commit: b21882a02b227d9345060b5d209a48f8b6dd7b0f Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> AuthorDate: Sun Apr 13 19:39:01 2025 +0000 Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> CommitDate: Mon Apr 14 21:14:55 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b21882a0
sci-biology/clustalx: treeclean Closes: https://bugs.gentoo.org/947634 (pkgremoved) Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org> profiles/package.mask | 6 - sci-biology/clustalx/Manifest | 2 - sci-biology/clustalx/clustalx-2.1-r3.ebuild | 55 ---- sci-biology/clustalx/files/clustalx-2.1-qt5.patch | 295 ---------------------- sci-biology/clustalx/metadata.xml | 8 - 5 files changed, 366 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 08388cf53530..40474ba88fc3 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -382,12 +382,6 @@ dev-vcs/notify-webhook # https://github.com/lkrg-org/lkrg/issues/364 =app-antivirus/lkrg-0.9.9 -# Andreas Sturmlechner <[email protected]> (2025-03-01) -# Last release 14 years ago, dead upstream, depends on Qt5 (and even that -# only by means of downstream patching). Bug #947634. -# Removal on 2025-04-15. -sci-biology/clustalx - # Eray Aslan <[email protected]> (2025-02-24) # Mask experimental software =mail-mta/postfix-3.11* diff --git a/sci-biology/clustalx/Manifest b/sci-biology/clustalx/Manifest deleted file mode 100644 index d7f84169aed4..000000000000 --- a/sci-biology/clustalx/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST clustalx-2.1.tar.gz 341649 BLAKE2B 43a740b278127d4745699a75479e422cc95a864bd55a9fe37eb68c0b36ae89e07848e8fdae2207ff9b3850eebc273b803df0261eefd3e7d96d8fa58c75af3adc SHA512 e8cbad783722161de6999ab01a91d555fc10db609197a8d2878f91e9d7dc998784c02d2ccb54c4936ee27b41321db6f4f37021221662f483b8b6d945b6e1c026 -DIST clustalx.png.xz 74808 BLAKE2B 3e0b7ba5d0c4e1013a1ea0146460384279e7116cccde1abdd2e34de16867d83b88c0a04fbc64524e340611fdc5a5df4dbc73f10af610a43fae65c0907b7ac25d SHA512 0907710c944fc1b883c58501cd7bc2abbc5bf171495b58dbe9829d60d7c3530c210f89a5bfafc3cec03808ae50f5c9a78ce37b9175c2e37590494e115e8e343a diff --git a/sci-biology/clustalx/clustalx-2.1-r3.ebuild b/sci-biology/clustalx/clustalx-2.1-r3.ebuild deleted file mode 100644 index ae15401a3488..000000000000 --- a/sci-biology/clustalx/clustalx-2.1-r3.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit desktop qmake-utils - -DESCRIPTION="Graphical interface for the ClustalW multiple alignment program" -HOMEPAGE="https://www.ebi.ac.uk/Tools/msa/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" - -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 -r 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 deleted file mode 100644 index 96b108c14474..000000000000 --- a/sci-biology/clustalx/files/clustalx-2.1-qt5.patch +++ /dev/null @@ -1,295 +0,0 @@ -Author: Andreas Tille <[email protected]> -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); diff --git a/sci-biology/clustalx/metadata.xml b/sci-biology/clustalx/metadata.xml deleted file mode 100644 index ccdff086e20b..000000000000 --- a/sci-biology/clustalx/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata>
![https://dev.gentoo.org/~jlec/distfiles/${PN}.png.xz"](https://dev.gentoo.org/~jlec/distfiles/${PN}.png.xz"){kind=link}