Merge branch 'master' into core-updates

20 files changed, 813 insertions, 1862 deletions

diff --git a/gnu/packages/patches/avogadro-boost148.patch b/gnu/packages/patches/avogadro-boost148.patch
deleted file mode 100644
index f244f14674..0000000000
--- a/gnu/packages/patches/avogadro-boost148.patch
+++ /dev/null
@@ -1,69 +0,0 @@
-Index: avogadro-1.2.0/libavogadro/src/pythonengine_p.h
-===================================================================
---- avogadro-1.2.0.orig/libavogadro/src/pythonengine_p.h
-+++ avogadro-1.2.0/libavogadro/src/pythonengine_p.h
-@@ -31,7 +31,9 @@
- 
- #include <avogadro/global.h>
- #include <avogadro/engine.h>
-+#ifndef Q_MOC_RUN
- #include <boost/python.hpp>
-+#endif
- 
- namespace Avogadro {
- 
-Index: avogadro-1.2.0/libavogadro/src/pythonextension_p.h
-===================================================================
---- avogadro-1.2.0.orig/libavogadro/src/pythonextension_p.h
-+++ avogadro-1.2.0/libavogadro/src/pythonextension_p.h
-@@ -33,7 +33,9 @@
- #include <avogadro/extension.h>
- #include <avogadro/primitive.h>
- #include <avogadro/glwidget.h>
-+#ifndef Q_MOC_RUN
- #include <boost/python.hpp>
-+#endif
- 
- #include <QWidget>
- #include <QList>
-Index: avogadro-1.2.0/libavogadro/src/pythontool_p.h
-===================================================================
---- avogadro-1.2.0.orig/libavogadro/src/pythontool_p.h
-+++ avogadro-1.2.0/libavogadro/src/pythontool_p.h
-@@ -31,7 +31,9 @@
- 
- #include <avogadro/global.h>
- #include <avogadro/tool.h>
-+#ifndef Q_MOC_RUN
- #include <boost/python.hpp>
-+#endif
- 
- #include <QObject>
- #include <QAction>
-Index: avogadro-1.2.0/libavogadro/src/pythoninterpreter.h
-===================================================================
---- avogadro-1.2.0.orig/libavogadro/src/pythoninterpreter.h
-+++ avogadro-1.2.0/libavogadro/src/pythoninterpreter.h
-@@ -26,7 +26,9 @@
- #define PYTHONINTERPRETER_H
- 
- #include <avogadro/global.h>
-+#ifndef Q_MOC_RUN
- #include <boost/python.hpp>
-+#endif
- #include <avogadro/primitive.h>
- #include <QString>
- 
-Index: avogadro-1.2.0/libavogadro/src/pythonscript.h
-===================================================================
---- avogadro-1.2.0.orig/libavogadro/src/pythonscript.h
-+++ avogadro-1.2.0/libavogadro/src/pythonscript.h
-@@ -27,6 +27,8 @@
- #define PYTHONSCRIPT_H
- 
- #include <avogadro/global.h>
-+#ifndef Q_MOC_RUN
- #include <boost/python.hpp>
-+#endif
- 
- #include "pythonerror.h"
diff --git a/gnu/packages/patches/avogadro-eigen3-update.patch b/gnu/packages/patches/avogadro-eigen3-update.patch
deleted file mode 100644
index a5f669292f..0000000000
--- a/gnu/packages/patches/avogadro-eigen3-update.patch
+++ /dev/null
@@ -1,603 +0,0 @@
-From 43af3c117b0b3220b15c2fe2895b94bbd83d3a60 Mon Sep 17 00:00:00 2001
-From: Claudio Fernandes <claudiosf.claudio@gmail.com>
-Date: Sun, 15 Jan 2017 21:23:39 -0200
-Subject: [PATCH] Adapt Avogadro to Eigen 3.3
-
----
- CMakeLists.txt                                     |  9 +------
- avogadro/src/mainwindow.cpp                        |  5 ++--
- libavogadro/src/camera.cpp                         | 10 ++++----
- libavogadro/src/camera.h                           | 14 +++++------
- libavogadro/src/engines/wireengine.cpp             |  4 ++--
- .../crystallography/crystallographyextension.cpp   |  2 +-
- .../crystallography/ui/ceviewoptionswidget.cpp     |  2 +-
- .../src/extensions/orca/orcaanalysedialog.cpp      |  1 -
- .../src/extensions/orca/orcainputdialog.cpp        |  1 -
- .../src/extensions/qtaim/qtaimmathutilities.cpp    |  1 +
- .../qtaim/qtaimwavefunctionevaluator.cpp           | 28 +++++++++++-----------
- .../extensions/surfaces/openqube/gamessukout.cpp   |  1 +
- .../src/extensions/surfaces/openqube/slaterset.cpp |  6 +++--
- libavogadro/src/glpainter_p.cpp                    | 14 +++++------
- libavogadro/src/glwidget.cpp                       |  4 ++--
- libavogadro/src/molecule.cpp                       | 26 ++++++++++++++++++--
- libavogadro/src/navigate.cpp                       |  2 +-
- libavogadro/src/tools/bondcentrictool.cpp          | 28 +++++++++++-----------
- libavogadro/src/tools/manipulatetool.cpp           | 17 +++++++------
- libavogadro/src/tools/navigatetool.cpp             |  3 ++-
- libavogadro/src/tools/skeletontree.cpp             |  7 +++---
- libavogadro/src/tools/skeletontree.h               |  2 +-
- 22 files changed, 102 insertions(+), 85 deletions(-)
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -231,14 +231,7 @@ if(NOT Linguist_FOUND)
-   message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations")
- endif()
- 
--find_package(Eigen3) # find and setup Eigen3 if available
--if(NOT EIGEN3_FOUND)
--   message(STATUS "Cannot find Eigen3, trying Eigen2")
--   find_package(Eigen2 REQUIRED) # Some version is required
--else()
--# Use Stage10 Eigen3 support
--   set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE)
--endif()
-+find_package(Eigen3 REQUIRED) # find and setup Eigen3 if available
- 
- find_package(ZLIB REQUIRED)
- find_package(OpenBabel2 REQUIRED) # find and setup OpenBabel
---- a/avogadro/src/mainwindow.cpp
-+++ b/avogadro/src/mainwindow.cpp
-@@ -115,7 +115,6 @@
- #include <QDebug>
- 
- #include <Eigen/Geometry>
--#include <Eigen/Array>
- #define USEQUAT
- // This is a "hidden" exported Qt function on the Mac for Qt-4.x.
- #ifdef Q_WS_MAC
-@@ -2775,7 +2774,7 @@ protected:
-     linearGoal.row(1) = linearGoal.row(2).cross(linearGoal.row(0));
- 
-     // calculate the translation matrix
--    Transform3d goal(linearGoal);
-+    Projective3d goal(linearGoal);
- 
-     goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
- 
-@@ -2840,7 +2839,7 @@ protected:
-     Matrix3d linearGoal = Matrix3d::Identity();
- 
-     // calculate the translation matrix
--    Transform3d goal(linearGoal);
-+    Projective3d goal(linearGoal);
- 
-     goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
- 
---- a/libavogadro/src/camera.cpp
-+++ b/libavogadro/src/camera.cpp
-@@ -47,7 +47,7 @@ namespace Avogadro
- 
-       CameraPrivate() {};
- 
--      Eigen::Transform3d modelview, projection;
-+      Eigen::Projective3d modelview, projection;
-       const GLWidget *parent;
-       double angleOfViewY;
-       double orthoScale;
-@@ -169,20 +169,20 @@ namespace Avogadro
- 
-   double Camera::distance(const Eigen::Vector3d & point) const
-   {
--    return ( d->modelview * point ).norm();
-+    return ( d->modelview * point.homogeneous() ).head<3>().norm();
-   }
- 
--  void Camera::setModelview(const Eigen::Transform3d &matrix)
-+  void Camera::setModelview(const Eigen::Projective3d &matrix)
-   {
-     d->modelview = matrix;
-   }
- 
--  const Eigen::Transform3d & Camera::modelview() const
-+  const Eigen::Projective3d & Camera::modelview() const
-   {
-     return d->modelview;
-   }
- 
--  Eigen::Transform3d & Camera::modelview()
-+  Eigen::Projective3d & Camera::modelview()
-   {
-     return d->modelview;
-   }
---- a/libavogadro/src/camera.h
-+++ b/libavogadro/src/camera.h
-@@ -101,16 +101,16 @@ namespace Avogadro {
-       double angleOfViewY() const;
-       /** Sets 4x4 "modelview" matrix representing the camera orientation and position.
