Fix compilation against glbc-2.1.4 (changed declaration of type for __malloc_initiali...

Package-Manager: portage-2.2.0_alpha77/cvs/Linux x86_64

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index b8367ea398597d528ae455e717491eefa23c49c1..b00919e4ef5f85bd1ec0a3784289749df5b4f906 100644 (file)
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/ncbi-tools++
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ChangeLog,v 1.21 2011/09/23 09:43:25 polynomial-c Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ChangeLog,v 1.22 2011/11/24 09:12:21 jlec Exp $
+
+  24 Nov 2011; Justin Lecher <jlec@gentoo.org>
+  ncbi-tools++-2010.06.15-r1.ebuild,
+  +files/ncbi-tools++-2010.06.15-glibc-214.patch:
+  Fix compilation against glbc-2.1.4 (changed declaration of type for
+  __malloc_initialize_hook from void to volatile
 
   23 Sep 2011; Lars Wendler <polynomial-c@gentoo.org>
   ncbi-tools++-2010.06.15-r1.ebuild,

diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest
index 7cc34f40eb6387f65bcabf03c076b75f70a3e00f..ae307db5a817f6a81f74d294da5a8322e62992f4 100644 (file)
--- a/sci-biology/ncbi-tools++/Manifest
+++ b/sci-biology/ncbi-tools++/Manifest
@@ -4,27 +4,18 @@ Hash: SHA512
 AUX ncbi-tools++-2009.05.15-asneeded.patch 3620 RMD160 393db694f0824b0d47571e3b64250b8398c33e58 SHA1 541f00f4d2170d9bb4721468f1c350dcc92552bb SHA256 71a4b2040417a9bfaa7254b5c6668d09ec69f5836a372f1b2bbc938f41ff7657
 AUX ncbi-tools++-2009.05.15-gcc44.patch 554 RMD160 57a23cbaad59b6011124f684db55f4ac2e4a43ab SHA1 7ed63addba554bf87a347d25ea2d4ea6b6552a1a SHA256 ddc2379ff636851e1bb4fb601930ee926c396819e06812b1ba76da001255d5c6
 AUX ncbi-tools++-2010.06.15-gcc46.patch 2304 RMD160 bec40073066b10a3ca95f5a125dccab2110eaaf4 SHA1 ff0675b263ba7f9f5e7abd33544e9b2fc88ff11b SHA256 ef20fbecab4c7223dd52855015b8cceed2599120ee0d99cf1dfbdb347725a199
+AUX ncbi-tools++-2010.06.15-glibc-214.patch 836 RMD160 62d84a8569dd3f189be69a307b25b323f7e0e376 SHA1 cb7cdae15c35d301aaccbcdc9d2b3f2656a640f2 SHA256 e8a6054fef2a25c594f626e773a990c9399a17210f1fee4ddcdc7e181ac8d6d8
 AUX ncbi-tools++-2010.06.15-libpng15.patch 1241 RMD160 3e8e55bd4ad309a7eda3517a36196d6a9ae4653e SHA1 8fcdd288fa5e4713331acbeb2dae580d277551fd SHA256 123e85198251ea21230f8afea0cc12b4aaa04adc9f4e1d421b3c14811c4b8f53
 DIST ncbi-tools++-2010.06.15-asneeded.patch.xz 4948 RMD160 ee82d427be00e029066126898db44d76bc2cbe0d SHA1 71cef7198fcd52eca16cb76ae7f8abd084cbd437 SHA256 8a39b46e1ef6ddae57151c3ffbb7da952e4cb6eea0f76a4ac74de981d88cb873
 DIST ncbi_cxx--Jun_15_2010.tar.gz 17297248 RMD160 35e2ffbe2f37856eb4368e7e98c48c2721848060 SHA1 43c007fb6b3a72389ca33e884c6abd7ad27dbbd0 SHA256 eb24230a9afe9bcf3c52aa6d5d9545dca04649a2569a1bb832ace54aec9d3c54
-EBUILD ncbi-tools++-2010.06.15-r1.ebuild 1877 RMD160 7992e916136493b3011b5dc520e5d84ca87db672 SHA1 9103cacde3683fe650b2bca1f98c540b9199a336 SHA256 10fae4b0802438cc23b8de9b146692c5493b00eae4a61537a434058c1eb3a33d
