gentoo resync : 17.08.2021

12 files changed, 52 insertions, 55 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 86ae7edb0a70..7771279063cb 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/bodr/Manifest b/sci-chemistry/bodr/Manifest
index d3f4c0ae9af1..2846d415c78a 100644
--- a/sci-chemistry/bodr/Manifest
+++ b/sci-chemistry/bodr/Manifest
@@ -1,3 +1,3 @@
 DIST bodr-10.tar.bz2 225671 BLAKE2B cda3d66da530cb28898389080807c4ed8602bb8871ee9e9ff75ba4a7a40ee676308539adb26d61b3361b53f37c099fa784438def9b768828a941c3693c7315a2 SHA512 a3e0e7195914938d8824127aa4777c4054c302ef7811d82d1e012d9be5d7a13d7f2225d4216f4a30ae7dbf70eb3b0b38571c3ee0dbe1d97af15f04171dd51bec
-EBUILD bodr-10.ebuild 585 BLAKE2B 645d4a136eebe975101b4b4b87e19db89157f62983c146d5891bb803205d175b96734962236192da71cbcaeb54ee5338b38b26d068519c28db9f39acb06882f2 SHA512 8faf4644cc5ec6afbca8fec153262db33a0e9804cc711d48a4a2a5ca48ff08d6dc74ffd7aacc7ca7a9006b1093d6522bd3988e25f8b8cdb3cdff9a42a1b0e508
+EBUILD bodr-10.ebuild 456 BLAKE2B 9d151b5ce46752ae361a21f1224b9fde5fe872e8bd18141fbbe5f94c2b17923fdbcd86a03e37303c9590c1c2cb77f0d6cf24b6d2cddff7102d92eda65c73d7e6 SHA512 88c69197d354522717c6d176c8b5c0b2572b40517332a42ae7969f17a2e0b440328383777230080b7347d078722eef17fbeb0c5237322beae930d9063b7f4642
 MISC metadata.xml 691 BLAKE2B 1cb2f68315ca1fc3ee1576ea5f13ffbac8ac3552090eac4ed36b85a7411e5d456da29f38627b1c36552d37e9a260a36ae62bd314b3b735c505931f2f9302c899 SHA512 40092a5f0956a1fb3ab8fcad065fbb3d3549d97c5687acf26fe68f07754ff4909b7c6bc84dcb2e097ab5637fecd11f7057026967fd86b4302a5a6f718cea3e1c
diff --git a/sci-chemistry/bodr/bodr-10.ebuild b/sci-chemistry/bodr/bodr-10.ebuild
index 4a8ecabc18c3..7a957c05b90d 100644
--- a/sci-chemistry/bodr/bodr-10.ebuild
+++ b/sci-chemistry/bodr/bodr-10.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=8
 
 DESCRIPTION="The Blue Obelisk Data Repository listing element and isotope properties"
 HOMEPAGE="https://sourceforge.net/projects/bodr"
@@ -10,17 +10,10 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~ppc-macos"
-IUSE=""
 
-DEPEND="dev-libs/libxslt"
-RDEPEND=""
-
-DOCS=( "THANKS" "AUTHORS" "README" "ChangeLog" )
+BDEPEND="dev-libs/libxslt"
 