-         * @param matrix the matrix to copy from
--        * @sa Eigen::Transform3d & modelview(), applyModelview() */
--      void setModelview(const Eigen::Transform3d &matrix);
-+        * @sa Eigen::Projective3d & modelview(), applyModelview() */
-+      void setModelview(const Eigen::Projective3d &matrix);
-       /** @return a constant reference to the 4x4 "modelview" matrix representing
-         *         the camera orientation and position
--        * @sa setModelview(), Eigen::Transform3d & modelview() */
--      const Eigen::Transform3d & modelview() const;
-+        * @sa setModelview(), Eigen::Projective3d & modelview() */
-+      const Eigen::Projective3d & modelview() const;
-       /** @return a non-constant reference to the 4x4 "modelview" matrix representing
-         *         the camera orientation and position
--        * @sa setModelview(), const Eigen::Transform3d & modelview() const */
--      Eigen::Transform3d & modelview();
-+        * @sa setModelview(), const Eigen::Projective3d & modelview() const */
-+      Eigen::Projective3d & modelview();
-       /** Calls gluPerspective() or glOrtho() with parameters automatically chosen
-         * for rendering the GLWidget's molecule with this camera. Should be called
-         * only in GL_PROJECTION matrix mode. Example code is given
-@@ -342,7 +342,7 @@ namespace Avogadro {
-        * @return {x/w, y/w, z/w} vector
-        */
-       Eigen::Vector3d V4toV3DivW(const Eigen::Vector4d & v4) {
--        return v4.start<3>()/v4.w();
-+        return v4.head<3>()/v4.w();
-       }
-   };
- 
---- a/libavogadro/src/engines/wireengine.cpp
-+++ b/libavogadro/src/engines/wireengine.cpp
-@@ -109,7 +109,7 @@ namespace Avogadro {
-     const Camera *camera = pd->camera();
- 
-     // perform a rough form of frustum culling
--    Eigen::Vector3d transformedPos = pd->camera()->modelview() * v;
-+    Eigen::Vector3d transformedPos = (pd->camera()->modelview() * v.homogeneous()).head<3>();
-     double dot = transformedPos.z() / transformedPos.norm();
-     if(dot > -0.8)
-       return true;
-@@ -167,7 +167,7 @@ namespace Avogadro {
-       map = pd->colorMap(); // fall back to global color map
- 
-     // perform a rough form of frustum culling
--    Eigen::Vector3d transformedEnd1 = pd->camera()->modelview() * v1;
-+    Eigen::Vector3d transformedEnd1 = (pd->camera()->modelview() * v1.homogeneous()).head<3>();
-     double dot = transformedEnd1.z() / transformedEnd1.norm();
-     if(dot > -0.8)
-       return true; // i.e., don't bother rendering
---- a/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
-+++ b/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
-@@ -1989,7 +1989,7 @@ namespace Avogadro
-     // fix coordinates
-     // Apply COB matrix:
-     Eigen::Matrix3d invCob;
--    cob.computeInverse(&invCob);
-+    invCob = cob.inverse();
-     for (QList<Eigen::Vector3d>::iterator
-            it = fcoords.begin(),
-            it_end = fcoords.end();
---- a/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
-+++ b/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
-@@ -139,7 +139,7 @@ namespace Avogadro
-   {
-     // View into a Miller plane
-     Camera *camera = m_glWidget->camera();
--    Eigen::Transform3d modelView;
-+    Eigen::Projective3d modelView;
-     modelView.setIdentity();
- 
-     // OK, so we want to rotate to look along the normal at the plane
---- a/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
-+++ b/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
-@@ -41,7 +41,6 @@
- #include <openbabel/mol.h>
- 
- #include <Eigen/Geometry>
--#include <Eigen/LeastSquares>
- 
- #include <vector>
- 
---- a/libavogadro/src/extensions/orca/orcainputdialog.cpp
-+++ b/libavogadro/src/extensions/orca/orcainputdialog.cpp
-@@ -33,7 +33,6 @@
- #include <openbabel/mol.h>
- 
- #include <Eigen/Geometry>
--#include <Eigen/LeastSquares>
- 
- #include <vector>
- 
---- a/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
-+++ b/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
-@@ -28,6 +28,7 @@
- 
- #include <cmath>
- #include <Eigen/QR>
-+#include <Eigen/Eigenvalues>
- 
- namespace Avogadro {
-   namespace QTAIMMathUtilities {
---- a/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
-+++ b/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
-@@ -35,21 +35,21 @@ namespace Avogadro
-     m_nprim=wfn.numberOfGaussianPrimitives();
-     m_nnuc=wfn.numberOfNuclei();
- 
--    m_nucxcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.xNuclearCoordinates(),m_nnuc);
--    m_nucycoord=Map<Matrix<qreal,Dynamic,1> >(wfn.yNuclearCoordinates(),m_nnuc);
--    m_nuczcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.zNuclearCoordinates(),m_nnuc);
--    m_nucz=Map<Matrix<qint64,Dynamic,1> >(wfn.nuclearCharges(),m_nnuc);
--    m_X0=Map<Matrix<qreal,Dynamic,1> >(wfn.xGaussianPrimitiveCenterCoordinates(),m_nprim,1);
--    m_Y0=Map<Matrix<qreal,Dynamic,1> >(wfn.yGaussianPrimitiveCenterCoordinates(),m_nprim,1);
--    m_Z0=Map<Matrix<qreal,Dynamic,1> >(wfn.zGaussianPrimitiveCenterCoordinates(),m_nprim,1);
--    m_xamom=Map<Matrix<qint64,Dynamic,1> >(wfn.xGaussianPrimitiveAngularMomenta(),m_nprim,1);
--    m_yamom=Map<Matrix<qint64,Dynamic,1> >(wfn.yGaussianPrimitiveAngularMomenta(),m_nprim,1);
--    m_zamom=Map<Matrix<qint64,Dynamic,1> >(wfn.zGaussianPrimitiveAngularMomenta(),m_nprim,1);
--    m_alpha=Map<Matrix<qreal,Dynamic,1> >(wfn.gaussianPrimitiveExponentCoefficients(),m_nprim,1);
-+    m_nucxcoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.xNuclearCoordinates()),m_nnuc);
-+    m_nucycoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.yNuclearCoordinates()),m_nnuc);
-+    m_nuczcoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.zNuclearCoordinates()),m_nnuc);
-+    m_nucz=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.nuclearCharges()),m_nnuc);
-+    m_X0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.xGaussianPrimitiveCenterCoordinates()),m_nprim,1);
-+    m_Y0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.yGaussianPrimitiveCenterCoordinates()),m_nprim,1);
-+    m_Z0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.zGaussianPrimitiveCenterCoordinates()),m_nprim,1);
-+    m_xamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.xGaussianPrimitiveAngularMomenta()),m_nprim,1);
-+    m_yamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.yGaussianPrimitiveAngularMomenta()),m_nprim,1);
-+    m_zamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.zGaussianPrimitiveAngularMomenta()),m_nprim,1);
-+    m_alpha=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.gaussianPrimitiveExponentCoefficients()),m_nprim,1);
-     // TODO Implement screening for unoccupied molecular orbitals.
--    m_occno=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalOccupationNumbers(),m_nmo,1);
--    m_orbe=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalEigenvalues(),m_nmo,1);
--    m_coef=Map<Matrix<qreal,Dynamic,Dynamic,RowMajor> >(wfn.molecularOrbitalCoefficients(),m_nmo,m_nprim);
-+    m_occno=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.molecularOrbitalOccupationNumbers()),m_nmo,1);
-+    m_orbe=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.molecularOrbitalEigenvalues()),m_nmo,1);
-+    m_coef=Map<Matrix<qreal,Dynamic,Dynamic,RowMajor> >(const_cast<qreal*>(wfn.molecularOrbitalCoefficients()),m_nmo,m_nprim);
-     m_totalEnergy=wfn.totalEnergy();
-     m_virialRatio=wfn.virialRatio();
- 
---- a/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
-+++ b/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
-@@ -19,6 +19,7 @@
- using Eigen::Vector3d;
- using std::vector;
- 
-+#include <iostream>
- #include <fstream>
- 
- namespace OpenQube
---- a/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
-+++ b/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
-@@ -25,9 +25,9 @@
- 
- #include "cube.h"
- 
--#include <Eigen/Array>
- #include <Eigen/LU>
- #include <Eigen/QR>
-+#include <Eigen/Eigenvalues>
- 
- #include <cmath>
- 
-@@ -250,7 +250,9 @@ bool SlaterSet::initialize()
- 
-   SelfAdjointEigenSolver<MatrixXd> s(m_overlap);
-   MatrixXd p = s.eigenvectors();
--  MatrixXd m = p * s.eigenvalues().cwise().inverse().cwise().sqrt().asDiagonal() * p.inverse();
-+  // TODO check if this is correct
-+  MatrixXd m1 = (s.eigenvalues().array().inverse().sqrt());
-+  MatrixXd m = p.array()*(m1.diagonal().array())*p.inverse().array();
-   m_normalized = m * m_eigenVectors;
- 
-   if (!(m_overlap*m*m).isIdentity())
---- a/libavogadro/src/glpainter_p.cpp
-+++ b/libavogadro/src/glpainter_p.cpp
-@@ -789,13 +789,13 @@ namespace Avogadro
-         } else {
-           points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
-         }
--        points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
-+        points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
-       }
- 
-     // Get vectors representing the points' positions in terms of the model view.
--    Eigen::Vector3d _origin = d->widget->camera()->modelview() * origin;
--    Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin+u);
--    Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin+v);
-+    Eigen::Vector3d _origin = (d->widget->camera()->modelview() * origin.homogeneous()).head<3>();
-+    Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin+u).homogeneous()).head<3>();
-+    Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin+v).homogeneous()).head<3>();
- 
-     glPushAttrib(GL_ALL_ATTRIB_BITS);
-     glPushMatrix();
-@@ -880,12 +880,12 @@ namespace Avogadro
-         } else {
-           points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
-         }
--        points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
-+        points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
-       }
- 
-     // Get vectors representing the points' positions in terms of the model view.
