coot -- fixes for gcc4.4 and glibc-2.10

9 files changed, 48 insertions, 132 deletions

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 071d9e18d..6a3089a30 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  -coot-0.6_pre1-r2041.ebuild, coot-0.6_pre1-r2042.ebuild,
+  +files/0.5.2-gcc-4.4.patch, +files/0.6_pre1-gcc4.4.patch,
+  coot-9999.ebuild, +files/9999-gcc4.4.patch, coot-0.5.2.ebuild:
+  fixes for gcc4.4 and glibc-2.10
+
 *coot-9999 (08 Jun 2009)
 
   08 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index 8e17d895f..20e651f5f 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -1,7 +1,10 @@
 AUX 0.5.2-as-needed.patch 19562 RMD160 7c242801251cbd11a8143df793a832a860c5aacb SHA1 a7d6552e5a3bbdf4e28ac995a31b3c3059241dab SHA256 9f5be12beb7691eb1e187923b95edc5890e385fecb2ef2ecb5eb9991858bebc1
 AUX 0.5.2-gcc-4.3.patch 260 RMD160 e6d72c24d7dc02e84c67198f3e82aa4215df9b77 SHA1 1dd99a49d35181808a9e30a1f41ab63b6077dda0 SHA256 2d215b8009449e2f234eeb6c1e08da1f2e7804fedcf5e1d69997a6d8355d37da
+AUX 0.5.2-gcc-4.4.patch 257 RMD160 d1ec251cda36ac201a8baa84d7dad542e72e0c7b SHA1 069af29c1de34e6af94ff463ca04e3fb3c19c209 SHA256 761db5b8cb4cc11050b833df1f87b9ea5d9ca8b3637d7e7b1f5b4f6b7d795177
 AUX 0.6_pre1-as-needed.patch 19465 RMD160 7bb47b98e929f7219cbe82d415dd94d27369ecdb SHA1 76aec121e7f3454cd38d5e3a1fb87126e15537f6 SHA256 d374ae451805701c08c9872e7a73f51062e75ae61cbf5cee6af2d9a6f64232d0
+AUX 0.6_pre1-gcc4.4.patch 257 RMD160 d1ec251cda36ac201a8baa84d7dad542e72e0c7b SHA1 069af29c1de34e6af94ff463ca04e3fb3c19c209 SHA256 761db5b8cb4cc11050b833df1f87b9ea5d9ca8b3637d7e7b1f5b4f6b7d795177
 AUX 9999-as-needed.patch 19465 RMD160 7bb47b98e929f7219cbe82d415dd94d27369ecdb SHA1 76aec121e7f3454cd38d5e3a1fb87126e15537f6 SHA256 d374ae451805701c08c9872e7a73f51062e75ae61cbf5cee6af2d9a6f64232d0
+AUX 9999-gcc4.4.patch 299 RMD160 75374bd38981d4383d926a3b6529ef955a18e893 SHA1 e05d1caeb3dd13d101d417e7f2613402b6712005 SHA256 02c18e695086d70152b923af5d0aecd334bc18f1b6b955d3133c2ae7b6f218af
 AUX fix-namespace-error.patch 1081 RMD160 ebecd51b87c39dc2c37e565f18fc88b7aa837d05 SHA1 f732df5f4795e728bdf217aac9c9f53952e2890c SHA256 fd271dd22eec5725fcbd20c68b57008eed0f435d1e0ac212fbfd389a0a970beb
 AUX glib.m4 8444 RMD160 f3f4b2987796f16d17758f2af3459279351d6f2c SHA1 201eb58c2b3f3c5395dacd3913a4fb9d950d3276 SHA256 ada4a0a46bd00eda39afe77f675b721f60cd20c0080170848f4d7e92b4ba4dc8
 AUX gtk.m4 8516 RMD160 3860fe211902d5b9290f0a70e7d75ebec6b0ec67 SHA1 98b93b820423a52ebd80e3f1822a8f2bd4b3f15d SHA256 4eb6e0bb2c6863139d1fb4ca2d1d0f0ef07e3a85fdbb5ba98d03373f610f0c37
@@ -9,11 +12,9 @@ AUX gtkgl.m4 1137 RMD160 9f9712aeaa4efaf07a8c1c483abd4098ac823ef7 SHA1 f7bb50edc
 AUX imlib.m4 11371 RMD160 4470d0cf2d0f8298bea6565069acda8a44e1cd9d SHA1 c983c372cb6cca546bb3fd739f68199a94a741c8 SHA256 04fcea84564608fff1b8049170f4dd571e9b30723c29c46e31855fab26b84a91