 src_prepare() {
+	default
 	sed -i -e "s/COPYING//g" Makefile.* || die
 }
-
-src_configure() {
-	econf --docdir="${EPREFIX}"/usr/share/doc/${PF}
-}
diff --git a/sci-chemistry/easychem/Manifest b/sci-chemistry/easychem/Manifest
index 0286e86d8a92..695a7f699cd8 100644
--- a/sci-chemistry/easychem/Manifest
+++ b/sci-chemistry/easychem/Manifest
@@ -1,4 +1,4 @@
 AUX 0.6-gentoo.patch 1695 BLAKE2B cff09334811f4f7f40c77edcfd9c160885f906d616d1b36d0a0c61b0c4d03982ebab91cbcacd55fab1e7b152dec6de26e8f6584b8436a20a3d9e8f43621888e4 SHA512 02b9880ff2b8d9ec81ddd8d96f64a9e1dc38810789eedd18ad7cacc0c594914334971fccf735a7103878c8d32e0a3765d5ff57016b4a4feb2e572915bd7c3eec
 DIST easychem-0.6.tar.gz 265458 BLAKE2B 673100e6d01653ea16a70a8384dc8c598c8e113e241851b19882b333c95e6118fc180a1123e770c021245417640310a05a9026e55a57ae589bde59cf9e5b4766 SHA512 83f877d1813287592a460f4dc3769feda88e45d8f77cd728c4055b60521babe253b4432033941ff429c753cfe675a642714052a01736534147398d6972e47051
-EBUILD easychem-0.6-r1.ebuild 807 BLAKE2B bbd891d60711b8d4fe68e17fa5f71016479c274bc077d277aa49fd4313046d676fc87514513c5468d3bd52a2408b83bacee0a18cce45cb1951f8d87d48fed644 SHA512 49514e7ac39bea63ea697fade31adb0b7b7dbae28867d7f0e3401d52ef9a5d37a431da0fcd61fb5e2f819cada9794f788f254f0b9c41ba1665946f9bb29887b6
+EBUILD easychem-0.6-r1.ebuild 819 BLAKE2B 3d44383de6e9bb19e085d2db5e3382a02b1f03e3c67e4656bdcc94c0a768b3969bb8f488a7e2982cc945a97e454dc4de21743457655600241f2107ec01e83d8c SHA512 ed6793460232ffc5711ce05baea50916e0f3212aeb72322f52e39bdda2c3d0746f4b654affc98df633b3dd6de116b024c33083690055a4c6bfec34097d5bc4d0
 MISC metadata.xml 758 BLAKE2B e03f2d584016eb1bf52a93b6bbcf0d77734e50ee7e1ab4fb15cfd15032bb28437d994698e9f221dec7dbe88ca7f3234734ec5819ffce8e103a03ca639984ee8e SHA512 e07eda8ec2fd7a721628cf0ccc1a50876f6cd8aff0a27903366ca03587d8c9dbb5cd830da9dfcfe2aa5d6b64eb577b36f3b5173b5fa6e39b19c6e97d8764a825
diff --git a/sci-chemistry/easychem/easychem-0.6-r1.ebuild b/sci-chemistry/easychem/easychem-0.6-r1.ebuild
index 9fbce1815123..4d9d43bcf619 100644
--- a/sci-chemistry/easychem/easychem-0.6-r1.ebuild
+++ b/sci-chemistry/easychem/easychem-0.6-r1.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=8
 
-inherit epatch toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Chemical structure drawing program - focused on presentation"
 HOMEPAGE="http://easychem.sourceforge.net/"
@@ -12,18 +12,22 @@ SRC_URI="mirror://sourceforge/easychem/${P}.tar.gz"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
 
 RDEPEND="
-	x11-libs/gtk+:2
 	app-text/ghostscript-gpl
-	media-gfx/pstoedit"
-DEPEND="${RDEPEND}
+	media-gfx/pstoedit
+	x11-libs/gtk+:2
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
 	dev-lang/perl
-	virtual/pkgconfig"
+	virtual/pkgconfig
+"
+
+PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch )
 
 src_prepare() {
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
+	default
 	tc-export CC
 }
 
