* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/dssp/, sci-chemistry/dssp/files/
@ 2015-08-15 14:41 Justin Lecher
0 siblings, 0 replies; 2+ messages in thread
From: Justin Lecher @ 2015-08-15 14:41 UTC (permalink / raw
To: gentoo-commits
commit: 11ee21569f870e70f3e8ff45d9b87210b224ac76
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Aug 15 13:56:05 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Aug 15 14:41:52 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=11ee2156
sci-chemistry/dssp: Add missing USE dep, bug #557840 drop old patches
Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-chemistry/dssp/dssp-2.2.1-r1.ebuild | 2 +-
sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch | 46 ----------------
sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch | 70 ------------------------
3 files changed, 1 insertion(+), 117 deletions(-)
diff --git a/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild
index 5e8b800..28f8ace 100644
--- a/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild
+++ b/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild
@@ -15,7 +15,7 @@ SLOT="0"
KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
IUSE=""
-RDEPEND="dev-libs/boost:="
+RDEPEND="dev-libs/boost:=[threads]"
DEPEND="${RDEPEND}"
src_prepare() {
diff --git a/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch b/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch
deleted file mode 100644
index 5db1437..0000000
--- a/sci-chemistry/dssp/files/dssp-2.0.4-gcc47.patch
+++ /dev/null
@@ -1,46 +0,0 @@
- src/matrix.h | 5 +++--
- src/primitives-3d.cpp | 1 +
- 2 files changed, 4 insertions(+), 2 deletions(-)
-
-diff --git a/src/matrix.h b/src/matrix.h
-index 1053ad9..d7dae5f 100644
---- a/src/matrix.h
-+++ b/src/matrix.h
-@@ -14,6 +14,7 @@
- #include <istream>
- #include <cassert>
- #include <stdexcept>
-+#include <unistd.h>
-
- // --------------------------------------------------------------------
- // uBlas compatible matrix types
-@@ -284,7 +285,7 @@ class identity_matrix : public matrix_base<T>
- template<typename T>
- matrix<T> operator*(const matrix_base<T>& lhs, const matrix_base<T>& rhs)
- {
-- matrix<T> result(min(lhs.dim_m(), rhs.dim_m()), min(lhs.dim_n(), rhs.dim_n()));
-+ matrix<T> result(std::min(lhs.dim_m(), rhs.dim_m()), std::min(lhs.dim_n(), rhs.dim_n()));
-
- for (uint32 i = 0; i < result.dim_m(); ++i)
- {
-@@ -310,7 +311,7 @@ matrix<T> operator*(const matrix_base<T>& lhs, T rhs)
- template<typename T>
- matrix<T> operator-(const matrix_base<T>& lhs, const matrix_base<T>& rhs)
- {
-- matrix<T> result(min(lhs.dim_m(), rhs.dim_m()), min(lhs.dim_n(), rhs.dim_n()));
-+ matrix<T> result(std::min(lhs.dim_m(), rhs.dim_m()), std::min(lhs.dim_n(), rhs.dim_n()));
-
- for (uint32 i = 0; i < result.dim_m(); ++i)
- {
-diff --git a/src/primitives-3d.cpp b/src/primitives-3d.cpp
-index b04e7c4..4532ecd 100644
---- a/src/primitives-3d.cpp
-+++ b/src/primitives-3d.cpp
-@@ -9,6 +9,7 @@
-
- #include <valarray>
- #include <cmath>
-+#include <unistd.h>
-
- #include <boost/foreach.hpp>
- #define foreach BOOST_FOREACH
diff --git a/sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch b/sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch
deleted file mode 100644
index 3db40f6..0000000
--- a/sci-chemistry/dssp/files/dssp-2.0.4-gentoo.patch
+++ /dev/null
@@ -1,70 +0,0 @@
- makefile | 24 ++++++++++++++----------
- 1 files changed, 14 insertions(+), 10 deletions(-)
-
-diff --git a/makefile b/makefile
-index df699b7..9d2167b 100644
---- a/makefile
-+++ b/makefile
-@@ -2,7 +2,7 @@
- #
- # Copyright Maarten L. Hekkelman, Radboud University 2008-2011.
- # Distributed under the Boost Software License, Version 1.0.