 AUX link-against-guile-gtk-properly.patch 800 RMD160 4215ea41c02e7db2c04dda191e0200cc1704d43c SHA1 5bd24ab8c651a147076289098956f545c6e431d6 SHA256 7805cdf4e34c532899a8c37eb19664fc95fc8bc440e770db7c87373a94e1fb2d
 DIST coot-0.5.2.tar.gz 10160364 RMD160 5cee5e8da6e4d2ce06016f6f8935b395e65ddbf9 SHA1 041cc947a68296701deb153c0932ee20a3437323 SHA256 6245f85dfb796ee7f3488c0790531f8d5e29a9f6ea18411ae539e3993e4ed2d6
-DIST coot-0.6-pre-1-revision-2041.tar.gz 10888604 RMD160 8cadfeba306aac8ebe16502d1a1f1de8ed0b2840 SHA1 bfc5a8540cc91851767be4ea8c39fff633eef7ed SHA256 63e47a7f1030d52ce63a46751d931594bd20051cbb3d391d34c0a905b195e010
 DIST coot-0.6-pre-1-revision-2042.tar.gz 10888679 RMD160 25fa2990351b13fb94d1a070d6310c1e0191ce2f SHA1 f21a24f55c0e99ba12b9cacf7e7e1908a9f3a7ab SHA256 bef648ac407b900af3383f63a138ddbdff96695542633b1ed88b5947e38a03e5
-EBUILD coot-0.5.2.ebuild 3193 RMD160 3e74d8b08a4042bb216cc20c72fe276de8d5e47c SHA1 a33e0396a8046ac48ec226cd5aa9ea3f57baba10 SHA256 d24848498dd19a2cda184ddd5e4278d80f5679e854279db639703aca5cfe1aa6
-EBUILD coot-0.6_pre1-r2041.ebuild 3246 RMD160 f5700bf0e09defe1a11a01faf871ff1c4bc88832 SHA1 a9396e0ca895b431ea8fca36058cb966f381ad96 SHA256 1726f17f68e6aa05abc50e30463b24c7b069b3ffd243a115fc27a8626bb69ed1
-EBUILD coot-0.6_pre1-r2042.ebuild 2867 RMD160 813a05ce3850b58bef0672b59298de5c514e5dca SHA1 e009f3b9f107c377543410d28beec5678fbb9941 SHA256 56abe4ede7b94331246dd52f154edcd9c415bc0d1d74f148f8c066b139c1b3a3
-EBUILD coot-9999.ebuild 3057 RMD160 e69d835f3bfa30cd8e6968dbe97bbd363e71552f SHA1 ffe756c480822b79e1722bd19bcd89ed819cd2ff SHA256 2786aeddd713bdcb3bef9dc690ee510a7f1a0ff97b531e969ca9d47e56fba706
-MISC ChangeLog 4276 RMD160 f89aeeb1b110de72b51417e26dcffa81598c178e SHA1 8032afc6c7925a0781c96079eaf17c5750d9e5bd SHA256 440f667eb7bd1bf00af93ef9017148ce971c2c95cc8088804c68f608d9cf6198
+EBUILD coot-0.5.2.ebuild 3234 RMD160 61dd2c58155350889e8120b0f7fe9361daf3aa7b SHA1 0ee99faaafc1c349569fb71342c8269732430c30 SHA256 b6a5ff0fdee3afa51befde1849cbb55bc9212067e43b88a37b3b82f9cbb10edf
+EBUILD coot-0.6_pre1-r2042.ebuild 2901 RMD160 f822c42328b42dcf6a07f5ee08809d9f6e237853 SHA1 76779628a94b71d90c824ace661c22715b15075b SHA256 5ca5ea32aca7f754fa8ef8aacf3fb80eaed06545036a64f67ac4f60e0987b1da
+EBUILD coot-9999.ebuild 3091 RMD160 4d48b70cdf1ff33fded4e99c63c1cf9d91179d75 SHA1 fd0a15024edaaa36c8530b00d5513d2a1d003153 SHA256 026a107fe87091b0f65378446598a42d8409e97789e00bb28977bc05fccd6991
+MISC ChangeLog 4552 RMD160 0ca2cb0cfeaa05c78ee8318d73b5e9ad51100e9f SHA1 e949642482ea67aef7368e2290bdef6e63020637 SHA256 7fd6a1d8cb27a4d0776007a87fc1195e8834afd6b4dcbc66dbda1429aebb0454
 MISC metadata.xml 316 RMD160 845cc100ac244efa5f02595717b5da635f87d2f1 SHA1 c870d2c52c44dee3bab8623e5b6095266f400813 SHA256 64f6dbcd3bb41b26fd7897089cd60ddb93f1ea7d75f9531bca94f28b07e21b2f
diff --git a/sci-chemistry/coot/coot-0.5.2.ebuild b/sci-chemistry/coot/coot-0.5.2.ebuild
index 10a8e68a6..5878affef 100644
--- a/sci-chemistry/coot/coot-0.5.2.ebuild
+++ b/sci-chemistry/coot/coot-0.5.2.ebuild
@@ -52,6 +52,7 @@ src_unpack() {
 