diff --git a/sci-chemistry/mopac7/Manifest b/sci-chemistry/mopac7/Manifest
index 274811a00582..ca9982c34338 100644
--- a/sci-chemistry/mopac7/Manifest
+++ b/sci-chemistry/mopac7/Manifest
@@ -2,5 +2,5 @@ AUX Makefile 387 BLAKE2B b0c4b3a009c8bf8c779953edf3e233434656033a661cb307079eebc
 DIST dcart.f 11044 BLAKE2B 7414804ecfab9a7cbddee664b85e6e2e8c1d8fe1e1f73d480dd1a387c5e349d26ec4ae1a37f27e38b7c051fcce2c1bdf77de12ec628298fd3edf79040a8a0c5a SHA512 788a184fd8419ff742e49c1a652d5ea093f9114dbe4f272665b8fb9eeac2afb7f7042628c288f2b81d0f54d8a7ef2f400490cd3aff39dda59a6d70a0deab5b80
 DIST gmxmop.f 38956 BLAKE2B e411feca5104e91ae8fd2008de61d18cc214beb3b2a7aa09a80269fb935e27ba1b1cb89fa30eedbfc4f6c4734c22d932e57d5905c175ae9f56c4affee7b0ca04 SHA512 38bb2e5749c4d3c8c24f15682f72e40cb4edb6517c7916cecee1d21675b1870c0fe331ba2ec40312408dec473141e7742d1e155d4b64f1c2a25bfa4e11885194
 DIST mopac7-1.15.tar.gz 764547 BLAKE2B 6e037862007221955d0ad65f3c002a3d2e461950a2bc0efac9d195cf1d9d856842d02bc380ce236c3d48f863a144875950f5c86f8f3ac936b8b098472f7f7a0d SHA512 e0ccd643caa6dbd7e156867530d79e50e10243f5e3b5f8bc57781e68e1daf26f2a0e6987fff00afe07eb0fcb98cbd9f01e4cfa5d20acc0d8ab3cca632968636e
-EBUILD mopac7-1.15-r1.ebuild 1814 BLAKE2B 6ceef187223119bdcc1d772981573756c6b591bd9ab4886fea99ac3bccd08f755a1687b15e524d0db4030955b0a0e85b2793478788e910c65963019f85b396b4 SHA512 44211bb723a2e39e4059309ceef512e49b4010d18b66fa8509f5538cac0c59d4d29eaba887eb1101710bf59d70863a15c1605fe32b5ce9734019099d3c6d64f0
+EBUILD mopac7-1.15-r1.ebuild 1851 BLAKE2B e3922c1a7937bb5a5ec85b7ef94a3c7eee007d6488e74bbed300c0f4904b83921aaea1b6e84932e869a5e1491a305b10b1123b3aacb36f5952505b2d70165b0f SHA512 bc58c9b43d6e63e8fa25c33d199bdc924b841cf60c2ac3e5b387b5912ead41153684f15fa7231b056cfe84b62c44d16c004c78137f4aa0e805ee2b503af57b35
 MISC metadata.xml 434 BLAKE2B 011dd4486a917b69a58d398027b3af606bae6a6ea2b470b2f3f3d15f64b6db46a8a77ae4a52d78249ac8917d1a25bcbbcb5af62bea6677c5d4b433e47e9a8356 SHA512 77b3e0b69436a4f199c5ae3d9382c9b6cf2049ffd98144a2dc291495de9e8daa9deb6141d77b917f6e29902ad862c9044e7661ca7f0ae5e4fc68983857b3f6f2
diff --git a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild
index 3cb18cba78fe..aaf87bceee5c 100644
--- a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild
+++ b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=8
 
 inherit autotools fortran-2 flag-o-matic toolchain-funcs
 
@@ -21,6 +21,8 @@ DEPEND="dev-libs/libf2c"
 RDEPEND="${DEPEND}"
 
 src_prepare() {
+	default
+
 	# Install the executable
 	sed -i \
 		-e "s:noinst_PROGRAMS = mopac7:bin_PROGRAMS = mopac7:g" \
@@ -44,11 +46,12 @@ src_compile() {
 	emake
 	if use gmxmopac7; then
 		einfo "Making mopac7 lib for gromacs"
-		mkdir "${S}"/fortran/libgmxmopac7 && cd "${S}"/fortran/libgmxmopac7
-		cp -f ../SIZES ../*.f "${FILESDIR}"/Makefile . || die
+		mkdir "${S}"/fortran/libgmxmopac7 || die
+		cd "${S}"/fortran/libgmxmopac7 || die
+		cp -n ../SIZES ../*.f "${FILESDIR}"/Makefile . || die
 		emake clean
-		cp -f "${DISTDIR}"/gmxmop.f "${DISTDIR}"/dcart.f . || die
-		sed "s:GENTOOVERSION:${PV}:g" -i Makefile
+		cp -n "${DISTDIR}"/gmxmop.f "${DISTDIR}"/dcart.f . || die
+		sed "s:GENTOOVERSION:${PV}:g" -i Makefile || die
 		emake FC=$(tc-getFC)
 	fi
 }
@@ -61,7 +64,7 @@ src_install() {
 	default
 
 	if use gmxmopac7; then
-		cd "${S}"/fortran/libgmxmopac7
+		cd "${S}"/fortran/libgmxmopac7 || die
 		dolib.so libgmxmopac7.so*
 	fi
 