--    Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin + u);
--    Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin + v);
-+    Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin + u).homogeneous()).head<3>();
-+    Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin + v).homogeneous()).head<3>();
- 
-     glPushAttrib(GL_ALL_ATTRIB_BITS);
-     glPushMatrix();
---- a/libavogadro/src/glwidget.cpp
-+++ b/libavogadro/src/glwidget.cpp
-@@ -765,7 +765,7 @@ namespace Avogadro {
-       GLfloat fogColor[4]= {static_cast<GLfloat>(d->background.redF()), static_cast<GLfloat>(d->background.greenF()),
-                             static_cast<GLfloat>(d->background.blueF()), static_cast<GLfloat>(d->background.alphaF())};
-       glFogfv(GL_FOG_COLOR, fogColor);
--      Vector3d distance = camera()->modelview() * d->center;
-+      Vector3d distance = (camera()->modelview() * d->center.homogeneous()).head<3>();
-       double distanceToCenter = distance.norm();
-       glFogf(GL_FOG_DENSITY, 1.0);
-       glHint(GL_FOG_HINT, GL_NICEST);
-@@ -1711,7 +1711,7 @@ namespace Avogadro {
- 
-       if (d->renderModelViewDebug) {
-         // Model view matrix:
--        const Eigen::Transform3d &modelview = d->camera->modelview();
-+        const Eigen::Projective3d &modelview = d->camera->modelview();
-         y += d->pd->painter()->drawText
-             (x, y, tr("ModelView row 1: %L1 %L2 %L3 %L4")
-              .arg(modelview(0, 0), 6, 'f', 2, ' ')
---- a/libavogadro/src/molecule.cpp
-+++ b/libavogadro/src/molecule.cpp
-@@ -38,7 +38,7 @@
- #include "zmatrix.h"
- 
- #include <Eigen/Geometry>
--#include <Eigen/LeastSquares>
-+#include <Eigen/Eigenvalues>
- 
- #include <vector>
- 
-@@ -1907,7 +1907,29 @@ namespace Avogadro{
-         }
-         d->center /= static_cast<double>(nAtoms);
-         Eigen::Hyperplane<double, 3> planeCoeffs;
--        Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
-+        //Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
-+
-+        // TODO check if this is OK
-+        /************************/
-+        typedef Eigen::Matrix<double,3,3> CovMatrixType;
-+        typedef Eigen::Vector3d VectorType;
-+        
-+        VectorType mean = d->center;
-+        int size=3;
-+        int numPoints=numAtoms();
-+        VectorType ** points=atomPositions;
-+        CovMatrixType covMat = CovMatrixType::Zero(size, size);
-+        VectorType remean = VectorType::Zero(size);
-+        for(int i = 0; i < numPoints; ++i)
-+        {
-+          VectorType diff = (*(points[i]) - mean).conjugate();
-+          covMat += diff * diff.adjoint();
-+        }
-+        Eigen::SelfAdjointEigenSolver<CovMatrixType> eig(covMat);
-+        planeCoeffs.normal() = eig.eigenvectors().col(0);
-+        /************************/
-+
-+
-         delete[] atomPositions;
-         d->normalVector = planeCoeffs.normal();
-       }
---- a/libavogadro/src/navigate.cpp
-+++ b/libavogadro/src/navigate.cpp
-@@ -40,7 +40,7 @@ namespace Avogadro {
-   void Navigate::zoom(GLWidget *widget, const Eigen::Vector3d &goal,
-                       double delta)
-   {
--    Vector3d transformedGoal = widget->camera()->modelview() * goal;
-+    Vector3d transformedGoal = (widget->camera()->modelview() * goal.homogeneous()).head<3>();
-     double distanceToGoal = transformedGoal.norm();
- 
-     double t = ZOOM_SPEED * delta;
---- a/libavogadro/src/tools/bondcentrictool.cpp
-+++ b/libavogadro/src/tools/bondcentrictool.cpp
-@@ -578,8 +578,8 @@ namespace Avogadro {
- 
-           Vector3d clicked = *m_clickedAtom->pos();
- 
--          Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
--                (widget->camera()->modelview() * center).z() ? -1 : 1));
-+          Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other.homogeneous()).z() >=
-+                (widget->camera()->modelview() * center.homogeneous()).z() ? -1 : 1));
- 
-           Vector3d centerProj = widget->camera()->project(center);
-           centerProj -= Vector3d(0,0,centerProj.z());
-@@ -673,8 +673,8 @@ namespace Avogadro {
- 
-           Vector3d clicked = *m_clickedAtom->pos();
- 
--          Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
--                (widget->camera()->modelview() * center).z() ? -1 : 1));
-+          Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other.homogeneous()).z() >=
-+                (widget->camera()->modelview() * center.homogeneous()).z() ? -1 : 1));
- 
-           Vector3d centerProj = widget->camera()->project(center);
-           centerProj -= Vector3d(0,0,centerProj.z());
-@@ -1362,10 +1362,10 @@ namespace Avogadro {
- 
-     planeVec = length * (planeVec / planeVec.norm());
- 
--    Vector3d topLeft = widget->camera()->modelview() * (left + planeVec);
--    Vector3d topRight = widget->camera()->modelview() * (right + planeVec);
--    Vector3d botRight = widget->camera()->modelview() * (right - planeVec);
--    Vector3d botLeft = widget->camera()->modelview() * (left - planeVec);
-+    Vector3d topLeft = (widget->camera()->modelview() * (left + planeVec).homogeneous()).head<3>();
-+    Vector3d topRight = (widget->camera()->modelview() * (right + planeVec).homogeneous()).head<3>();
-+    Vector3d botRight = (widget->camera()->modelview() * (right - planeVec).homogeneous()).head<3>();
-+    Vector3d botLeft = (widget->camera()->modelview() * (left - planeVec).homogeneous()).head<3>();
- 
-     float alpha = 0.4;
-     double lineWidth = 1.5;
-@@ -1444,10 +1444,10 @@ namespace Avogadro {
-       C = D + ((C-D).normalized() * minWidth);
-     }
- 
--    Vector3d topLeft = widget->camera()->modelview() * D;
--    Vector3d topRight = widget->camera()->modelview() * C;
--    Vector3d botRight = widget->camera()->modelview() * B;
--    Vector3d botLeft = widget->camera()->modelview() * A;
-+    Vector3d topLeft = (widget->camera()->modelview() * D.homogeneous()).head<3>();
-+    Vector3d topRight = (widget->camera()->modelview() * C.homogeneous()).head<3>();
-+    Vector3d botRight = (widget->camera()->modelview() * B.homogeneous()).head<3>();
-+    Vector3d botLeft = (widget->camera()->modelview() * A.homogeneous()).head<3>();
- 
-     float alpha = 0.4;
-     double lineWidth = 1.5;
-@@ -1506,12 +1506,12 @@ namespace Avogadro {
-       Vector3d positionVector)
-   {
-     //Rotate skeleton around a particular axis and center point
--    Eigen::Transform3d rotation;
-+    Eigen::Projective3d rotation;
-     rotation = Eigen::AngleAxisd(angle, rotationVector);
-     rotation.pretranslate(centerVector);
-     rotation.translate(-centerVector);
- 
--    return rotation*positionVector;
-+    return (rotation*positionVector.homogeneous()).head<3>();
-   }
- 
-   // ##########  showAnglesChanged  ##########
---- a/libavogadro/src/tools/manipulatetool.cpp
-+++ b/libavogadro/src/tools/manipulatetool.cpp
-@@ -40,7 +40,6 @@
- #include <QAbstractButton>
- 
- using Eigen::Vector3d;
--using Eigen::Transform3d;
- using Eigen::AngleAxisd;
- 
- namespace Avogadro {
-@@ -138,7 +137,7 @@ namespace Avogadro {
-     double yRotate = m_settingsWidget->yRotateSpinBox->value() * DEG_TO_RAD;
-     double zRotate = m_settingsWidget->zRotateSpinBox->value() * DEG_TO_RAD;
- 
--    Eigen::Transform3d rotation;
-+    Eigen::Projective3d rotation;
-     rotation.matrix().setIdentity();
-     rotation.translation() = center;
-     rotation.rotate(AngleAxisd(xRotate, Vector3d::UnitX())
-@@ -152,12 +151,12 @@ namespace Avogadro {
-         if (p->type() == Primitive::AtomType) {
-           Atom *atom = static_cast<Atom*>(p);
-           tempPos = translate + *(atom->pos());
--          atom->setPos(rotation * tempPos);
-+          atom->setPos((rotation * tempPos.homogeneous()).head<3>());
-         }
-     } else {
-       foreach(Atom *atom, widget->molecule()->atoms()) {
-         tempPos = translate + *(atom->pos());
--        atom->setPos(rotation * tempPos);
-+        atom->setPos((rotation * tempPos.homogeneous()).head<3>());
-       }
-     }
- 
-@@ -199,7 +198,7 @@ namespace Avogadro {
-     widget->setCursor(Qt::SizeVerCursor);
- 
-     // Move the selected atom(s) in to or out of the screen
--    Vector3d transformedGoal = widget->camera()->modelview() * *goal;
-+    Vector3d transformedGoal = (widget->camera()->modelview() * goal->homogeneous()).head<3>();
-     double distanceToGoal = transformedGoal.norm();
- 
-     double t = ZOOM_SPEED * delta;
-@@ -255,7 +254,7 @@ namespace Avogadro {
- 
-     // Rotate the selected atoms about the center
-     // rotate only selected primitives
--    Transform3d fragmentRotation;
-+    Eigen::Projective3d fragmentRotation;
-     fragmentRotation.matrix().setIdentity();
-     fragmentRotation.translation() = *center;
-     fragmentRotation.rotate(
-@@ -266,7 +265,7 @@ namespace Avogadro {
- 
-     foreach(Primitive *p, widget->selectedPrimitives())
-       if (p->type() == Primitive::AtomType)
--        static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
-+        static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
-     widget->molecule()->update();
-   }
- 
-@@ -274,7 +273,7 @@ namespace Avogadro {
-                             double delta) const
-   {
-     // Tilt the selected atoms about the center
--    Transform3d fragmentRotation;
-+    Eigen::Projective3d fragmentRotation;
-     fragmentRotation.matrix().setIdentity();
-     fragmentRotation.translation() = *center;
-     fragmentRotation.rotate(AngleAxisd(delta * ROTATION_SPEED, widget->camera()->backTransformedZAxis()));
-@@ -282,7 +281,7 @@ namespace Avogadro {
- 
-     foreach(Primitive *p, widget->selectedPrimitives())
-       if (p->type() == Primitive::AtomType)
--        static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
-+        static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
-     widget->molecule()->update();
-   }
- 
---- a/libavogadro/src/tools/navigatetool.cpp
-+++ b/libavogadro/src/tools/navigatetool.cpp
-@@ -92,7 +92,8 @@ namespace Avogadro {
-       double sumOfWeights = 0.;
-       QList<Atom*> atoms = widget->molecule()->atoms();
-       foreach (Atom *atom, atoms) {
--        Vector3d transformedAtomPos = widget->camera()->modelview() * *atom->pos();
-+        Vector3d transformedAtomPos = (widget->camera()->modelview() *
-+                                       atom->pos()->homogeneous()).head<3>();
-         double atomDistance = transformedAtomPos.norm();
-         double dot = transformedAtomPos.z() / atomDistance;
-         double weight = exp(-30. * (1. + dot));
---- a/libavogadro/src/tools/skeletontree.cpp
-+++ b/libavogadro/src/tools/skeletontree.cpp
-@@ -29,6 +29,7 @@
- #include <avogadro/atom.h>
- #include <avogadro/bond.h>
- #include <avogadro/molecule.h>
-+#include <iostream>
- 
- using namespace Eigen;
- using namespace std;
-@@ -221,7 +222,7 @@ namespace Avogadro {
-   {
-     if (m_rootNode) {
-       //Rotate skeleton around a particular axis and center point
--      Eigen::Transform3d rotation;
-+      Eigen::Projective3d rotation;
-       rotation = Eigen::AngleAxisd(angle, rotationAxis);
-       rotation.pretranslate(centerVector);
-       rotation.translate(-centerVector);
-@@ -248,11 +249,11 @@ namespace Avogadro {
-   // ##########  recursiveRotate  ##########
- 
-   void SkeletonTree::recursiveRotate(Node* n,
--                                     const Eigen::Transform3d &rotationMatrix)
-+                                     const Eigen::Projective3d &rotationMatrix)
-   {
-     // Update the root node with the new position
-     Atom* a = n->atom();
--    a->setPos(rotationMatrix * (*a->pos()));
-+    a->setPos((rotationMatrix * (*a->pos()).homogeneous()).head<3>());
-     a->update();
- 
-     // Now update the children
---- a/libavogadro/src/tools/skeletontree.h
-+++ b/libavogadro/src/tools/skeletontree.h
-@@ -230,6 +230,6 @@ namespace Avogadro {
-        * @param centerVector Center location to rotate around.
