From df16b5637477cfa861db3608016cc2f1fa118020 Mon Sep 17 00:00:00 2001 From: Kacper Kowalik Date: Mon, 21 Nov 2011 17:33:09 +0000 Subject: [PATCH] Fix implicits and array out of bounds Package-Manager: portage-2.2.0_alpha75/cvs/Linux x86_64 --- sci-libs/hdf5/ChangeLog | 7 +- sci-libs/hdf5/Manifest | 32 +++---- .../hdf5/files/hdf5-1.8.8-array_bounds.patch | 22 +++++ .../hdf5/files/hdf5-1.8.8-implicits.patch | 85 +++++++++++++++++++ sci-libs/hdf5/hdf5-1.8.8.ebuild | 6 +- 5 files changed, 134 insertions(+), 18 deletions(-) create mode 100644 sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch create mode 100644 sci-libs/hdf5/files/hdf5-1.8.8-implicits.patch diff --git a/sci-libs/hdf5/ChangeLog b/sci-libs/hdf5/ChangeLog index 115613f1a475..68ec612baf02 100644 --- 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 + +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 799417ef3f34..1701c9127bec 100644 --- 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.18 (GNU/Linux) -iQIcBAEBCAAGBQJOxPvjAAoJEF0huFKJUZL5k+wP/001mXTV4lhTFRiKU/3z892B -fY3rotP2oeEk5Qr4AB30NL8Gi93jZcLxWq5RrHXYf7KhsEQGaLm//SIKW5mo7RFC -qrkr1ODDg7NsMhKt/xYwFsSTAycDSJW3eaqXTRLa/C64HRwisP0rH5GiBaw0M3gQ -Bh48DXQDxg3fbVtfubMd3JyQ6wVvDiOQmwWaVGcJP02s4cd0VU1HXdwl8D+JwZ9G -1Q4A1t0ODMdYkFsaqFi4GYMgLzEBB2YMST4SgNuDjW4ZsZ9LibrKF6/9WSq92PN6 -8tuUYg7hUAifTkFxJtx1ekBKWGOM16I4lDg4zG3LJzGPIEeFsVB0nZCI03x3Z3Wd -QG+79q/jzn7SmSqvRccXzauLIdMjLNYIcC1FbsNtALed6N+YzWirSZmhQARofWyU -qF8CbTRrPPpgd8T2Op9Cqcdq0ZqWuUUbJtWDF/qx7OLvQVYSKDnNkMALrPjoQ5so -LtAUmUAoYFeM5idYsHzkifdqBqjRy++m7ml6z67bxF5fuliCnDOAm/SUiJxaxnUh -bdpb8JvpG/A+qyXfbWFbX4vPrvOV+fP5eucFLSwMOJiCU3+6AMEMsATZQ1Wt2PnZ -mrVTPdYy1j4FbAUwt0GUf5aO3e8TSi/UnnlkgOFZ50d66I4Tq84OjFScF0D+FBBz -Pp0RjdOiZKv8BjhkQM9+ -=7efn +iQIcBAEBCAAGBQJOyotfAAoJEF0huFKJUZL5KO0QAI68Fo2MPakK7IOcaGBmH9EX +t2PSytvxQIrOlWfxYeMqxgMTd/D2HbfQoHbvqcNYygU9qI9MzAMuejchBPpe1mxu +NGBvrDqEkh93qokoluc8VmThxluQj8N10RWXYbeCEzR0/GwxF43ZGyifP+iRrdjD +BHnzYRlPzHZ7sbzjEomt2OffKSlyuD3P3PVwpiudT61G1kjBmy3RxIlTD+o2lBSF +llEPo/eivhWNyIe8WW0zRzEQYJNavi71W94nIICNQQpQ1uGTTvjq3hAAsB25L4uY +5xjCELqZxYBLi5Qhbo5GM/TGlmW08yX2Dgk1PJGwTRuGEP65FKF1BaFjJDGJydqG +mIWnHAZDOO7Z+OZATqHeCc4TZ0NOXFiaJ9nptPzoN2EFFwbhSe+wr5YiCPw/jZJy +nxXzLVro5sD+o1xW5kOOGG+62+0iPqAuiyIeBnmPD6sAecRiGBTlvxfPzRp4Mjyo +qpSNxzc3BhAF4I1ZsTD5JxdUwTa4ail+wLTE5oPWOsuGXrckEFNwFsZlI3K3rplg +/aBKynwCF6Cjamr2h0AnMpo2+465Dx3/dg+5M0cdGIkdI0VNfyvIKkBx1ceJWwvx +vtSRP67K/Y1Jl75HAa/hvTgONyi/dsM86KbZFxujVBfcuFFpih3R5DWm+lekPMGj +9uyvFzGLB+lHzEpieGnt +=xNCQ -----END PGP SIGNATURE----- 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 index 000000000000..042d012d1621 --- /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 index 000000000000..d1217e83a989 --- /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 ++#include "H5pubconf.h" + #ifdef H5_HAVE_UNISTD_H + #include + #endif + diff --git a/sci-libs/hdf5/hdf5-1.8.8.ebuild b/sci-libs/hdf5/hdf5-1.8.8.ebuild index 3310cb052610..abf3331123e7 100644 --- 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" \ -- 2.26.2