diff --git a/sci-chemistry/mustang/Manifest b/sci-chemistry/mustang/Manifest
index 7fbdd268c336..b94ffa43278d 100644
--- a/sci-chemistry/mustang/Manifest
+++ b/sci-chemistry/mustang/Manifest
@@ -1,4 +1,4 @@
-AUX mustang-3.2.1-gcc-4.7.patch 477 BLAKE2B 1e380b3b4bd96c61e316b7aa150f1e5e290dbb2e9d93876ef31adf6cdb482f5390eb630e34a4a1851bd7f5dfea5d93cadedbb320ad336f48fa87c8a4dbd8be81 SHA512 169e68335093d3400c3294a38246d5e9264f77bbaeab7c047318f8db5934cfed24ae5f0f421f2483e2c9fe8df1db40b8ab48c0dac1c20867f4119011b3e4f52e
+AUX mustang-3.2.1-gcc-4.7.patch 286 BLAKE2B 93f16865b51cc5b510ac98a1f45bf02f0d0543c96df40ea54f9b33ce6905985760f201c6beda95dcaaa8a620f257c2d9dd448f315f5dee67dec1aae07d91b304 SHA512 7f2f113a28439c6646582ce154ccffea9df6a01254335a5915456609ecba2edaeefb9b16f02973624c3a046ae29865c2beb8eb6eb0c53d8209a56ea9f6946426
 DIST mustang_v3.2.2.tgz 141940 BLAKE2B b90b42df782bd1dbdb387d0d0ab42430c5212b439da84f56a33ca2c746c8937ae330dfb8d634e7d1c5ffd0f6959cd9e4be0efe8f569c452930a3481894c68ec5 SHA512 cb862f860f3cdb3349743c6005a29acc14cde5269df9d61f1100ffdc9a22c1d8e3dd46771371557b823724e79783f8fcb7356c63c6f0c0a09aac09bee407a26d
-EBUILD mustang-3.2.2.ebuild 1103 BLAKE2B 0d56516a4ffc44784786ab9b10759dc04bb08ecd906cb281b8174ac4f0af44e67d7f340bfcada2dbf465ee986a3fce0fe9b4cca9fc7dcada3d00d8711649be3e SHA512 9b6e784bd46029c575d68b472693bc98ec788cdc1b415ddc27d492b4a88967af25e2c1d865db3b57307c2ce6a8b863a3a576b178b863646be8aa1c47db9f8263
+EBUILD mustang-3.2.2.ebuild 1101 BLAKE2B 7d7cf0ac042e03bd199b4c23d2c24f9a3ad18b74a4e199c0748029c0238df4bb2389922fdb930d66a2896e47ca6a4350f3c753a7b77b85c198dc942219e0f0a9 SHA512 1b4229362d019bd73e6dc57da94d2a62fb034ebcb27ea2e53f3e5df96479224c8ffefdd0d4e5be57e6eab8014c485ca9cf85df092f244a2ca875cc913cbd62a1
 MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a
diff --git a/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch b/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch
index 9e5dea85afeb..20bd300db89e 100644
--- a/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch
+++ b/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch
@@ -1,8 +1,3 @@
- src/superpose_on_core_2.cpp |    2 ++
- 1 files changed, 2 insertions(+), 0 deletions(-)
-
-diff --git a/src/superpose_on_core_2.cpp b/src/superpose_on_core_2.cpp
-index ae137de..059dfe3 100644
 --- a/src/superpose_on_core_2.cpp
 +++ b/src/superpose_on_core_2.cpp
 @@ -55,6 +55,8 @@ using std::ofstream ;
diff --git a/sci-chemistry/mustang/mustang-3.2.2.ebuild b/sci-chemistry/mustang/mustang-3.2.2.ebuild
index c82add5410d0..d15a60e83945 100644
--- a/sci-chemistry/mustang/mustang-3.2.2.ebuild
+++ b/sci-chemistry/mustang/mustang-3.2.2.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=8
 
