gentoo resync : 18.08.2019

7 files changed, 41 insertions, 35 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 096f21431427..65a1a8d0bc0e 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/sim4/Manifest b/sci-biology/sim4/Manifest
index 8ead2531796b..61fa823043dd 100644
--- a/sci-biology/sim4/Manifest
+++ b/sci-biology/sim4/Manifest
@@ -1,4 +1,4 @@
 AUX sim4-20030921-fix-build-system.patch 491 BLAKE2B 87842374146fa44c2788ce7444480cb7be244d04f0e2f2d22bdc5cca766b4bd610b94a5d6088c58ce2005b8e7664fab6ec4b0ea598e833a34fa1edff29e413da SHA512 fdc737ccacd7cb4f7c5534af49587d7958f62dbe66a5197c38bda89af3cdd572231c10af75e8bb59120fa116f856f1ca5ba95279f9a2fe07228543588552f915
-DIST sim4.tar.gz 60814 BLAKE2B 2a6aeaf56cbec7b3d5e8cb0c0405afd3b1325977d1b68ba319347dbc38461bde9bdb028e92d8b463a593a2fdc8d72d65db27c8e30462901ce8921632201ad038 SHA512 de7ee4094830262cb7ea8ed2f4573beed96df4b12f2915f669c52fd3fa40f5a4894cd94224e575bfb2588f9a6f19c0b73a38d6209d92a1dc644639a4927aa6b5
-EBUILD sim4-20030921-r2.ebuild 553 BLAKE2B f7f2009a850ccd08bb6d9d0eb3cd9f82e5701bcbc3c1e7bedd84109eaa63a6063dc76c0f6c893cc661a1a5d728918c8ebf05e203564a9eed4367c1ac9664473b SHA512 51fd5d759f62b005bc33b2fc37dbf8dc3f8b993d461d5dc2722ed93f8a8e51c19d21ea82105c3544ed23ad831c7e2d5c86e5c63aa3aa19937c4c354426e37f71
+DIST sim4-20030921.tar.gz 60814 BLAKE2B 2a6aeaf56cbec7b3d5e8cb0c0405afd3b1325977d1b68ba319347dbc38461bde9bdb028e92d8b463a593a2fdc8d72d65db27c8e30462901ce8921632201ad038 SHA512 de7ee4094830262cb7ea8ed2f4573beed96df4b12f2915f669c52fd3fa40f5a4894cd94224e575bfb2588f9a6f19c0b73a38d6209d92a1dc644639a4927aa6b5
+EBUILD sim4-20030921-r2.ebuild 542 BLAKE2B 12b61e595117218379fdf7e02c5e389cd7dd6ddb4fdb51f1d6fe48c8a3c7e45d6c531b84e5ebb9757253f55ff97ca75618d274eea3759fb2097007d7715881fc SHA512 9497feebbd6f978dd3801c156bc4112d634f842aa056323d84cc6148f51f8ee42e0a3f85a7f07faf495e395d37b61515a6168a94f05182328dc31c6a5dbba485
 MISC metadata.xml 1228 BLAKE2B e3e87915a4b710b37be351835010d57cea2b044160a7e0a5651366c07127509e6bf422f4b20b314a0810a86eae33d44612a758e1081f7dcd194476c30a784c1f SHA512 417eff4c0d22bb4bef9bd027c79171375f9638e7efd452444d2c2a40b79a02c24f69b6158448420970a86e87358ed6bd397307b227cbe1b3bbf6813b6433d565
diff --git a/sci-biology/sim4/sim4-20030921-r2.ebuild b/sci-biology/sim4/sim4-20030921-r2.ebuild
index 204ec82210ae..9ea005c9a35e 100644
--- a/sci-biology/sim4/sim4-20030921-r2.ebuild
+++ b/sci-biology/sim4/sim4-20030921-r2.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit toolchain-funcs
 
 DESCRIPTION="A program to align cDNA and genomic DNA"
 HOMEPAGE="http://globin.cse.psu.edu/html/docs/sim4.html"
-SRC_URI="http://globin.cse.psu.edu/ftp/dist/sim4/sim4.tar.gz"
+SRC_URI="mirror://gentoo/${PN}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
diff --git a/sci-biology/stride/Manifest b/sci-biology/stride/Manifest
index 53fba32cc4e5..4230976b6793 100644
--- a/sci-biology/stride/Manifest