-        */
-       void recursiveRotate(Node* n,
--                           const Eigen::Transform3d &rotationMatrix);
-+                           const Eigen::Projective3d &rotationMatrix);
- 
-   };
- } // End namespace Avogadro
\ No newline at end of file
diff --git a/gnu/packages/patches/avogadro-python-eigen-lib.patch b/gnu/packages/patches/avogadro-python-eigen-lib.patch
deleted file mode 100644
index ac9f2e30af..0000000000
--- a/gnu/packages/patches/avogadro-python-eigen-lib.patch
+++ /dev/null
@@ -1,161 +0,0 @@
-From 2d4be7ede177a8df7340fe3b209698d591ee8a04 Mon Sep 17 00:00:00 2001
-From: Claudio Fernandes <claudiosf.claudio@gmail.com>
-Date: Mon, 16 Jan 2017 19:48:23 -0200
-Subject: [PATCH] Adapt libavogadro/python to Eigen 3.3
-
----
- libavogadro/src/python/camera.cpp |  2 +-
- libavogadro/src/python/eigen.cpp  | 60 +++++++++++++++++++--------------------
- 2 files changed, 31 insertions(+), 31 deletions(-)
-
-diff --git a/libavogadro/src/python/camera.cpp b/libavogadro/src/python/camera.cpp
-index 69ca87bf8..30b32af7d 100644
---- a/libavogadro/src/python/camera.cpp
-+++ b/libavogadro/src/python/camera.cpp
-@@ -10,7 +10,7 @@ using namespace Avogadro;
- void export_Camera()
- {
- 
--  const Eigen::Transform3d& (Camera::*modelview_ptr)() const = &Camera::modelview;
-+  const Eigen::Projective3d& (Camera::*modelview_ptr)() const = &Camera::modelview;
-   Eigen::Vector3d (Camera::*unProject_ptr1)(const Eigen::Vector3d&) const = &Camera::unProject;
-   Eigen::Vector3d (Camera::*unProject_ptr2)(const QPoint&, const Eigen::Vector3d&) const = &Camera::unProject;
-   Eigen::Vector3d (Camera::*unProject_ptr3)(const QPoint&) const = &Camera::unProject;
-diff --git a/libavogadro/src/python/eigen.cpp b/libavogadro/src/python/eigen.cpp
-index c1faedbcc..20b4e719d 100644
---- a/libavogadro/src/python/eigen.cpp
-+++ b/libavogadro/src/python/eigen.cpp
-@@ -305,9 +305,9 @@ template <> struct ScalarTraits<double>
-     struct innerclass
-     {
-       //
--      //  Eigen::Transform3d --> python array (4x4)
-+      //  Eigen::Projective3d --> python array (4x4)
-       //
--      static PyObject* convert(Eigen::Transform3d const &trans)
-+      static PyObject* convert(Eigen::Projective3d const &trans)
-       {
-         npy_intp dims[2] = { 4, 4 };
-         PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
-@@ -321,9 +321,9 @@ template <> struct ScalarTraits<double>
-         return incref(result);
-       }
-       //
--      //  Eigen::Transform3d* --> python array (4x4)
-+      //  Eigen::Projective3d* --> python array (4x4)
-       //
--      static PyObject* convert(Eigen::Transform3d *trans)
-+      static PyObject* convert(Eigen::Projective3d *trans)
-       {
-         npy_intp dims[2] = { 4, 4 };
-         PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
-@@ -337,9 +337,9 @@ template <> struct ScalarTraits<double>
-         return incref(result);
-       }
-       //
--      //  const Eigen::Transform3d* --> python array (4x4)
-+      //  const Eigen::Projective3d* --> python array (4x4)
-       //
--      static PyObject* convert(const Eigen::Transform3d *trans)
-+      static PyObject* convert(const Eigen::Projective3d *trans)
-       {
-         npy_intp dims[2] = { 4, 4 };
-         PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
-@@ -358,10 +358,10 @@ template <> struct ScalarTraits<double>
-     Transform3d_to_python_array()
-     {
-       #ifndef WIN32
--      to_python_converter<Eigen::Transform3d, innerclass>();
-+      to_python_converter<Eigen::Projective3d, innerclass>();
-       #endif
--      to_python_converter<Eigen::Transform3d*, innerclass>();
--      to_python_converter<const Eigen::Transform3d*, innerclass>();
-+      to_python_converter<Eigen::Projective3d*, innerclass>();
-+      to_python_converter<const Eigen::Projective3d*, innerclass>();
-     }
- 
-   };
-@@ -373,17 +373,17 @@ template <> struct ScalarTraits<double>
-       // Insert an rvalue from_python converter at the tail of the
-       // chain. Used for implicit conversions
-       //
--      //  python array --> Eigen::Transform3d
-+      //  python array --> Eigen::Projective3d
-       //
-       // used for:
-       //
--      //  void function(Eigen::Transform3d vec)
--      //  void function(Eigen::Transform3d & vec)
--      //  void function(const Eigen::Transform3d & vec)
-+      //  void function(Eigen::Projective3d vec)
-+      //  void function(Eigen::Projective3d & vec)
-+      //  void function(const Eigen::Projective3d & vec)
-       //
--      converter::registry::push_back( &convertible, &construct, type_id<Eigen::Transform3d>() );
-+      converter::registry::push_back( &convertible, &construct, type_id<Eigen::Projective3d>() );
-       
--      converter::registry::insert( &convert, type_id<Eigen::Transform3d>() );
-+      converter::registry::insert( &convert, type_id<Eigen::Projective3d>() );
-     }
- 
-     static void* convert(PyObject *obj_ptr)
-@@ -401,7 +401,7 @@ template <> struct ScalarTraits<double>
-         throw_error_already_set(); // the 1D array does not have exactly 3 elements
- 
-       double *values = reinterpret_cast<double*>(array->data);
--      Eigen::Transform3d *c_obj = new Eigen::Transform3d();
-+      Eigen::Projective3d *c_obj = new Eigen::Projective3d();
-       double *dataPtr = c_obj->data();
- 
-       for (int i = 0; i < 16; ++i)
-@@ -432,7 +432,7 @@ template <> struct ScalarTraits<double>
-       // I think this is a better way to get at the double array, where is this
-       // deleted though? Does Boost::Python do it?
