gentoo resync : 09.03.2018

6 files changed, 358 insertions, 6 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index ec4f5e09ff11..d3e2e55bcd81 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest
index cf9af10bddd2..0749a737c777 100644
--- a/sci-biology/amos/Manifest
+++ b/sci-biology/amos/Manifest
@@ -4,5 +4,5 @@ AUX amos-3.1.0-goBambus2.py-indent-and-cleanup.patch 1057 BLAKE2B fde1011da76275
 AUX amos-3.1.0-qa-Wformat.patch 4511 BLAKE2B 64064175db625a098a528f0c8036196968c58dae445edd3c98fc5627e3a84d593abc438958573ef7a28193d0d2fc76db30fe16a180a383dec9bae5084305505d SHA512 de0382f9128b46fef8e87d14de75bbc9f0af3e8bcbb915edab26a883186109ab29ddbb31c5cf70fc8d37700abe36fb73a7bdca46c29672052d01ebebffd52abe
 DIST amos-3.1.0-fix-c++14.patch.bz2 8033 BLAKE2B 942248f64906253205392df71010bf41105d2985fc8112e7443975d776cc484a4e2b6cf34284d4c384145bf32601892c06f156a0b0ccf0f2ce721de242e02e9b SHA512 76e26ca48a009cbf637d9462878223633e9b21cbd12d58a19e9a561f2cf4805791becc0b5f7aaf81975ca1e02b263cdd9d5ff310c4594670922ea65885ad9634
 DIST amos-3.1.0.tar.gz 2094268 BLAKE2B b9fb80d4e7b7e9e7769081c2680a3cba26591f00a4d9fdb17ad602e581dea5e8e2add4b0d9d3821a7f8a4ec1a45dfd867037baf35ecd401584f030c86b2b0f83 SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491
-EBUILD amos-3.1.0-r3.ebuild 1189 BLAKE2B d0e36265d14eb3b3c0da7e21edc63bc75e3176d52ec0a117fefa394d234f29954809626bd0517a9210b7fa104dae9c72f962b3cde12386da04890f039a5af8a2 SHA512 b2e0386fc5bd65884f4f9ccbdb74ec0f42c37c157cf52c17195fbf390156f242f9c77780323b40fa33e6f5be52863fb0beddd23048695c3e40a65f2272dce7c7
+EBUILD amos-3.1.0-r4.ebuild 1110 BLAKE2B 4730d6a04ba727fd72ea825c6c57d65079ae9ddb29411f0a26aa94653309364ddec742104783044549adc2a60f06a7452f76e392145aa02db472042dde05e1d5 SHA512 7cb40d45dabc4e6cc188d3edf8347f34578d1f955b2d522273f3b551be6974023145e35a443f0e4495d70746aa40b6c451cedf999c102f1f8f7ffbab09748d61
 MISC metadata.xml 345 BLAKE2B 750928cf3e96c24e2af8e84d5889100c1954eb140596368dc00d479f63898c82e3bb0e07a9e970c6c12eb36ed3ae84c6bcc7913cf3ed56e2d71120185d24a4f0 SHA512 a31ba5660e524b70517f2644bb929d4bc0428d1ea682752ca2ddefd3b5a8a5c8aabf7a9877fa61e8fe12599da65e9f0a6c1e7db90d61729e26c33b76303ff497
diff --git a/sci-biology/amos/amos-3.1.0-r3.ebuild b/sci-biology/amos/amos-3.1.0-r4.ebuild
index 33c30995b11b..0dbcaffd81da 100644
--- a/sci-biology/amos/amos-3.1.0-r3.ebuild
+++ b/sci-biology/amos/amos-3.1.0-r4.ebuild
@@ -5,7 +5,7 @@ EAPI=6
 
 PYTHON_COMPAT=( python2_7 )
 
-inherit autotools flag-o-matic python-single-r1 qmake-utils
+inherit autotools flag-o-matic python-single-r1
 
 DESCRIPTION="A Modular, Open-Source whole genome assembler"
 HOMEPAGE="http://amos.sourceforge.net/"
@@ -15,10 +15,10 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz
 LICENSE="Artistic"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="qt4"
+IUSE=""
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
-DEPEND="qt4? ( dev-qt/qtcore:4 )"
+DEPEND=""
 RDEPEND="${DEPEND}
 	${PYTHON_DEPS}
 	dev-perl/DBI
@@ -43,8 +43,7 @@ src_prepare() {
 }
 
 src_configure() {
-	econf \
-		--with-qmake-qt4=$(usex qt4 $(qt4_get_bindir)/qmake no)
+	econf --with-qmake-qt4=no
 }
 
 src_install() {