+++ b/sci-biology/stride/Manifest
@@ -1,5 +1,5 @@
-AUX stride-LDFLAGS.patch 280 BLAKE2B e33e6b77463be3e1e58864b70ab931b9983107d69b86c89988bf20a163744350d28a47e36a134ddebfe1cc6734ca2dd3e9cddcea2e56820fe7afe54539735300 SHA512 d3fc5fec53066fc5f015a2b741bf5e3a236db4eee04ae7908912036c0be004e9827228b9153188f2304c91eb44e9d029996b4d86eee7baf0d109ae87776504f8
+AUX stride-20011129-fix-buildsystem.patch 807 BLAKE2B df077f9234808abe3a9346af6c4a8bde92812cc9f782ad37b75b060166b35686cbcdc2f4b12c26263127dbd3c488660bb2cf70bc553c267cb3e9f70eba68082d SHA512 2afba4707d8371da1fc79c5bfa6f476ac76682d67e52287462eabfcecd394f89a9fe68810045098c48107ed7f33b8c44c566f609c647f71a7918375cfc9dc220
+DIST stride-20011129.tar.gz 56441 BLAKE2B 4d4cd3f9f6cef997fff10571aecb70cb21056e88c5130e7dfdafe15a6fb353656d0635b4d65895ef115479a87dcf600b659455d15460344c838543a2e356bfae SHA512 cbd40fce4684728f363520540132fc1a0003126954a145d59aeff48adb20fdaa66520bd12b56ee5d2906e8ea97bf78a225204105b820f7f368aee5e790a6471b
 DIST stride-20060723-update.patch.bz2 5621 BLAKE2B 266a7371c0963a996430c1f809b46196e8bf179fcf2afb4380f6eccd092c03b29d5b09b8a8438ee7848d0f411920db2e4465ef646c75a406197412f35e880179 SHA512 e06eb68b907615e12dc1a9981be157400e9ffed9391a906cb4eb3ef4067b7027c26cc600298053bfc5d2bbbebbbfefe0e6b18d0e4f6fef2172768e6f95498af1
-DIST stride.tar.gz 56441 BLAKE2B 4d4cd3f9f6cef997fff10571aecb70cb21056e88c5130e7dfdafe15a6fb353656d0635b4d65895ef115479a87dcf600b659455d15460344c838543a2e356bfae SHA512 cbd40fce4684728f363520540132fc1a0003126954a145d59aeff48adb20fdaa66520bd12b56ee5d2906e8ea97bf78a225204105b820f7f368aee5e790a6471b
-EBUILD stride-20011129-r1.ebuild 917 BLAKE2B fc125782bd5edf45f8e6048383ab048ec7c86eb8ec1076ad76327a36c6a68e454f79bab0007cc68a55996f3ec6b29762e9c55d4fa1f5187b238abd7b7143a56a SHA512 633e21ef055594d0fdefd0d852b68b1585bda766616ab53fb3c69ee88e73161fea34d2c5428bc1b51261c04f65d760beeb7217eba61177fa108c4c505d4f013b
+EBUILD stride-20011129-r1.ebuild 822 BLAKE2B 34f7f410901818525c884457031a5ed16a1a467ca2b406db76102560ba94458693dc7fb7822b3c5d4fccc75f42a31b794b3f18ce726a2abc928ce8082301d691 SHA512 0fc9734abddfbbb22727c1de5021b7c544ce4a9d03e53c567d9f1eb1133936058eca9c1a862e6d964695e04d985349cd7698a27e63646f5a8c4658d8e18c626a
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
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 000000000000..ec4415ec45d4
--- /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 1761b12129bd..000000000000
--- 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 c76883b861e1..678887de925e 100644
--- a/sci-biology/stride/stride-20011129-r1.ebuild
+++ b/sci-biology/stride/stride-20011129-r1.ebuild
@@ -1,35 +1,31 @@
-# Copyright 1999-2015 Gentoo Foundation
+# 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/"
 SRC_URI="
-	ftp://ftp.ebi.ac.uk/pub/software/unix/${PN}/src/${PN}.tar.gz
+	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() {