-       double *values = reinterpret_cast<double*>(array->data);
--      Eigen::Transform3d *storage = new Eigen::Transform3d();
-+      Eigen::Projective3d *storage = new Eigen::Projective3d();
-       double *dataPtr = storage->data();
- 
-       for (int i = 0; i < 16; ++i)
-@@ -467,21 +467,21 @@ class EigenUnitTestHelper
-     void set_vector3d_ptr(Eigen::Vector3d* vec)                 { m_vector3d = *vec; }
-     void set_const_vector3d_ptr(const Eigen::Vector3d* const vec) { m_vector3d = *vec; }
- 
--    //Eigen::Transform3d             transform3d()              { return m_transform3d; }
--    //Eigen::Transform3d&            transform3d_ref()          { return m_transform3d; }
--    const Eigen::Transform3d&      const_transform3d_ref()    { return m_transform3d; }
--    Eigen::Transform3d*            transform3d_ptr()          { return &m_transform3d; }
--    const Eigen::Transform3d*      const_transform3d_ptr()    { return &m_transform3d; }
--
--    //void set_transform3d(Eigen::Transform3d vec)                      { m_transform3d = vec; }
--    //void set_transform3d_ref(Eigen::Transform3d& vec)                 { m_transform3d = vec; }
--    void set_const_transform3d_ref(const Eigen::Transform3d& vec)     { m_transform3d = vec; }
--    void set_transform3d_ptr(Eigen::Transform3d* vec)                 { m_transform3d = *vec; }
--    void set_const_transform3d_ptr(const Eigen::Transform3d* const vec) { m_transform3d = *vec; }
-+    //Eigen::Projective3d             transform3d()              { return m_transform3d; }
-+    //Eigen::Projective3d&            transform3d_ref()          { return m_transform3d; }
-+    const Eigen::Projective3d&      const_transform3d_ref()    { return m_transform3d; }
-+    Eigen::Projective3d*            transform3d_ptr()          { return &m_transform3d; }
-+    const Eigen::Projective3d*      const_transform3d_ptr()    { return &m_transform3d; }
-+
-+    //void set_transform3d(Eigen::Projective3d vec)                      { m_transform3d = vec; }
-+    //void set_transform3d_ref(Eigen::Projective3d& vec)                 { m_transform3d = vec; }
-+    void set_const_transform3d_ref(const Eigen::Projective3d& vec)     { m_transform3d = vec; }
-+    void set_transform3d_ptr(Eigen::Projective3d* vec)                 { m_transform3d = *vec; }
-+    void set_const_transform3d_ptr(const Eigen::Projective3d* const vec) { m_transform3d = *vec; }
-  
-   private:
-     Eigen::Vector3d m_vector3d;
--    Eigen::Transform3d m_transform3d;
-+    Eigen::Projective3d m_transform3d;
- 
- };
- #endif
-@@ -529,6 +529,6 @@ void export_Eigen()
-   Vector3x_to_python_array<Eigen::Vector3i>();
-   Vector3x_from_python_array<Eigen::Vector3i>();
- 
--  // Eigen::Transform3d
-+  // Eigen::Projective3d
-   Transform3d_to_python_array();
-   Transform3d_from_python_array();
diff --git a/gnu/packages/patches/c++-gsl-find-system-gtest.patch b/gnu/packages/patches/c++-gsl-find-system-gtest.patch
new file mode 100644
index 0000000000..2def650292
--- /dev/null
+++ b/gnu/packages/patches/c++-gsl-find-system-gtest.patch
@@ -0,0 +1,96 @@
+From f5cf01083baf7e8dc8318db3648bc6098dc32d67 Mon Sep 17 00:00:00 2001
+From: Nicholas Guriev <guriev-ns@ya.ru>
+Date: Sat, 18 Apr 2020 13:30:17 +0300
+Subject: [PATCH] Search for GoogleTest via pkg-config first
+
+---
+ tests/CMakeLists.txt | 55 ++++++++++++++++++++++++--------------------
+ 1 file changed, 30 insertions(+), 25 deletions(-)
+
+diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
+index 02193197..53d475c2 100644
+--- a/tests/CMakeLists.txt
++++ b/tests/CMakeLists.txt
+@@ -1,36 +1,41 @@
+ cmake_minimum_required(VERSION 3.0.2)
+ 
+ project(GSLTests CXX)
++include(FindPkgConfig)
+ 
+ # will make visual studio generated project group files
+ set_property(GLOBAL PROPERTY USE_FOLDERS ON)
+ 
+-configure_file(CMakeLists.txt.in googletest-download/CMakeLists.txt)
+-execute_process(
+-    COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
+-    RESULT_VARIABLE result
+-    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download
+-)
+-if(result)
+-    message(FATAL_ERROR "CMake step for googletest failed: ${result}")
+-endif()
++pkg_search_module(GTestMain gtest_main)
++if (NOT GTestMain_FOUND)
++    configure_file(CMakeLists.txt.in googletest-download/CMakeLists.txt)
++    execute_process(
++        COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
++        RESULT_VARIABLE result
++        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download
++    )
++    if(result)
++        message(FATAL_ERROR "CMake step for googletest failed: ${result}")
++    endif()
+ 
+-execute_process(
+-    COMMAND ${CMAKE_COMMAND} --build .
+-    RESULT_VARIABLE result
+-    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download
+-)
+-if(result)
+-    message(FATAL_ERROR "CMake step for googletest failed: ${result}")
+-endif()
++    execute_process(
++        COMMAND ${CMAKE_COMMAND} --build .
++        RESULT_VARIABLE result
++        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download
++    )
++    if(result)
++        message(FATAL_ERROR "CMake step for googletest failed: ${result}")
++    endif()
+ 
+-set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
++    set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
++    set(GTestMain_LIBRARIES gtest_main)
+ 
+-add_subdirectory(
+-    ${CMAKE_CURRENT_BINARY_DIR}/googletest-src
+-    ${CMAKE_CURRENT_BINARY_DIR}/googletest-build
+-    EXCLUDE_FROM_ALL
+-)
++    add_subdirectory(
++        ${CMAKE_CURRENT_BINARY_DIR}/googletest-src
++        ${CMAKE_CURRENT_BINARY_DIR}/googletest-build
++        EXCLUDE_FROM_ALL
++    )
++endif()
+ 
+ if (MSVC AND (GSL_CXX_STANDARD EQUAL 17))
+     set(GSL_CPLUSPLUS_OPT -Zc:__cplusplus -permissive-)
+@@ -149,7 +154,7 @@ function(add_gsl_test name)
+     target_link_libraries(${name}
+         GSL
+         gsl_tests_config
+-        gtest_main
++        ${GTestMain_LIBRARIES}
+     )
+     add_test(
+         ${name}
+@@ -254,7 +259,7 @@ function(add_gsl_test_noexcept name)
+     target_link_libraries(${name}
+         GSL
+         gsl_tests_config_noexcept
+-        gtest_main
++        ${GTestMain_LIBRARIES}
+     )
+     add_test(
+       ${name}
diff --git a/gnu/packages/patches/freebayes-devendor-deps.patch b/gnu/packages/patches/freebayes-devendor-deps.patch
new file mode 100644
index 0000000000..9886de11fb
--- /dev/null
+++ b/gnu/packages/patches/freebayes-devendor-deps.patch
@@ -0,0 +1,152 @@
+This patch is original to Guix, ongoing work to upstream bits as possible.
+
+From 9acc56db5e7469f5976be38b52ba4993de98ee38 Mon Sep 17 00:00:00 2001
+From: Efraim Flashner <efraim@flashner.co.il>
+Date: Sun, 17 Jan 2021 13:27:17 +0200
+Subject: [PATCH] devendor-dependants
+
+---
+ meson.build | 84 +++++++++++++++++++++++++++++++++++++++++------------
+ 1 file changed, 66 insertions(+), 18 deletions(-)
+
+diff --git a/meson.build b/meson.build
+index f6bf242..bded4af 100644
+--- a/meson.build
++++ b/meson.build
+@@ -9,8 +9,13 @@ project('freebayes', ['cpp', 'c'],
+ 
+ zlib_dep = dependency('zlib')
+ lzma_dep = dependency('liblzma')
++simde_dep = dependency('simde')
+ bzip2_dep = dependency('bz2lib', required: false)
+ htslib_dep = dependency('htslib', required : false)
++tabixpp_dep = dependency('tabixpp', required : false)
++fastahack_dep = dependency('fastahack', required : false)
++smithwaterman_dep = dependency('smithwaterman', required : false)
++vcflib_dep = dependency('vcflib', required: false)
+ thread_dep = dependency('threads')
+ 
+ if htslib_dep.found()
+@@ -59,6 +64,56 @@ else
+ ]
+ endif
+ 
++if tabixpp_dep.found()
++  tabixpp_includes = ''
++  tabixpp_src = []
++else
++  tabixpp_includes = [
++    'vcflib/tabixpp',
++    ]
++  tabixpp_src = [
++    'vcflib/tabixpp/tabix.cpp',
++    ]
++endif
++
++if vcflib_dep.found()
++  vcflib_includes = ''
++  vcflib_src = []
++else
++  vcflib_includes = [
++    'vcflib/src',
++    'vcflib/multichoose',
++    'vcflib/filevercmp',
++    ]
++  vcflib_src = [
++    'vcflib/src/Variant.cpp',
++    ]
++endif
++
++if fastahack_dep.found()
++  fastahack_src = []
++else
++  fastahack_src = [
++    'vcflib/fastahack/Fasta.cpp',
++    'vcflib/src/split.cpp',
++    ]
++endif
++
++if smithwaterman_dep.found()
++  smithwaterman_includes = ''
++  smithwaterman_src = []
++else
++  smithwaterman_includes = [
++    'vcflib/smithwaterman',
++    ]
++  smithwaterman_src = [
++    'vcflib/smithwaterman/SmithWatermanGotoh.cpp',
++    'vcflib/smithwaterman/disorder.cpp',
++    'vcflib/smithwaterman/Repeats.cpp',
++    'vcflib/smithwaterman/LeftAlign.cpp',
