix implicits and array out of bounds
 
 *hdf5-1.8.8 (17 Nov 2011)
 

diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest
index 799417ef3f34c5fe65c284a238d6c41fcfccb2ba..1701c9127bec4462685c551bb58188fbde62f690 100644 (file)
--- a/sci-libs/hdf5/Manifest
+++ b/sci-libs/hdf5/Manifest
@@ -9,30 +9,32 @@ AUX hdf5-1.8.4-scaleoffset.patch 1098 RMD160 4983755ff2d284c73f8479cbf11a19b1bf4
 AUX hdf5-1.8.4-sigbus.patch 779 RMD160 ba4c92e0ba5ef95b1459d4b570d9113acbc65613 SHA1 3fc4c90ac42b9a59f26a459e6faf6f7410b87a9a SHA256 69c0ef464d99b6c2bd3a959b8210e7772a662054b481bed7775ec21c731bf106
 AUX hdf5-1.8.5-implicits.patch 1782 RMD160 968ff2c36606ca85644e23200d90bb566b67a418 SHA1 eda61db0fafdc738db992fc055a9ad9626743872 SHA256 cd352f026daabba1c1a17725ebbc21a59015d3103697fd6e1181ea1998c07bb3
 AUX hdf5-1.8.5-noreturn.patch 1477 RMD160 52c0e72b78b00effe3337f6016f716b425d29f03 SHA1 88eee2a0bb02512795a61f0ceb9d54f8df454e31 SHA256 7278c504b0e252ea5d0a9d7de5b332f0f1c0981a441efb286864b9599790c0b2
+AUX hdf5-1.8.8-array_bounds.patch 624 RMD160 cdbda024424e3eb6a08fd6bc226a28a1da5b9c8e SHA1 0b818c8aa78b54a82e9089ed22b77cec1653d628 SHA256 849df1a9fed1d6225b0032507294fbd4eec13f7514e1175907f2c9c00aafb48c
 AUX hdf5-1.8.8-buildsystem.patch 1410 RMD160 a88c63145bf088b018d4dcf327415938d467914e SHA1 f8a48e3602967ef15ceabab9ad499a8f6b3aa009 SHA256 a97a7a82197eb4f3c9d43836f24c2c2ae14962970a0b680e5305a977b8c611a5
+AUX hdf5-1.8.8-implicits.patch 2005 RMD160 3eb7faffe476dec3f3cf49be0d285fef3c43fd2f SHA1 842fa0e605ba6ba5fa6c3134902c192c64584b13 SHA256 1fec9a12f20f28484a9047e39b4bb56694af394d9e591abf442046aed96d4b5c
 AUX mpd.conf 48 RMD160 289de9bb40759e3f71229cf47e4d2af83703a85f SHA1 244eee76dbf4ff269e4489d5cc7c3577c6c1fa6b SHA256 ae740cacaf2cb798921cb2092f5af98de67445e27af3f88858f3e6d2bbb127f4
 DIST hdf5-1.8.4.tar.gz 7181176 RMD160 e448e2326b55aa89ff0bd7488cd4291d6c5485ee SHA1 37877e29c49a6af3e23aa9ad798ef12b8ba1c05c SHA256 a992fce9387a17f175b3b188dc2a42f545a3057aeb141beb3fc3361c7521f465
 DIST hdf5-1.8.7.tar.bz2 5710170 RMD160 34641bf8e664c3b3382d1346a65e2f5c3eb485ee SHA1 be1daff26f066aca0b5be52d86dada6757fc4b95 SHA256 771761c9bec30b9a4137fa59ef88fdafdb0f4f35d1db0fd655f2591d19570fec
 DIST hdf5-1.8.8.tar.bz2 5827394 RMD160 077580c9828747473836cc39f8cb3fd4e5e045d9 SHA1 1bc16883ecd631840b70857bea637a06eb0155da SHA256 b0ebb0b5478c6c0427631d4ad08f96e39f1b09fde615aa98d2a1b8fb7f6dced3