diff --git a/sci-biology/clustalx/Manifest b/sci-biology/clustalx/Manifest
index 7d3cf91d5636..aae876b740a0 100644
--- a/sci-biology/clustalx/Manifest
+++ b/sci-biology/clustalx/Manifest
@@ -1,5 +1,7 @@
+AUX clustalx-2.1-qt5.patch 8173 BLAKE2B dca2d4f7531ac38510cc9c2aa788244293c436940d38945c906c76b7a29d395179190833517c01cbe48d450111d3f115427fb55536ab55dd01fc0617ff9e7bc2 SHA512 d8c9e9e1aade86f6ba4aa88618ace305152b819cf445119c82b4d4e56c7923e25876c83fd74c8dc91715ce484ff0ea3111b13ed7d8219c1222ad60e09b72d29e
 DIST clustalx-2.1.tar.gz 341649 BLAKE2B 43a740b278127d4745699a75479e422cc95a864bd55a9fe37eb68c0b36ae89e07848e8fdae2207ff9b3850eebc273b803df0261eefd3e7d96d8fa58c75af3adc SHA512 e8cbad783722161de6999ab01a91d555fc10db609197a8d2878f91e9d7dc998784c02d2ccb54c4936ee27b41321db6f4f37021221662f483b8b6d945b6e1c026
 DIST clustalx.png.xz 74808 BLAKE2B 3e0b7ba5d0c4e1013a1ea0146460384279e7116cccde1abdd2e34de16867d83b88c0a04fbc64524e340611fdc5a5df4dbc73f10af610a43fae65c0907b7ac25d SHA512 0907710c944fc1b883c58501cd7bc2abbc5bf171495b58dbe9829d60d7c3530c210f89a5bfafc3cec03808ae50f5c9a78ce37b9175c2e37590494e115e8e343a
 EBUILD clustalx-2.1-r1.ebuild 1093 BLAKE2B 369910c48ad315148d210bf616980a483ca37ec9a27e227876e4057faed667db1ca4bc8dfd760dcce2ccb1d54a3fa7d4fdf3d762bdc7b89908c8bdcbcd2610e6 SHA512 997c71482dff6f73841ba912904b9ea34992ffd9dc90466e233017857a93c11a2f930ff242bfc0b1309bedbf4e6be2556bf26efa9a9f7dfe83d0e96abc06e8a0
 EBUILD clustalx-2.1-r2.ebuild 1225 BLAKE2B 458fb581439821d8eabffc507148a830a74e593f84679757699348d65f1bbe076e5fcba21f0fd2d083256d0de63498378ab87f4a3d74d5f3166fbddd93437954 SHA512 6d0d46521bc2511dca32363e7faf6ff550de74f6e6fcf22f0d3ebd7cbe0f10884dbdb52fcfcba034b4185419d2109663bf1e589d072937b6bbc012fe5ad5c250
+EBUILD clustalx-2.1-r3.ebuild 1336 BLAKE2B 0116719c2b776feedeaae20148ee41c5b8cc1d3ddcb006f1899f0db198d2c8e8ab4b8dc8813a806775c367db2a863df769032f02e35584c3aadef78c60f1f90f SHA512 587d03c86f6faf24bbb49cbc9328923fd9d9634a1bd2360669d1c2e25329ad996c6bc63c717af044fc816f009bab482953a5efcb0d11adff161664da930b1fc6
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/clustalx/clustalx-2.1-r3.ebuild b/sci-biology/clustalx/clustalx-2.1-r3.ebuild
new file mode 100644
index 000000000000..0f9366bee7f5
--- /dev/null
+++ b/sci-biology/clustalx/clustalx-2.1-r3.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit desktop qmake-utils
+
+DESCRIPTION="Graphical interface for the ClustalW multiple alignment program"
+HOMEPAGE="http://www.ebi.ac.uk/tools/clustalw2/"
+SRC_URI="
+	http://www.clustal.org/download/current/${P}.tar.gz
+	https://dev.gentoo.org/~jlec/distfiles/${PN}.png.xz"
+
+LICENSE="GPL-3 LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="
+	dev-qt/qtcore:5
+	dev-qt/qtgui:5
+	dev-qt/qtwidgets:5
+	dev-qt/qtxml:5
+"
+RDEPEND="${DEPEND}
+	>=sci-biology/clustalw-${PV}
+"
+
+PATCHES=( "${FILESDIR}/${P}"-qt5.patch ) # kindly borrowed from Debian
+
+src_prepare() {
+	default
+	sed \
+		-e "s|colprot.xml|${EPREFIX}/usr/share/${PN}/colprot.xml|" \
+		-e "s|coldna.xml|${EPREFIX}/usr/share/${PN}/coldna.xml|" \
+		-e "s|colprint.xml|${EPREFIX}/usr/share/${PN}/colprint.xml|" \
+		-i ClustalQtParams.h || \
+		die "Failed to patch shared files location."