++    'vcflib/smithwaterman/IndelAllele.cpp',
++    ]
++endif
+ 
+ 
+ #
+@@ -105,23 +160,18 @@ seqlib_src = [
+ ]
+ 
+ vcflib_src = [
+-    'vcflib/tabixpp/tabix.cpp',
+-    'vcflib/src/Variant.cpp',
+-    'vcflib/smithwaterman/SmithWatermanGotoh.cpp',
+-    'vcflib/smithwaterman/disorder.cpp',
+-    'vcflib/smithwaterman/Repeats.cpp',
+-    'vcflib/smithwaterman/LeftAlign.cpp',
+-    'vcflib/smithwaterman/IndelAllele.cpp',
++    vcflib_src,
++    tabixpp_src,
++    smithwaterman_src,
+ ]
+ 
+ bamleftalign_src = [
+     'src/bamleftalign.cpp',
+     'src/IndelAllele.cpp',
+     'contrib/SeqLib/src/BamWriter.cpp',
+-    'vcflib/fastahack/Fasta.cpp',
+-    'vcflib/smithwaterman/LeftAlign.cpp',
+-    'vcflib/smithwaterman/IndelAllele.cpp',
+-    'vcflib/src/split.cpp',
++    fastahack_src,
++    smithwaterman_src,
++    vcflib_src,
+     'src/LeftAlign.cpp',
+ ]
+ 
+@@ -134,11 +184,9 @@ incdir = include_directories(
+     'ttmath',
+     'contrib',
+     'contrib/SeqLib',
+-    'vcflib/src',
+-    'vcflib/tabixpp',
+-    'vcflib/smithwaterman',
+-    'vcflib/multichoose',
+-    'vcflib/filevercmp')
++    tabixpp_includes,
++    smithwaterman_includes,
++    vcflib_includes)
+ 
+ c_args = ['-fpermissive','-w']
+ cpp_args = ['-fpermissive','-w','-Wc++14-compat']
+@@ -152,7 +200,7 @@ executable('freebayes',
+            include_directories : incdir,
+            cpp_args : cpp_args,
+            c_args :   c_args,
+-           dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep],
++           dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, smithwaterman_dep, vcflib_dep, thread_dep],
+            install: true
+           )
+ 
+@@ -165,7 +213,7 @@ executable('bamleftalign',
+            include_directories : incdir,
+            cpp_args : cpp_args,
+            c_args :   c_args,
+-           dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep],
++           dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, fastahack_dep, smithwaterman_dep, vcflib_dep, thread_dep],
+            install: true
+           )
+ 
+-- 
+2.30.0
+
diff --git a/gnu/packages/patches/gst-plugins-good-fix-test.patch b/gnu/packages/patches/gst-plugins-good-fix-test.patch
new file mode 100644
index 0000000000..38ec0ba802
--- /dev/null
+++ b/gnu/packages/patches/gst-plugins-good-fix-test.patch
@@ -0,0 +1,94 @@
+Fix a broken test:
+
+https://gitlab.freedesktop.org/gstreamer/gst-plugins-good/-/issues/803
+
+Patches copied from upstream source repository:
+
+https://gitlab.freedesktop.org/gstreamer/gst-plugins-good/-/commit/2ce5909f3a0b0da3abb7b794215d6b8b72a3b7fa
+https://gitlab.freedesktop.org/gstreamer/gst-plugins-good/-/commit/f5310ce346180a717f091f2f09bcbb3ddfb15436
+
+From 2ce5909f3a0b0da3abb7b794215d6b8b72a3b7fa Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Tim-Philipp=20M=C3=BCller?= <tim@centricular.com>
+Date: Thu, 12 Nov 2020 23:38:21 +0000
+Subject: [PATCH 1/2] tests: qtdemux: fix crash on 32-bit architectures
+
+Fixes https://gitlab.freedesktop.org/gstreamer/gst-plugins-good/-/issues/803
+
+Part-of: <https://gitlab.freedesktop.org/gstreamer/gst-plugins-good/-/merge_requests/815>
+---
+ tests/check/elements/qtdemux.c | 14 ++++++++------
+ 1 file changed, 8 insertions(+), 6 deletions(-)
+
+diff --git a/tests/check/elements/qtdemux.c b/tests/check/elements/qtdemux.c
+index 5271c6576..0c748278b 100644
+--- a/tests/check/elements/qtdemux.c
++++ b/tests/check/elements/qtdemux.c
+@@ -797,9 +797,10 @@ GST_START_TEST (test_qtdemux_pad_names)
+       "protection-system", G_TYPE_STRING,
+       "9a04f079-9840-4286-ab92-e65be0885f95", NULL);
+   caps =
+-      gst_caps_new_simple ("video/quicktime", "variant", G_TYPE_STRING,
+-      "mss-fragmented", "timesacle", G_TYPE_UINT64, 10000000, "media-caps",
+-      GST_TYPE_CAPS, mediacaps, NULL);
++      gst_caps_new_simple ("video/quicktime",
++      "variant", G_TYPE_STRING, "mss-fragmented",
++      "timesacle", G_TYPE_UINT64, G_GUINT64_CONSTANT (10000000),
++      "media-caps", GST_TYPE_CAPS, mediacaps, NULL);
+ 
+   /* Send segment event* */
+   event = gst_event_new_caps (caps);
+@@ -852,9 +853,10 @@ GST_START_TEST (test_qtdemux_pad_names)
+       "protection-system", G_TYPE_STRING,
+       "9a04f079-9840-4286-ab92-e65be0885f95", NULL);
+   caps =
+-      gst_caps_new_simple ("video/quicktime", "variant", G_TYPE_STRING,
+-      "mss-fragmented", "timesacle", G_TYPE_UINT64, 10000000, "media-caps",
+-      GST_TYPE_CAPS, mediacaps, NULL);
++      gst_caps_new_simple ("video/quicktime",
++      "variant", G_TYPE_STRING, "mss-fragmented",
++      "timesacle", G_TYPE_UINT64, G_GUINT64_CONSTANT (10000000),
++      "media-caps", GST_TYPE_CAPS, mediacaps, NULL);
+ 
+   /* Send segment event* */
+   event = gst_event_new_caps (caps);
+-- 
+2.30.0
+
+
+From f5310ce346180a717f091f2f09bcbb3ddfb15436 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Tim-Philipp=20M=C3=BCller?= <tim@centricular.com>
+Date: Thu, 12 Nov 2020 23:39:21 +0000
+Subject: [PATCH 2/2] tests: qtdemux: fix typo in caps field
+
+timesacle -> timescale
+
+Part-of: <https://gitlab.freedesktop.org/gstreamer/gst-plugins-good/-/merge_requests/815>
+---
+ tests/check/elements/qtdemux.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/tests/check/elements/qtdemux.c b/tests/check/elements/qtdemux.c
+index 0c748278b..4a14c45c0 100644
+--- a/tests/check/elements/qtdemux.c
++++ b/tests/check/elements/qtdemux.c
+@@ -799,7 +799,7 @@ GST_START_TEST (test_qtdemux_pad_names)
+   caps =
+       gst_caps_new_simple ("video/quicktime",
+       "variant", G_TYPE_STRING, "mss-fragmented",
+-      "timesacle", G_TYPE_UINT64, G_GUINT64_CONSTANT (10000000),
++      "timescale", G_TYPE_UINT64, G_GUINT64_CONSTANT (10000000),
+       "media-caps", GST_TYPE_CAPS, mediacaps, NULL);
+ 
+   /* Send segment event* */
+@@ -855,7 +855,7 @@ GST_START_TEST (test_qtdemux_pad_names)
+   caps =
+       gst_caps_new_simple ("video/quicktime",
+       "variant", G_TYPE_STRING, "mss-fragmented",
+-      "timesacle", G_TYPE_UINT64, G_GUINT64_CONSTANT (10000000),
++      "timescale", G_TYPE_UINT64, G_GUINT64_CONSTANT (10000000),
+       "media-caps", GST_TYPE_CAPS, mediacaps, NULL);
+ 
+   /* Send segment event* */
+-- 
+2.30.0
+
diff --git a/gnu/packages/patches/icecat-makeicecat.patch b/gnu/packages/patches/icecat-makeicecat.patch
index 3f16880260..edd1ced257 100644
--- a/gnu/packages/patches/icecat-makeicecat.patch
+++ b/gnu/packages/patches/icecat-makeicecat.patch
@@ -25,7 +25,7 @@ index 8be2362..48716f2 100755
 -wget -N https://ftp.mozilla.org/pub/mozilla.org/firefox/releases/${FFVERSION}esr/source/firefox-${FFVERSION}esr.source.tar.xz.asc
 -gpg --recv-keys --keyserver keyserver.ubuntu.com 14F26682D0916CDD81E37B6D61B7B526D98F0353
 -gpg --verify firefox-${FFVERSION}esr.source.tar.xz.asc
--echo -n 0d07b74cb66b94018e3d7f11531f95c76a955e0016a3c401241d0d85062ae7ce firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c -
+-echo -n 1aa041db28cd742e93d663a9da8defd33040b38d8b9470350538473251621643 firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c -
 -
 -echo Extracting Firefox tarball
 -tar -xf firefox-${FFVERSION}esr.source.tar.xz
@@ -37,7 +37,7 @@ index 8be2362..48716f2 100755
 +# wget -N https://ftp.mozilla.org/pub/mozilla.org/firefox/releases/${FFVERSION}esr/source/firefox-${FFVERSION}esr.source.tar.xz.asc
 +# gpg --recv-keys --keyserver keyserver.ubuntu.com 14F26682D0916CDD81E37B6D61B7B526D98F0353
 +# gpg --verify firefox-${FFVERSION}esr.source.tar.xz.asc
-+# echo -n 0d07b74cb66b94018e3d7f11531f95c76a955e0016a3c401241d0d85062ae7ce firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c -
++# echo -n 1aa041db28cd742e93d663a9da8defd33040b38d8b9470350538473251621643 firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c -
 +# 
 +# echo Extracting Firefox tarball
 +# tar -xf firefox-${FFVERSION}esr.source.tar.xz
diff --git a/gnu/packages/patches/idris-disable-test.patch b/gnu/packages/patches/idris-disable-test.patch
new file mode 100644
index 0000000000..ec8c7c8451
--- /dev/null
+++ b/gnu/packages/patches/idris-disable-test.patch
@@ -0,0 +1,19 @@
+The "pkg010" test output depends on the version of optparse-applicative being
+used.  The expected output requires optparse-applicative >= 0.15.1.0.  Skip
+the test for now.
+
+--- idris-1.3.3/test/TestData.hs	2021-01-19 23:05:24.238958262 -0600
++++ idris-1.3.3/test/TestData.hs	2021-01-19 23:10:33.314390997 -0600
+@@ -212,8 +212,10 @@
+       (  5, ANY  ),
+       (  6, ANY  ),
+       (  7, ANY  ),
+-      (  8, ANY  ),
+-      ( 10, ANY  )]),
++      (  8, ANY  )]),
++--      FIXME: Expected output depends on optparse-applicative version.