 EBUILD hdf5-1.8.4-r1.ebuild 3134 RMD160 6dfc52e18b8d0005560f6c543b9641daeb20a11e SHA1 9f01a942144e3a1cdf8d9eea9b3e3620cd180892 SHA256 89aa8ed18e2d68e4c55d8f24c0db221f6e3f13d056f4f14eb29016dffddcdda7
 EBUILD hdf5-1.8.7.ebuild 3150 RMD160 dd97bcfbd37b1a8ccc58b68f132924524ef48ad7 SHA1 8be1115834e11ebead352ca696b95739709ff5d5 SHA256 64352ffb1767130ba79d14c6a4ba89b5a37065c7f9e09a2c282e4dc0298c1314
-EBUILD hdf5-1.8.8.ebuild 3099 RMD160 7b17f388bcee774a374f371e6b3fcf981ce8b7e4 SHA1 ed38932cd77076e542bb8761d6f357210e6d5f38 SHA256 2e10b20a0680627186f2678ef2f72570542dce52cb12d54a79752cb011efddb3
-MISC ChangeLog 15411 RMD160 b6f8bfe9bc9fa4dacaba695e91e2c3120a4f27f0 SHA1 eab434b6cf89e13d6a59e218b546d370c17933e4 SHA256 f3951dea5dc19857f46a9598e2406121d79d464d093b1ecc25e5ce822852f86b
+EBUILD hdf5-1.8.8.ebuild 3180 RMD160 dc1dfe7b23de81179bd9f42002a6d994667c2621 SHA1 39fbbb5cace946d6f0d972de8af899c4c6d8cc13 SHA256 f55fc3bd5d11e37df8635a9ee9a7b7eac07b3c9f5b1666f9409adf1bfd867b1f
+MISC ChangeLog 15602 RMD160 695be9fa15ee6609c0e663fa3ade7fe324ee0bf8 SHA1 2abf4c2339a7c2751c575c362955afc6b66faf46 SHA256 52a1e551b193445704f86ed9e73c2c9e7a26d0a6a595700191e524172c399314
 MISC metadata.xml 728 RMD160 3863f8962e54ddbd28c78256e03feedc571148a7 SHA1 f4ac101d9b30cca655a89a87185364dd4a24816b SHA256 1a503997c6e2248b43a36eccd2c09337a0e02b498926b4430b9d8df059e638ba
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diff --git a/sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch b/sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch
new file mode 100644 (file)
index 0000000..042d012
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch
@@ -0,0 +1,22 @@
+--- a/perform/pio_engine.c
++++ b/perform/pio_engine.c
+@@ -454,7 +454,7 @@
+         subdir = (user ? user : login);
+ 
+         if (subdir) {
+-            for (i = 0; i < size && prefix[i]; i++)
++            for (i = 0; i < size-1 && prefix[i]; i++)
+                 fullname[i] = prefix[i];
+ 
+             fullname[i++] = '/';
+--- a/perform/sio_engine.c
++++ b/perform/sio_engine.c
+@@ -353,7 +353,7 @@
+     subdir = (user ? user : login);
+ 
+     if (subdir) {
+-        for (i = 0; i < size && prefix[i]; i++)
++        for (i = 0; i < size-1 && prefix[i]; i++)
+         fullname[i] = prefix[i];
+ 
+         fullname[i++] = '/';

