[gentoo-commits] repo/gentoo:master commit in: sci-biology/stride/files/, sci-biology/stride/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/stride/files/, sci-biology/stride/

[David Seifert]

commit:     bcc75ebcff4cfb8a99a5a5f418f3b73174da7e11
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Aug 17 11:19:19 2019 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Aug 17 11:19:19 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bcc75ebc

sci-biology/stride: Port to EAPI 7

Package-Manager: Portage-2.3.71, Repoman-2.3.17
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 .../files/stride-20011129-fix-buildsystem.patch    | 21 +++++++++++++++++++
 sci-biology/stride/files/stride-LDFLAGS.patch      | 11 ----------
 sci-biology/stride/stride-20011129-r1.ebuild       | 24 +++++++++-------------
 3 files changed, 31 insertions(+), 25 deletions(-)

diff --git a/sci-biology/stride/files/stride-20011129-fix-buildsystem.patch b/sci-biology/stride/files/stride-20011129-fix-buildsystem.patch
new file mode 100644
index 00000000000..ec4415ec45d
--- /dev/null
+++ b/sci-biology/stride/files/stride-20011129-fix-buildsystem.patch
@@ -0,0 +1,21 @@
+--- a/Makefile
++++ b/Makefile
+@@ -1,4 +1,3 @@
+-CC = gcc -g
+ FLAGS = -lm  -o
+ 
+ SOURCE = stride.c splitstr.c rdpdb.c initchn.c geometry.c thr2one.c one2thr.c filename.c tolostr.c strutil.c place_h.c hbenergy.c memory.c helix.c sheet.c rdmap.c phipsi.c command.c molscr.c die.c hydrbond.c mergepat.c fillasn.c escape.c p_jrnl.c p_rem.c p_atom.c p_helix.c p_sheet.c p_turn.c p_ssbond.c p_expdta.c p_model.c p_compnd.c report.c nsc.c area.c ssbond.c chk_res.c chk_atom.c turn.c pdbasn.c dssp.c outseq.c chkchain.c elem.c measure.c asngener.c p_endmdl.c stred.c contact_order.c contact_map.c
+@@ -7,12 +6,9 @@
+ 
+ BINDIR = .
+ 
+-.c.o: 
+-	$(CC) -c $< -o $@
+-
+ 
+ stride : $(OBJECT)
+-	$(CC) $(OBJECT) $(FLAGS)  $(BINDIR)/stride
++	$(CC) $(LDFLAGS) $(OBJECT) $(FLAGS) $(BINDIR)/stride
+ 
+ $(OBJECT) : stride.h protot.h
+ 

diff --git a/sci-biology/stride/files/stride-LDFLAGS.patch b/sci-biology/stride/files/stride-LDFLAGS.patch
deleted file mode 100644
index 1761b12129b..00000000000
--- a/sci-biology/stride/files/stride-LDFLAGS.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- Makefile	2009-10-27 21:18:45.000000000 +0100
-+++ Makefile.new	2009-10-27 21:19:00.000000000 +0100
-@@ -12,7 +12,7 @@
- 
- 
- stride : $(OBJECT)
--	$(CC) $(OBJECT) $(FLAGS)  $(BINDIR)/stride
-+	$(CC) $(LDFLAGS) $(OBJECT) $(FLAGS)  $(BINDIR)/stride
- 
- $(OBJECT) : stride.h protot.h
- 

diff --git a/sci-biology/stride/stride-20011129-r1.ebuild b/sci-biology/stride/stride-20011129-r1.ebuild
index 77a19f3ea89..678887de925 100644
--- a/sci-biology/stride/stride-20011129-r1.ebuild
+++ b/sci-biology/stride/stride-20011129-r1.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Protein secondary structure assignment from atomic coordinates"
 HOMEPAGE="http://webclu.bio.wzw.tum.de/stride/"
@@ -11,25 +11,21 @@ SRC_URI="
 	ftp://ftp.ebi.ac.uk/pub/software/unix/${PN}/src/${PN}.tar.gz -> ${P}.tar.gz
 	https://dev.gentoo.org/~jlec/distfiles/${PN}-20060723-update.patch.bz2"
 
-SLOT="0"
 LICENSE="STRIDE"
+SLOT="0"
 KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE=""
-
-S="${WORKDIR}"
-
 RESTRICT="mirror bindist"
 
-src_prepare() {
+S="${WORKDIR}"
+PATCHES=(
 	# this patch updates the source to the most recent
 	# version which was kindly provided by the author
-	epatch \
-		"${DISTDIR}/${PN}-20060723-update.patch.bz2" \
-		"${FILESDIR}"/${PN}-LDFLAGS.patch
+	"${S}"/${PN}-20060723-update.patch
+	"${FILESDIR}"/${PN}-20011129-fix-buildsystem.patch
+)
 
-	# fix makefile
-	sed -e "/^CC/s|gcc -g|$(tc-getCC) ${CFLAGS}|" -i Makefile || \
-		die "Failed to fix Makefile"
+src_configure() {
+	tc-export CC
 }
 
 src_install() {

[gentoo-commits] repo/gentoo:master commit in: sci-biology/stride/files/, sci-biology/stride/

[Ionen Wolkens]

commit:     e3f47e5d698809e572c10bda6e4929f2794f9860
Author:     Ionen Wolkens <ionen <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 15 14:20:17 2022 +0000
Commit:     Ionen Wolkens <ionen <AT> gentoo <DOT> org>
CommitDate: Sat Oct 15 20:06:44 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e3f47e5d

sci-biology/stride: fix build w/ upcoming clang16

Note that the implicit int is part of the update patch.

Closes: https://bugs.gentoo.org/874069
Signed-off-by: Ionen Wolkens <ionen <AT> gentoo.org>

 sci-biology/stride/files/stride-20011129-clang16.patch | 15 +++++++++++++++
 sci-biology/stride/stride-20011129-r1.ebuild           |  3 ++-
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/sci-biology/stride/files/stride-20011129-clang16.patch b/sci-biology/stride/files/stride-20011129-clang16.patch
new file mode 100644
index 000000000000..e1e4383a3281
--- /dev/null
+++ b/sci-biology/stride/files/stride-20011129-clang16.patch
@@ -0,0 +1,15 @@
+https://bugs.gentoo.org/874069
+--- a/hydrbond.c
++++ b/hydrbond.c
+@@ -293,3 +293,3 @@
+   int dc, ac, ccd, cca, cc, hc=0, i;
+-  void (*HBOND_Energy)();
++  void (*HBOND_Energy)(float*, float*, float*, float*, float*, COMMAND*, HBOND*);
+   BUFFER Text;
+--- a/p_atom.c
++++ b/p_atom.c
+@@ -11,3 +11,3 @@
+   RESIDUE *r;
+-  register i;
++  register int i;
+ 

diff --git a/sci-biology/stride/stride-20011129-r1.ebuild b/sci-biology/stride/stride-20011129-r1.ebuild
index a8681b7f924e..9638fd559b55 100644
--- a/sci-biology/stride/stride-20011129-r1.ebuild
+++ b/sci-biology/stride/stride-20011129-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -22,6 +22,7 @@ PATCHES=(
 	# version which was kindly provided by the author
 	"${S}"/${PN}-20060723-update.patch
 	"${FILESDIR}"/${PN}-20011129-fix-buildsystem.patch
+	"${FILESDIR}"/${PN}-20011129-clang16.patch
 )
 
 src_configure() {