++--      See https://github.com/idris-lang/Idris-dev/issues/4896
++--      ( 10, ANY  )]),
+   ("prelude",         "Prelude",
+     [ (  1, ANY  )]),
+   ("primitives",      "Primitive types",
diff --git a/gnu/packages/patches/ipxe-reproducible-geniso.patch b/gnu/packages/patches/ipxe-reproducible-geniso.patch
new file mode 100644
index 0000000000..ff6aa1da94
--- /dev/null
+++ b/gnu/packages/patches/ipxe-reproducible-geniso.patch
@@ -0,0 +1,77 @@
+From 052d24d8217c51c572c2f6cbb4a687be2e8ba52d Mon Sep 17 00:00:00 2001
+From: Brice Waegeneire <brice@waegenei.re>
+Date: Fri, 5 Jun 2020 14:38:43 +0200
+Subject: [PATCH] [geniso] Make it reproducible
+
+Some timestamps get embedded in the generated ISO, making it
+unreproducible so we overwrite those timestamps to be at the UNIX epoch.
+---
+ src/util/geniso | 24 +++++++++++++++++++++---
+ 1 file changed, 21 insertions(+), 3 deletions(-)
+
+diff --git a/src/util/geniso b/src/util/geniso
+index ff090d4a..e032ffb0 100755
+--- a/src/util/geniso
++++ b/src/util/geniso
+@@ -11,6 +11,13 @@ function help() {
+ 	echo " -o FILE  save iso image to file"
+ }
+ 
++function reset_timestamp() {
++	for f in "$1"/*; do
++		touch -t 197001010100 "$f"
++	done
++	touch -t 197001010100 "$1"
++}
++
+ LEGACY=0
+ FIRST=""
+ 
+@@ -37,8 +44,9 @@ if [ -z "${OUT}" ]; then
+ 	exit 1
+ fi
+ 
+-# There should either be mkisofs or the compatible genisoimage program
+-for command in genisoimage mkisofs; do
++# There should either be mkisofs, xorriso or the compatible genisoimage
++# program
++for command in xorriso genisoimage mkisofs; do
+ 	if ${command} --version >/dev/null 2>/dev/null; then
+ 		mkisofs=(${command})
+ 		break
+@@ -46,8 +54,10 @@ for command in genisoimage mkisofs; do
+ done
+ 
+ if [ -z "${mkisofs}" ]; then
+-	echo "${0}: mkisofs or genisoimage not found, please install or set PATH" >&2
++	echo "${0}: mkisofs, xorriso or genisoimage not found, please install or set PATH" >&2
+ 	exit 1
++elif [ "$mkisofs" = "xorriso" ]; then
++	 mkisofs+=(-as mkisofs)
+ fi
+ 
+ dir=$(mktemp -d bin/iso.dir.XXXXXX)
+@@ -115,6 +125,8 @@ case "${LEGACY}" in
+ 			exit 1
+ 		fi
+ 
++		reset_timestamp "$dir"
++
+ 		# generate the iso image
+ 		"${mkisofs[@]}" -b boot.img -output ${OUT} ${dir}
+ 		;;
+@@ -127,6 +139,12 @@ case "${LEGACY}" in
+ 			cp ${LDLINUX_C32} ${dir}
+ 		fi
+ 
++		reset_timestamp "$dir"
++
++		if [ "${mkisofs[0]}" = "xorriso" ]; then
++			mkisofs+=(-isohybrid-mbr "$SYSLINUX_MBR_DISK_PATH")
++		fi
++
+ 		# generate the iso image
+ 		"${mkisofs[@]}" -b isolinux.bin -no-emul-boot -boot-load-size 4 -boot-info-table -output ${OUT} ${dir}
+ 
+-- 
+2.26.2
diff --git a/gnu/packages/patches/mesa-skip-disk-cache-test.patch b/gnu/packages/patches/mesa-skip-disk-cache-test.patch
deleted file mode 100644
index 190f6b6ee1..0000000000
--- a/gnu/packages/patches/mesa-skip-disk-cache-test.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-disk_cache_create() here looks up the users home directory from <pwd.h>
-which resolves to "/" in the build environment. I could not find an easy
-way to set the home directory to something else, so we disable this test
-for now.
-
---- a/src/compiler/glsl/tests/cache_test.c
-+++ b/src/compiler/glsl/tests/cache_test.c
-@@ -170,11 +170,6 @@
-    unsetenv("MESA_GLSL_CACHE_DIR");
-    unsetenv("XDG_CACHE_HOME");
- 
--   cache = disk_cache_create("test", "make_check", 0);
--   expect_non_null(cache, "disk_cache_create with no environment variables");
--
--   disk_cache_destroy(cache);
--
-    /* Test with XDG_CACHE_HOME set */
-    setenv("XDG_CACHE_HOME", CACHE_TEST_TMP "/xdg-cache-home", 1);
-    cache = disk_cache_create("test", "make_check", 0);
diff --git a/gnu/packages/patches/mesa-skip-tests.patch b/gnu/packages/patches/mesa-skip-tests.patch
new file mode 100644
index 0000000000..2622d5d312
--- /dev/null
+++ b/gnu/packages/patches/mesa-skip-tests.patch
@@ -0,0 +1,49 @@
+disk_cache_create() here looks up the users home directory from <pwd.h>
+which resolves to "/" in the build environment. I could not find an easy
+way to set the home directory to something else, so we disable this test
+for now.
+
+--- a/src/compiler/glsl/tests/cache_test.c
++++ b/src/compiler/glsl/tests/cache_test.c
+@@ -170,11 +170,6 @@
+    unsetenv("MESA_GLSL_CACHE_DIR");
+    unsetenv("XDG_CACHE_HOME");
+ 
+-   cache = disk_cache_create("test", "make_check", 0);
+-   expect_non_null(cache, "disk_cache_create with no environment variables");
+-
+-   disk_cache_destroy(cache);
+-
+    /* Test with XDG_CACHE_HOME set */
+    setenv("XDG_CACHE_HOME", CACHE_TEST_TMP "/xdg-cache-home", 1);
+    cache = disk_cache_create("test", "make_check", 0);
+
+This test fails on i686-linux. I couldn't come up with a regex that
+could be used to disable it just on i686-linux, so we disable it
+completely with this patch:
+
+https://gitlab.freedesktop.org/mesa/mesa/-/issues/4091
+
+diff --git a/src/util/meson.build b/src/util/meson.build
+index 0893f64..909b3e0 100644
+--- a/src/util/meson.build
++++ b/src/util/meson.build
+@@ -289,18 +289,6 @@ if with_tests
+      suite : ['util'],
+   )   
+ 
+-  test(
+-    'u_debug_stack',
+-    executable(
+-      'u_debug_stack_test',
+-      files('u_debug_stack_test.cpp'),
+-      include_directories : [inc_include, inc_src, inc_mapi, inc_mesa, inc_gallium, inc_gallium_aux],
+-      dependencies : [idep_mesautil, idep_gtest],
+-      c_args : [c_msvc_compat_args],
+-    ),
+-     suite : ['util'],
+-  )
+-
+   process_test_exe = executable(
+     'process_test',
+     files('process_test.c'),
diff --git a/gnu/packages/patches/obs-modules-location.patch b/gnu/packages/patches/obs-modules-location.patch
new file mode 100644
index 0000000000..18b286d006
--- /dev/null
+++ b/gnu/packages/patches/obs-modules-location.patch
@@ -0,0 +1,33 @@
+From d250434e6c8eb4f8c8cb47ef3cc6e6de8fa8f828 Mon Sep 17 00:00:00 2001
+From: Alexey Abramov <levenson@mmer.org>
+Date: Fri, 15 Jan 2021 17:07:17 +0100
+Subject: [PATCH] Use environment variable for a default module location
+
+diff --git a/libobs/obs-nix.c b/libobs/obs-nix.c
+index 382fa0546..481ea0f14 100644
+*** a/libobs/obs-nix.c
+--- b/libobs/obs-nix.c
+@@ -66,8 +66,19 @@
+ 
+ void add_default_module_paths(void)
+ {
+-	for (int i = 0; i < module_patterns_size; i++)
+-		obs_add_module_path(module_bin[i], module_data[i]);
++	char *bin_directory = getenv("OBS_PLUGINS_DIRECTORY");
++	char *data_directory = getenv("OBS_PLUGINS_DATA_DIRECTORY");
++	if (bin_directory && data_directory) {
++		struct dstr dstr_data_directory;
++		dstr_init_copy(&dstr_data_directory, data_directory);
++		dstr_cat(&dstr_data_directory, "/%module%");
++		obs_add_module_path(bin_directory, dstr_data_directory.array);
++		dstr_free(&dstr_data_directory);
++
++	} else {
++		for (int i = 0; i < module_patterns_size; i++)
++			obs_add_module_path(module_bin[i], module_data[i]);
++	}
+ }
+ 
+ /*
+-- 
+2.29.2
\ No newline at end of file
diff --git a/gnu/packages/patches/pinentry-efl.patch b/gnu/packages/patches/pinentry-efl.patch
deleted file mode 100644
index 5ba79e28df..0000000000
--- a/gnu/packages/patches/pinentry-efl.patch
+++ /dev/null
@@ -1,798 +0,0 @@
-https://git.gnupg.org/cgi-bin/gitweb.cgi?p=pinentry.git;a=commit;h=948105b7a34ec9a9e5479d376b7c86bafee50a01
-This patch can be removed with the next release of pinentry.
-
-From 948105b7a34ec9a9e5479d376b7c86bafee50a01 Mon Sep 17 00:00:00 2001
-From: "William L. Thomson Jr" <wlt@o-sinc.com>
-Date: Tue, 29 May 2018 22:50:47 +0100
-Subject: [PATCH] efl: Add an EFL-based pinentry.
-
-* NEWS: Update.
-* Makefile.am: Add new efl subdirectory.
-* configure.ac: Add --enable-pinentry-efl option.
-* efl/Makefile.am: New file.
-* efl/pinentry-efl.c: New file.