 	# To send upstream
 	epatch "${FILESDIR}"/${PV}-gcc-4.3.patch
+	epatch "${FILESDIR}"/${PV}-gcc-4.4.patch
 
 	epatch "${FILESDIR}"/${PV}-as-needed.patch
 	epatch "${FILESDIR}"/link-against-guile-gtk-properly.patch
@@ -102,7 +103,6 @@ src_compile() {
 		--with-pygtk \
 		|| die "econf failed"
 
-
 	# Regenerate wrappers, otherwise at least gtk-2 build fails
 	pushd src
 	rm -f coot_wrap_python.cc coot_wrap_python_pre.cc \
diff --git a/sci-chemistry/coot/coot-0.6_pre1-r2041.ebuild b/sci-chemistry/coot/coot-0.6_pre1-r2041.ebuild
deleted file mode 100644
index 6af6fab5c..000000000
--- a/sci-chemistry/coot/coot-0.6_pre1-r2041.ebuild
+++ /dev/null
@@ -1,125 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit autotools eutils versionator
-
-MY_S2_PV=$(replace_version_separator 2 - ${PV})
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
-MY_S_P=${MY_S2_P}-${PR/r/revision-}
-MY_PV=${PV}
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~emsley/coot/"
-if [[ ${MY_PV} = *pre* ]]; then
-	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/pre-release/${MY_S_P}.tar.gz"
-else
-	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${MY_P}.tar.gz"
-fi
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-RDEPEND=">=sci-libs/gsl-1.3
-	>=x11-libs/gtk+-2.2
-	gnome-base/libgnomecanvas
-	=x11-libs/guile-gtk-2.1
-	x11-libs/gtkglext
-	virtual/glut
-	virtual/opengl
-	dev-lang/python
-	dev-scheme/guile-gui
-	dev-scheme/net-http
-	dev-scheme/goosh
-	dev-scheme/guile-www
-	>=dev-scheme/guile-lib-0.1.6
-	sci-libs/coot-data
-	sci-chemistry/reduce
-	sci-chemistry/refmac
-	sci-chemistry/probe
-	>=sci-libs/ccp4-libs-6.1
-	>=sci-libs/clipper-20090210
-	dev-python/pygtk
-	gnome-base/librsvg
-	>=dev-libs/gmp-4.2.2-r2"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-#S="${WORKDIR}/${MY_P}"
-S="${WORKDIR}/${MY_S2_P}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	epatch "${FILESDIR}"/${PV}-as-needed.patch
-	epatch "${FILESDIR}"/link-against-guile-gtk-properly.patch
-	epatch "${FILESDIR}"/fix-namespace-error.patch
-
-	# Link against single-precision fftw
-	sed -i \
-		-e "s:lfftw:lsfftw:g" \
-		-e "s:lrfftw:lsrfftw:g" \
-		"${S}"/macros/clipper.m4
-
-	# Fix where it looks for some binaries
-	sed -i \
-		-e "s:/y/people/emsley/coot/Linux/bin/probe.2.11.050121.linux.RH9:/usr/bin/probe:g" \
-		-e "s:/y/people/emsley/coot/Linux/bin/reduce.2.21.030604:/usr/bin/reduce:g" \
-		"${S}"/scheme/group-settings.scm
-
-	# Look for clipper slotted with '-2' suffix
-#	sed -i \
-#		-e "s~\(-lclipper[[:alnum:]-]*\)~\1-2~g" \
-#		"${S}"/macros/clipper.m4 \
-#		|| die "sed to find -2 slotted libraries failed"
-#	grep 'include.*clipper' -rl . \
-#		| xargs sed -i \
-#			-e "s~\(include.*clipper\)/~\1-2/~g" \
-#			|| die "sed to find -2 slotted headers failed"
-
-	# So we don't need to depend on crazy old gtk and friends
-	cp "${FILESDIR}"/*.m4 "${S}"/macros/
-
-	cd "${S}"
-	eautoreconf
-}
-
-src_compile() {
-	# All the --with's are used to activate various parts.
-	# Yes, this is broken behavior.
-	econf \
-		--includedir='${prefix}/include/coot' \
-		--with-gtkcanvas-prefix=/usr \
-		--with-clipper-prefix=/usr \
-		--with-mmdb-prefix=/usr \
-		--with-ssmlib-prefix=/usr \
-		--with-guile \
-		--with-python=/usr \
-		--with-guile-gtk \
-		--with-gtk2 \
-		--with-pygtk \
-		|| die "econf failed"
-
-
-	# Regenerate wrappers, otherwise at least gtk-2 build fails
-	pushd src
-	rm -f coot_wrap_python.cc coot_wrap_python_pre.cc \
-		&& emake coot_wrap_python.cc \
-		|| die "failed to regenerate python wrapper"
-
-	rm -f coot_wrap_guile.cc coot_wrap_guile_pre.cc \
-		&& emake coot_wrap_guile.cc \
-		||die "failed to regenerate guile wrapper"
-	popd
-
-	emake || die "emake failed"
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die "install failed"
-
-	# Install misses this
-	insinto /usr/share/coot/python
-	doins "${S}"/src/coot.py
-}
diff --git a/sci-chemistry/coot/coot-0.6_pre1-r2042.ebuild b/sci-chemistry/coot/coot-0.6_pre1-r2042.ebuild
index c8e487428..cd9d4026f 100644
--- a/sci-chemistry/coot/coot-0.6_pre1-r2042.ebuild
+++ b/sci-chemistry/coot/coot-0.6_pre1-r2042.ebuild
@@ -54,6 +54,7 @@ S="${WORKDIR}/${MY_S2_P}"
 