--# (See accompanying file LICENSE_1_0.txt or copy at
-+# (See aCXXompanying file LICENSE_1_0.txt or copy at
- # http://www.boost.org/LICENSE_1_0.txt)
- #
- # This makefile includes a file called make.config. It will create a
-@@ -24,22 +24,23 @@ BOOST_LIBS = thread regex filesystem program_options date_time iostreams math_
- LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2
-
- DEFINES = USE_COMPRESSION LINUX VERSION='"$(VERSION)"'
--CC = c++
-+CXX ?= c++
-
--CFLAGS = $(INC_DIR:%=-I%) -iquote src -g -Wall -Wno-multichar -pthread
--LDOPTS = $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -g -pthread
-+CPPFLAGS += $(INC_DIR:%=-I%) -iquote src
-+CXXFLAGS += -Wall -Wno-multichar -pthread
-+LDOPTS = $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -pthread
-
- OBJ_DIR = obj
-
- ifeq ($(DEBUG),1)
- OBJ_DIR := $(OBJ_DIR).dbg
--CFLAGS += -g3
-+CFLAGS +=
- else
- DEFINES += NDEBUG
--CFLAGS += -O3
-+CFLAGS +=
- endif
-
--CFLAGS += $(DEFINES:%=-D%)
-+CPPFLAGS += $(DEFINES:%=-D%)
-
- DIST_NAME = dssp-$(VERSION)
-
-@@ -49,17 +50,20 @@ OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ
-
- mkdssp: $(OBJECTS)
- @ echo linking $@
-- @ $(CC) -static -o $@ $^ $(LDOPTS)
-+ $(CXX) $(LDFLAGS) -o $@ $^ $(LDOPTS)
- @ echo OK
-
- include $(OBJECTS:%.o=%.d)
-
- $(OBJECTS:.o=.d):
-
--$(OBJ_DIR)/%.o: %.cpp
-+OBJ_DIR:
- @ if [ ! -d $(OBJ_DIR) ]; then mkdir $(OBJ_DIR); fi
-+
-+
-+$(OBJ_DIR)/%.o: %.cpp OBJ_DIR
- @ echo compiling $@
-- @ $(CC) -MD -c -o $@ $< $(CFLAGS)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -MD -c -o $@ $<
-
- clean:
- rm -rf $(OBJ_DIR)/* mkdssp
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/dssp/, sci-chemistry/dssp/files/
@ 2021-09-02 12:01 Pacho Ramos
0 siblings, 0 replies; 2+ messages in thread
From: Pacho Ramos @ 2021-09-02 12:01 UTC (permalink / raw
To: gentoo-commits
commit: 86a55f2707b1daa78e8d7e0666756e95ef588d47
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 2 11:48:56 2021 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Thu Sep 2 12:00:44 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=86a55f27
sci-chemistry/dssp: Fix boost compat for dssp-2
dssp-2 is still needed by gromacs, try to keep it whenever possible then
Closes: https://bugs.gentoo.org/802417
Closes: https://bugs.gentoo.org/808669
Package-Manager: Portage-3.0.22, Repoman-3.0.3
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>
sci-chemistry/dssp/dssp-2.2.1-r3.ebuild | 41 +++++++++++++++++++++++++++++++++
sci-chemistry/dssp/files/30-dssp | 1 +
2 files changed, 42 insertions(+)
diff --git a/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild
new file mode 100644
index 00000000000..17a89bb51ff
--- /dev/null
+++ b/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="The protein secondary structure standard"
+HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/"
+SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/${P}.tgz"
+
+LICENSE="Boost-1.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="dev-libs/boost:=[threads(+)]"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-2.1.0-gentoo.patch
+ "${FILESDIR}"/${PN}-2.2.1-boost-1.65-tr1-removal.patch
+)
+
+src_configure() {
+ tc-export CXX
+
+ cat >> make.config <<- EOF || die
+ BOOST_LIB_DIR = "${EPREFIX}/usr/$(get_libdir)"
+ BOOST_INC_DIR = "${EPREFIX}/usr/include"
+ EOF
+}
+
+src_install() {
+ dobin mkdssp
+ dosym mkdssp /usr/bin/dssp
+ doman doc/mkdssp.1
+ dodoc README.txt changelog
+
+ doenvd "${FILESDIR}"/30-${PN}
+}
diff --git a/sci-chemistry/dssp/files/30-dssp b/sci-chemistry/dssp/files/30-dssp
new file mode 100644
index 00000000000..e0a5e0ce562
--- /dev/null
+++ b/sci-chemistry/dssp/files/30-dssp
@@ -0,0 +1 @@
+DSSP=/usr/bin/dssp
\ No newline at end of file
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