+	sed \
+		-e "s|clustalx.hlp|${EPREFIX}/usr/share/${PN}/clustalx.hlp|" \
+		-i HelpDisplayWidget.cpp || \
+		die "Failed to patch help file location."
+	rm -rf usr || die
+}
+
+src_configure() {
+	eqmake5
+}
+
+src_install() {
+	dobin clustalx
+	insinto /usr/share/${PN}
+	doins colprot.xml coldna.xml colprint.xml clustalx.hlp
+	make_desktop_entry ${PN} ClustalX
+	doicon "${WORKDIR}"/${PN}.png
+}
diff --git a/sci-biology/clustalx/files/clustalx-2.1-qt5.patch b/sci-biology/clustalx/files/clustalx-2.1-qt5.patch
new file mode 100644
index 000000000000..96b108c14474
--- /dev/null
+++ b/sci-biology/clustalx/files/clustalx-2.1-qt5.patch
@@ -0,0 +1,295 @@
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 11 Sep 2017 09:30:38 +0200
+Description: Porting to Qt5 following the hints at
+   https://wiki.qt.io/Transition_from_Qt_4.x_to_Qt5#QtWidgets_as_a_Separate_Module
+   https://wiki.qt.io/Transition_from_Qt_4.x_to_Qt5#toAscii.28.29_and_fromAscii.28.29_Methods_are_deprecated
+
+--- a/clustalx.pro
++++ b/clustalx.pro
+@@ -6,6 +6,7 @@ TEMPLATE = app
+ TARGET = clustalx
+ CONFIG += release static
+ QT += xml
++QT += widgets
+ VERSION = 2.1
+ win32 {
+    DEFINES += OS_WINDOWS
+--- a/AlignOutputFileNames.cpp
++++ b/AlignOutputFileNames.cpp
+@@ -20,7 +20,7 @@
+ #include <QGridLayout>
+ #include <QSizePolicy>
+ #include <QComboBox>
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QLabel>
+ #include <iostream>
+ #include "AlignOutputFileNames.h"
+--- a/AlignmentFormatOptions.cpp
++++ b/AlignmentFormatOptions.cpp
+@@ -5,7 +5,7 @@
+ #include <QGridLayout>
+ #include <QSizePolicy>
+ #include <QComboBox>
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QLabel>
+ #include "AlignmentFormatOptions.h"
+ #include "clustalW/general/userparams.h"
+--- a/AlignmentParameters.cpp
++++ b/AlignmentParameters.cpp
+@@ -11,7 +11,7 @@
+ #include <QGridLayout>
+ #include <QSizePolicy>
+ #include <QComboBox>
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QLabel>
+ #include <QButtonGroup>
+ #include <QLineEdit>
+--- a/AlignmentViewerWidget.cpp
++++ b/AlignmentViewerWidget.cpp
+@@ -60,7 +60,7 @@
+  *****************************************************************************/
+ 
+ 
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QFile>
+ #include <QTextStream>
+ #include "AlignmentViewerWidget.h"
+--- a/AlignmentWidget.cpp
++++ b/AlignmentWidget.cpp
+@@ -45,7 +45,7 @@
+  *
+  ****************************************************************************/
+ 
+-#include <QtGui>
++#include <QtWidgets>
+ #include "AlignmentWidget.h"
+ #include "clustalW/general/userparams.h"
+ #include "ClustalQtParams.h"
+--- a/BootstrapTreeDialog.cpp
++++ b/BootstrapTreeDialog.cpp
+@@ -12,7 +12,7 @@
+ #include <QGridLayout>
+ #include <QSizePolicy>
+ #include <QComboBox>
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QLabel>
+ #include <iostream>
+ #include "BootstrapTreeDialog.h"
+--- a/ColorFileXmlParser.cpp
++++ b/ColorFileXmlParser.cpp
+@@ -1,4 +1,4 @@
+-#include <QtGui>
++#include <QtWidgets>
+ 