 PATCHES=(
 	"${FILESDIR}"/${PV}-as-needed.patch
+	"${FILESDIR}"/${PV}-gcc4.4.patch
 	"${FILESDIR}"/link-against-guile-gtk-properly.patch
 	"${FILESDIR}"/fix-namespace-error.patch
 	)
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 3e6704b50..11eb246cd 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -59,6 +59,7 @@ PATCHES=(
 	"${FILESDIR}"/${PV}-as-needed.patch
 	"${FILESDIR}"/link-against-guile-gtk-properly.patch
 	"${FILESDIR}"/fix-namespace-error.patch
+	"${FILESDIR}"/${PV}-gcc4.4.patch
 	)
 
 src_prepare() {
diff --git a/sci-chemistry/coot/files/0.5.2-gcc-4.4.patch b/sci-chemistry/coot/files/0.5.2-gcc-4.4.patch
new file mode 100644
index 000000000..d754a519c
--- /dev/null
+++ b/sci-chemistry/coot/files/0.5.2-gcc-4.4.patch
@@ -0,0 +1,11 @@
+--- coot-utils/coot-utils.cc	2008-12-10 01:22:01.000000000 +0100
++++ coot-utils/coot-utils.cc.new	2009-08-06 00:31:18.000000000 +0200
+@@ -47,7 +47,7 @@
+ 
+ #include "clipper/core/hkl_compute.h"
+ #include "coot-utils.hh"
+-
++#include <cstdio>
+ 
+ 
+ std::string
diff --git a/sci-chemistry/coot/files/0.6_pre1-gcc4.4.patch b/sci-chemistry/coot/files/0.6_pre1-gcc4.4.patch
new file mode 100644
index 000000000..d754a519c
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6_pre1-gcc4.4.patch
@@ -0,0 +1,11 @@
+--- coot-utils/coot-utils.cc	2008-12-10 01:22:01.000000000 +0100
++++ coot-utils/coot-utils.cc.new	2009-08-06 00:31:18.000000000 +0200
+@@ -47,7 +47,7 @@
+ 
+ #include "clipper/core/hkl_compute.h"
+ #include "coot-utils.hh"
+-
++#include <cstdio>
+ 
+ 
+ std::string
diff --git a/sci-chemistry/coot/files/9999-gcc4.4.patch b/sci-chemistry/coot/files/9999-gcc4.4.patch
new file mode 100644
index 000000000..b7cd75662
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-gcc4.4.patch
@@ -0,0 +1,10 @@
+--- coot-utils/coot-utils.cc	2009-08-06 00:02:51.000000000 +0200
++++ coot-utils/coot-utils.cc.new	2009-08-06 00:06:13.000000000 +0200
+@@ -25,6 +25,7 @@
+ 
+ #include <stdexcept> // for string_to_int.
+ #include <sstream>   // ditto.
++#include <cstdio>
+ 
+ #include "coot-sysdep.h"
+ #if defined _MSC_VER