-inherit epatch toolchain-funcs
+inherit toolchain-funcs
 
 MY_PN="MUSTANG"
 SRC_P="${PN}_v${PV}"
@@ -12,16 +12,16 @@ MY_P="${MY_PN}_v${PV}"
 DESCRIPTION="MUltiple STructural AligNment AlGorithm"
 HOMEPAGE="http://www.csse.monash.edu.au/~karun/Site/mustang.html"
 SRC_URI="http://www.csse.monash.edu.au/~karun/${PN}/${PN}_v${PV}.tgz"
+S="${WORKDIR}/${MY_P}"
 
 LICENSE="BSD"
 SLOT="0"
 KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE=""
 
-S="${WORKDIR}/${MY_P}"
+PATCHES=( "${FILESDIR}"/${PN}-3.2.1-gcc-4.7.patch )
 
 src_prepare() {
-	epatch "${FILESDIR}"/${PN}-3.2.1-gcc-4.7.patch
+	default
 	sed -e 's:3.2.1:3.2.2:g' -i Makefile || die
 }
 
diff --git a/sci-chemistry/theseus/Manifest b/sci-chemistry/theseus/Manifest
index 66b55599c691..c4c13d26de42 100644
--- a/sci-chemistry/theseus/Manifest
+++ b/sci-chemistry/theseus/Manifest
@@ -1,3 +1,3 @@
 DIST theseus_3.3.0.tar.gz 22548124 BLAKE2B 0ad49f768e1584bf40e90ff6fd0d884b6b27ee59ad31ce75050293b817a3747969ab0c4b4ff982aadbdc5301c1c56522540b78aab045e841c099a80dd546c8e9 SHA512 1fba3e8019a40214defdae13d4721d170ee698337d8efd4e872af22f8ab3cb1fdd52fa9f19a858ee51bc98150692af0c6016033feb0d76f29acaf7fffbb430e2
-EBUILD theseus-3.3.0-r1.ebuild 1510 BLAKE2B 8527637cfbeb666aa84112bf01867ba14d34e819ccb8f372bfc032315eb8e00645af56588262d0a088db1976d439531f96ffaee8af5a42e99fe8eebb60dd6e5d SHA512 ce61c47d06d624ef6b8c70dba821715e7fe8ef2a82ccacfd16c53bd2e76b77343299ead01a78267dd7d7c4fb9b8894d0fa58bd86234ce011011e99dcb1229116
+EBUILD theseus-3.3.0-r1.ebuild 1526 BLAKE2B 487eb12d25750eebb2ed066216111cfcdea94ad35860a70bc135e3f31d351058221bd9bb327bd562cb625deb608ae7b99d6e2e53f195315e01710b8e76136c89 SHA512 bdb6578de0350773930645ab8e6e0b852115c2568fa45f182b4e88516891299b6ff042d00e2c71eea6e0abc8e015f5dd9c0455959eaac684ad3ca53266f12c97
 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/theseus/theseus-3.3.0-r1.ebuild b/sci-chemistry/theseus/theseus-3.3.0-r1.ebuild
index f9e62b3916d7..fe012719670a 100644
--- a/sci-chemistry/theseus/theseus-3.3.0-r1.ebuild
+++ b/sci-chemistry/theseus/theseus-3.3.0-r1.ebuild
@@ -1,40 +1,42 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=8
 
-inherit multilib toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures"
 HOMEPAGE="http://www.theseus3d.org/"
 SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz"
+S="${WORKDIR}"/${PN}_src
 
-SLOT="0"
 LICENSE="GPL-3"
+SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="examples"
 
 RDEPEND="
 	sci-libs/gsl:=
 	|| (
+		sci-biology/clustalw:2
+		sci-biology/kalign
+		sci-biology/mafft
 		sci-biology/muscle
 		sci-biology/probcons
-		sci-biology/mafft
 		sci-biology/t-coffee
-		sci-biology/kalign
-		sci-biology/clustalw:2
-		)"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}"/${PN}_src/
+	)
+"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
 
 src_prepare() {
-	cat >> make.inc <<- EOF
+	default
+
+	cat >> make.inc <<- EOF || die
 	ARCH = $(tc-getAR)
 	ARCHFLAGS = -rvs
 	RANLIB = $(tc-getRANLIB)
-	LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir)
+	LOCALLIBDIR = "${EPREFIX}"/usr/$(get_libdir)
 	SYSLIBS = $($(tc-getPKG_CONFIG) --libs gsl) -lpthread
 	LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
 	LIBDIR = -L./lib