+ #include "ColorFileXmlParser.h"
+ #include "ClustalQtParams.h"
+--- a/ColumnScoreParams.cpp
++++ b/ColumnScoreParams.cpp
+@@ -11,7 +11,7 @@
+ #include <QGridLayout>
+ #include <QSizePolicy>
+ #include <QComboBox>
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QLabel>
+ #include <QButtonGroup>
+ #include <QLineEdit>
+--- a/HelpDisplayWidget.cpp
++++ b/HelpDisplayWidget.cpp
+@@ -16,7 +16,7 @@
+ #include <QTextEdit>
+ #include <iostream>
+ #include <fstream>
+-#include <QtGui>
++#include <QtWidgets>
+ #include "Resources.h"
+ 
+ const string HelpDisplayWidget::helpFileName = "/usr/share/clustalx/clustalx.hlp";
+--- a/HistogramWidget.cpp
++++ b/HistogramWidget.cpp
+@@ -21,7 +21,7 @@
+  ****************************************************************************/
+ 
+ #include "HistogramWidget.h"
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QImage>
+ //#include <QPixmap>
+ #include <QPoint>
+--- a/LowScoringSegParams.cpp
++++ b/LowScoringSegParams.cpp
+@@ -12,7 +12,7 @@
+ #include <QHBoxLayout>
+ #include <QSizePolicy>
+ #include <QComboBox>
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QLabel>
+ #include <QButtonGroup>
+ #include <QLineEdit>
+--- a/PSPrinter.cpp
++++ b/PSPrinter.cpp
+@@ -16,7 +16,7 @@
+ #include <ctime>
+ #include <iomanip>
+ #include <sstream>
+-#include <QtGui>
++#include <QtWidgets>
+ #include "PSPrinter.h"
+ #include "ColorFileXmlParser.h"
+ #include "clustalW/general/userparams.h"
+@@ -594,7 +594,7 @@ void PSPrinter::printHeaderLine(ofstream
+     {
+         psX = blockLeft + (i - fr) * CHARWIDTH; 
+         (*psOutFile) << "(";
+-        (*psOutFile) << data->seqHeader[ix][i].toAscii();
++        (*psOutFile) << data->seqHeader[ix][i].toLatin1();
+         (*psOutFile) << ") ";
+         (*psOutFile) << psX << " " << psY << " " << psX << " " 
+                      << psY << " 1.0 1.0 1.0 color_inv\n";
+--- a/PairwiseParams.cpp
++++ b/PairwiseParams.cpp
+@@ -18,7 +18,7 @@
+ #include <QRadioButton>
+ #include <QMessageBox>
+ #include <QHBoxLayout>
+-#include <QtGui>
++#include <QtWidgets>
+ #include "clustalW/general/userparams.h"
+ #include "clustalW/substitutionMatrix/globalmatrix.h"
+ #include "FileDialog.h"
+--- a/ProteinGapParameters.cpp
++++ b/ProteinGapParameters.cpp
+@@ -5,7 +5,7 @@
+ #include <QGridLayout>
+ #include <QSizePolicy>
+ #include <QComboBox>
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QLabel>
+ #include <QString>
+ #include <QMessageBox>
+--- a/SaveSeqFile.cpp
++++ b/SaveSeqFile.cpp
+@@ -18,7 +18,7 @@
+ #include <QGridLayout>
+ #include <QSizePolicy>
+ #include <QComboBox>
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QLabel>
+ #include "SaveSeqFile.h"
+ #include "clustalW/general/userparams.h"
+--- a/SecStructOptions.cpp
++++ b/SecStructOptions.cpp
+@@ -5,7 +5,7 @@
+ #include <QGridLayout>
+ #include <QSizePolicy>
+ #include <QComboBox>
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QLabel>
+ #include <QLineEdit>
+ #include "SecStructOptions.h"
+--- a/SeqNameWidget.cpp
++++ b/SeqNameWidget.cpp
+@@ -55,7 +55,7 @@