diff --git a/sci-libs/hdf5/files/hdf5-1.8.8-implicits.patch b/sci-libs/hdf5/files/hdf5-1.8.8-implicits.patch
new file mode 100644 (file)
index 0000000..d1217e8
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.8.8-implicits.patch
@@ -0,0 +1,85 @@
+--- b/configure.in
++++ a/configure.in
+@@ -1499,6 +1499,9 @@
+     dnl though we do not do this as it breaks the big test on older versions
+     dnl of linux (CentOS 4.6) using newer versions of gcc (4.6.2).
+     AM_CPPFLAGS="-D_BSD_SOURCE $AM_CPPFLAGS"
++
++    dnl _GNU_SOURCE is needed for vasprintf
++    AM_CPPFLAGS="-D_GNU_SOURCE $AM_CPPFLAGS"
+     ;;
+ esac
+ 
+--- a/test/cache_common.h
++++ b/test/cache_common.h
+@@ -702,5 +702,9 @@
+                          hbool_t compare_init,
+                          int test_num);
+ 
++hbool_t resize_configs_are_equal(const H5C_auto_size_ctl_t *a,
++                                 const H5C_auto_size_ctl_t *b,
++                                 hbool_t compare_init);
++
+ #endif /* _CACHE_COMMON_H */
+ 
+--- a/tools/misc/talign.c
++++ b/tools/misc/talign.c
+@@ -23,6 +23,7 @@
+ 
+ #include "hdf5.h"
+ #include "H5private.h"
++#include "h5tools.h"
+ 
+ const char *fname = "talign.h5";
+ const char *setname = "align";
+--- a/tools/h5repack/testh5repack_detect_szip.c
++++ b/tools/h5repack/testh5repack_detect_szip.c
+@@ -17,6 +17,7 @@
+ #include "h5repack.h"
+ #include "h5tools.h"
+ #include "h5test.h"
++#include "h5tools_utils.h"
+ 
+ 
+ /* Name of tool */
+--- a/tools/h5jam/h5jam.c
++++ b/tools/h5jam/h5jam.c
+@@ -15,6 +15,7 @@
+ 
+ #include "hdf5.h"
+ #include "H5private.h"
++#include "h5tools.h"
+ #include "h5tools_utils.h"
+ 
+ /* Name of tool */
+--- a/tools/h5jam/h5unjam.c
++++ b/tools/h5jam/h5unjam.c
+@@ -15,6 +15,7 @@
+ 
+ #include "hdf5.h"
+ #include "H5private.h"
++#include "h5tools.h"
+ #include "h5tools_utils.h"
+ 
+ /* Name of tool */
+--- a/tools/h5copy/h5copygentest.c
++++ b/tools/h5copy/h5copygentest.c
+@@ -20,6 +20,7 @@
+ #include "hdf5.h"
+ #include "H5private.h"
+ #include "h5tools.h"
++#include "h5tools_utils.h"
+ 
+ /* Name of tool */
+ #define PROGRAMNAME "h5copygentest"
+--- a/hl/src/H5LTanalyze.c
++++ b/hl/src/H5LTanalyze.c
+@@ -49,7 +49,8 @@
+ #define YY_FLEX_MINOR_VERSION 5
+ 
+ #include <stdio.h>
++#include "H5pubconf.h"
+ #ifdef H5_HAVE_UNISTD_H
+ #include <unistd.h>
+ #endif
+ 

diff --git a/sci-libs/hdf5/hdf5-1.8.8.ebuild b/sci-libs/hdf5/hdf5-1.8.8.ebuild
index 3310cb052610bc89edb575f68732544205534be5..abf3331123e7458b4f1c4c607e7e147b2f0b830e 100644 (file)
--- a/sci-libs/hdf5/hdf5-1.8.8.ebuild
+++ b/sci-libs/hdf5/hdf5-1.8.8.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.8.8.ebuild,v 1.1 2011/11/17 12:19:37 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.8.8.ebuild,v 1.2 2011/11/21 17:33:09 xarthisius Exp $
 
 EAPI=4
 
@@ -48,7 +48,9 @@ pkg_setup() {
 }
 
 src_prepare() {
-       epatch "${FILESDIR}"/${P}-buildsystem.patch
+       epatch "${FILESDIR}"/${P}-buildsystem.patch \
+               "${FILESDIR}"/${P}-array_bounds.patch \
+               "${FILESDIR}"/${P}-implicits.patch
        # respect gentoo examples directory
        sed \
                -e "s:hdf5_examples:doc/${PF}/examples:g" \