+EBUILD ncbi-tools++-2010.06.15-r1.ebuild 1908 RMD160 b0b9cdc80ce8edc0679231d753e96e14fdf7f7ed SHA1 4a6bcb9a09555d1918570f73aa78ed6e6dcde6d7 SHA256 19ff31f98df9b5a3cc42d345f7927b37ad716413b11af8870cea826f256e0563
 EBUILD ncbi-tools++-2010.06.15.ebuild 1653 RMD160 6653b7ca063cd7abaaa2a1ccba6a2fc4a0cae841 SHA1 0f93842404e562a127179db6ab52ea7f84c38801 SHA256 06b52157803e3f3c7c8bc78d875c26828ff94b514d7fe651ff67999b29e24c43
-MISC ChangeLog 4155 RMD160 78addba391bb217a4d93c0bf6f4b933126abf650 SHA1 66ac882154b9d024cb146ecb30109e17fbc757df SHA256 57ead376b38cf3bd682370cffd721f1cb06edbef6d95f243b2b93e8159a734bb
+MISC ChangeLog 4401 RMD160 c8ddc2a66eff8b2241c9b1bd0cad9255c981a212 SHA1 9ffb5de66600a3f7bd888a8feabe125b404e28ef SHA256 ad9516b763573fdd13324a5b24fb61b1eb2722b7019afdc276b649b56ab31f33
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-glibc-214.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-glibc-214.patch
new file mode 100644 (file)
index 0000000..2275cde
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-glibc-214.patch
@@ -0,0 +1,22 @@
+ src/app/netcache/nc_memory.cpp |    8 +++++++-
+ 1 files changed, 7 insertions(+), 1 deletions(-)
+
+diff --git a/src/app/netcache/nc_memory.cpp b/src/app/netcache/nc_memory.cpp
+index bb602ee..468b44d 100644
+--- a/src/app/netcache/nc_memory.cpp
++++ b/src/app/netcache/nc_memory.cpp
+@@ -3329,7 +3329,13 @@ void s_NCInitMallocHook(void)
+     __free_hook    = s_NCFreeHook;
+ }
+ 
+-void (*__malloc_initialize_hook) (void) = s_NCInitMallocHook;
++/* GNU libc 2.14 defines this macro to declare hook variables as volatile.
++   Define it as empty for older libc versions.  */
++#ifndef __MALLOC_HOOK_VOLATILE
++# define __MALLOC_HOOK_VOLATILE
++#endif
++
++void (*__MALLOC_HOOK_VOLATILE __malloc_initialize_hook) (void) = s_NCInitMallocHook;
+ 
+ #elif !defined(NCBI_OS_MSWIN)
+ // Changing of C library allocation functions on Windows is very tricky (if

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild
index 2b5a6cd58f3cd89a8244b892117fe8d4e54194ed..3c395d397c4ac76315c2bc0f48ec2cf5c30ec91c 100644 (file)
--- a/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.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-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild,v 1.3 2011/09/23 09:43:25 polynomial-c Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild,v 1.4 2011/11/24 09:12:21 jlec Exp $
 
 EAPI="3"
 
@@ -37,7 +37,8 @@ src_prepare() {
        epatch \
                "${FILESDIR}"/${P}-gcc46.patch \
                "${WORKDIR}"/${P}-asneeded.patch \
-               "${FILESDIR}"/${P}-libpng15.patch
+               "${FILESDIR}"/${P}-libpng15.patch \
+               "${FILESDIR}"/${P}-glibc-214.patch
 }
 
 src_configure() {