+  * 
+  ****************************************************************************/
+ 
+-#include <QtGui>
++#include <QtWidgets>
+ #include "SeqNameWidget.h"
+ #include "KeyController.h" //- nige
+ #include "clustalW/alignment/Alignment.h"
+--- a/TreeFormatOptions.cpp
++++ b/TreeFormatOptions.cpp
+@@ -4,7 +4,7 @@
+ #include <QGridLayout>
+ #include <QSizePolicy>
+ #include <QComboBox>
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QLabel>
+ #include <QCheckBox>
+ #include "TreeFormatOptions.h"
+--- a/TreeOutputFileNames.cpp
++++ b/TreeOutputFileNames.cpp
+@@ -11,7 +11,7 @@
+ #include <QGridLayout>
+ #include <QSizePolicy>
+ #include <QComboBox>
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QLabel>
+ #include <iostream>
+ #include "TreeOutputFileNames.h"
+--- a/WritePostscriptFile.cpp
++++ b/WritePostscriptFile.cpp
+@@ -18,7 +18,7 @@
+ #include <QGridLayout>
+ #include <QSizePolicy>
+ #include <QComboBox>
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QLabel>
+ #include <iostream>
+ #include "WritePostscriptFile.h"
+--- a/mainwindow.cpp
++++ b/mainwindow.cpp
+@@ -87,7 +87,7 @@
+  *
+  ****************************************************************************/
+ 
+-#include <QtGui>
++#include <QtWidgets>
+ #include <QPixmap>
+ #include <QFile>
+ #include <iostream>
+--- a/ColorParameters.cpp
++++ b/ColorParameters.cpp
+@@ -154,8 +154,8 @@ QColor ColorParameters::getResidueColor(
+ {
+     int i, j;
+     QChar colorParRes;
+-    char showRes = res.toAscii();
+-    char showCon = consensus.toAscii();
++    char showRes = res.toLatin1();
++    char showCon = consensus.toLatin1();
+     
+     for(i = 0; i < colorPar.size(); i++)
+     {
+@@ -171,7 +171,7 @@ QColor ColorParameters::getResidueColor(
+                 
+                 for(j = 0; j < colorPar[i].consensusConditionList.size(); j++)
+                 {
+-                    char temp = colorPar[i].consensusConditionList[j].toAscii();
++                    char temp = colorPar[i].consensusConditionList[j].toLatin1();
+                     if(consensus == colorPar[i].consensusConditionList[j])
+                     {
+                         return colorPar[i].color;
+@@ -191,8 +191,8 @@ int ColorParameters::getResidueColorNum(
+ {
+     int i, j;
+     QChar colorParRes;
+-    char showRes = res.toAscii();
+-    char showCon = consensus.toAscii();
++    char showRes = res.toLatin1();
++    char showCon = consensus.toLatin1();
+     
+     for(i = 0; i < colorPar.size(); i++)
+     {
+@@ -208,7 +208,7 @@ int ColorParameters::getResidueColorNum(
+                 
+                 for(j = 0; j < colorPar[i].consensusConditionList.size(); j++)
+                 {
+-                    char temp = colorPar[i].consensusConditionList[j].toAscii();
++                    char temp = colorPar[i].consensusConditionList[j].toLatin1();
+                     if(consensus == colorPar[i].consensusConditionList[j])
+                     {
+                         return getIndexOfColor(colorPar[i].color);