-
-Signed-off-by: Damien Goutte-Gattat <dgouttegattat@incenp.org>
----
- Makefile.am        |   8 +-
- configure.ac       |  44 +++-
- efl/Makefile.am    |  38 ++++
- efl/pinentry-efl.c | 623 +++++++++++++++++++++++++++++++++++++++++++++++++++++
- 6 files changed, 716 insertions(+), 2 deletions(-)
- create mode 100644 efl/Makefile.am
- create mode 100644 efl/pinentry-efl.c
-
-diff --git a/Makefile.am b/Makefile.am
-index 8c8b8e5..b8fd0e1 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -82,10 +82,16 @@ else
- pinentry_fltk =
- endif
- 
-+if BUILD_PINENTRY_EFL
-+pinentry_efl = efl
-+else
-+pinentry_efl =
-+endif
-+
- SUBDIRS = m4 secmem pinentry ${pinentry_curses} ${pinentry_tty} \
- 	${pinentry_emacs} ${pinentry_gtk_2} ${pinentry_gnome_3} \
- 	${pinentry_qt} ${pinentry_tqt} ${pinentry_w32} \
--	${pinentry_fltk} doc
-+	${pinentry_fltk} ${pinentry_efl} doc
- 
- 
- install-exec-local:
-diff --git a/configure.ac b/configure.ac
-index ff6c2e0..e305e44 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -419,6 +419,42 @@ fi
- 
- 
- dnl
-+dnl Check for EFL pinentry programs.
-+dnl
-+AC_ARG_ENABLE(pinentry-efl,
-+            AC_HELP_STRING([--enable-pinentry-efl], [build EFL pinentry]),
-+            pinentry_efl=$enableval, pinentry_efl=maybe)
-+
-+dnl check for pkg-config
-+if test "$pinentry_efl" != "no"; then
-+	AC_PATH_PROG(PKG_CONFIG, pkg-config, no)
-+	if test x"${PKG_CONFIG}" = xno ; then
-+		pinentry_efl=no
-+	fi
-+fi
-+
-+if test "$pinentry_efl" != "no"; then
-+	AC_MSG_CHECKING([for efl])
-+	"${PKG_CONFIG}" --exists 'elementary >= 1.18'
-+	if test $? -ne 0 ; then
-+		AC_MSG_RESULT([no])
-+		AC_MSG_WARN([efl >= 1.18 is required for efl pinentry])
-+		pinentry_efl=no
-+	else
-+		AC_MSG_RESULT([yes])
-+		EFL_CFLAGS=`"${PKG_CONFIG}" --cflags ecore-x elementary`
-+		EFL_LIBS=`"${PKG_CONFIG}" --libs ecore-x elementary`
-+		AC_SUBST(EFL_CFLAGS)
-+		AC_SUBST(EFL_LIBS)
-+		if test "$pinentry_efl" != "no"
-+		then
-+			pinentry_efl=yes
-+		fi
-+	fi
-+fi
-+AM_CONDITIONAL(BUILD_PINENTRY_EFL, test "$pinentry_efl" = "yes")
-+
-+dnl
- dnl Check for GTK+-2 / GNOME3 pinentry programs.
- dnl
- AC_ARG_ENABLE(pinentry-gtk2,
-@@ -645,7 +681,11 @@ else
-               if test "$pinentry_tqt" = "yes"; then
-                 PINENTRY_DEFAULT=pinentry-tqt
-               else
--                AC_MSG_ERROR([[No pinentry enabled.]])
-+                if test "$pinentry_efl" = "yes"; then
-+                  PINENTRY_DEFAULT=pinentry-efl
-+                else
-+                  AC_MSG_ERROR([[No pinentry enabled.]])
-+                fi
-               fi
-             fi
-           fi
-@@ -721,6 +761,7 @@ secmem/Makefile
- pinentry/Makefile
- curses/Makefile
- tty/Makefile
-+efl/Makefile
- emacs/Makefile
- gtk+-2/Makefile
- gnome3/Makefile
-@@ -744,6 +785,7 @@ AC_MSG_NOTICE([
- 	Curses Pinentry ..: $pinentry_curses
- 	TTY Pinentry .....: $pinentry_tty
- 	Emacs Pinentry ...: $pinentry_emacs
-+	EFL Pinentry .....: $pinentry_efl
- 	GTK+-2 Pinentry ..: $pinentry_gtk_2
- 	GNOME 3 Pinentry .: $pinentry_gnome_3
- 	Qt Pinentry ......: $pinentry_qt $pinentry_qt_lib_version
-diff --git a/efl/Makefile.am b/efl/Makefile.am
-new file mode 100644
-index 0000000..b986a04
---- /dev/null
-+++ b/efl/Makefile.am
-@@ -0,0 +1,38 @@
-+# Makefile.am - PIN entry EFL frontend.
-+# Copyright (C) 2017 Obsidian-Studios, Inc.
-+# Author William L. Thomson Jr. <wlt@o-sinc.com>
-+#
-+# This file is part of PINENTRY.
-+#
-+# PINENTRY is free software; you can redistribute it and/or modify
-+# it under the terms of the GNU General Public License as published by
-+# the Free Software Foundation; either version 2 of the License, or
-+# (at your option) any later version.
-+#
-+# PINENTRY is distributed in the hope that it will be useful,
-+# but WITHOUT ANY WARRANTY; without even the implied warranty of
-+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-+# GNU General Public License for more details.
-+#
-+# You should have received a copy of the GNU General Public License
-+# along with this program; if not, write to the Free Software
-+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA
-+
-+## Process this file with automake to produce Makefile.in
-+
-+bin_PROGRAMS = pinentry-efl
-+
-+if FALLBACK_CURSES
-+ncurses_include = $(NCURSES_INCLUDE)
-+libcurses = ../pinentry/libpinentry-curses.a $(LIBCURSES) $(LIBICONV)
-+else
-+ncurses_include =
-+libcurses =
-+endif
-+
-+AM_CPPFLAGS = $(COMMON_CFLAGS) $(EFL_CFLAGS) $(ncurses_include) \
-+	-I$(top_srcdir)/secmem -I$(top_srcdir)/pinentry
-+LDADD = ../pinentry/libpinentry.a ../secmem/libsecmem.a \
-+	$(COMMON_LIBS) $(LIBCAP) $(EFL_LIBS) $(libcurses)
-+
-+pinentry_efl_SOURCES = pinentry-efl.c
-diff --git a/efl/pinentry-efl.c b/efl/pinentry-efl.c
-new file mode 100644
-index 0000000..ca99693
---- /dev/null
-+++ b/efl/pinentry-efl.c
-@@ -0,0 +1,623 @@
-+/* pinentry-efl.c
-+   Copyright (C) 2017 Obsidian-Studios, Inc.
-+     Author William L. Thomson Jr. <wlt@o-sinc.com>
-+
-+   Based on pinentry-gtk2.c
-+   Copyright (C) 1999 Robert Bihlmeyer <robbe@orcus.priv.at>
-+   Copyright (C) 2001, 2002, 2007, 2015 g10 Code GmbH
-+   Copyright (C) 2004 by Albrecht Dreß <albrecht.dress@arcor.de>
-+
-+   pinentry-efl is a pinentry application for the EFL widget set.
-+   It tries to follow the Gnome Human Interface Guide as close as
-+   possible.
-+
-+   This program is free software; you can redistribute it and/or modify
-+   it under the terms of the GNU General Public License as published by
-+   the Free Software Foundation; either version 2 of the License, or
-+   (at your option) any later version.
-+
-+   This program is distributed in the hope that it will be useful,
-+   but WITHOUT ANY WARRANTY; without even the implied warranty of
-+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-+   GNU General Public License for more details.
-+
-+   You should have received a copy of the GNU General Public License
-+   along with this program; if not, write to the Free Software
-+   Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-+ */
-+
-+#ifdef HAVE_CONFIG_H
-+#include "config.h"
-+#endif
-+#include <Elementary.h>
-+#include <Ecore_X.h>
-+#include <gpg-error.h>
-+#if __GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 7)
-+#pragma GCC diagnostic push
-+#pragma GCC diagnostic ignored "-Wstrict-prototypes"
-+#endif
-+#if __GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 7)
-+#pragma GCC diagnostic pop
-+#endif
-+
-+#ifdef HAVE_GETOPT_H
-+#include <getopt.h>
-+#else
-+#include "getopt.h"
-+#endif /* HAVE_GETOPT_H */
-+
-+#include "pinentry.h"
-+
-+#ifdef FALLBACK_CURSES
-+#include "pinentry-curses.h"
-+#endif
-+
-+#define PGMNAME "pinentry-efl"
-+
-+#ifndef VERSION
-+#define VERSION
-+#endif
-+
-+#define ENTRY_HIDE "Hide entry"
-+#define ENTRY_SHOW "Show entry"
-+
-+typedef enum { CONFIRM_CANCEL, CONFIRM_OK, CONFIRM_NOTOK } confirm_value_t;
-+
-+static const int WIDTH = 480;
-+static const int BUTTON_HEIGHT = 27;
-+static const int BUTTON_WIDTH = 70;
-+static const int BUTTON_ICON_SIZE = 13;
-+static const int PADDING = 5;
-+
-+static Eina_Bool got_input;
-+static Ecore_Timer *timer;
-+static Evas_Object *check_label;
-+static Evas_Object *error_label;
-+static Evas_Object *entry;
-+static Evas_Object *repeat_entry;
-+static Evas_Object *qualitybar;
-+static Evas_Object *win;
-+static char **pargv;
-+static int grab_failed;
-+static int passphrase_ok;
-+static int confirm_mode;
-+static int pargc;
-+static confirm_value_t confirm_value;
-+static pinentry_t pinentry;
-+
-+pinentry_cmd_handler_t pinentry_cmd_handler;
-+
-+static void
-+quit (void)
-+{
-+  evas_object_del(win);
-+  elm_exit();
-+  ecore_main_loop_quit ();
-+}
-+
-+static void
-+delete_event (void *data EINA_UNUSED,
-+              Evas_Object *obj EINA_UNUSED,
-+              void *event EINA_UNUSED)
-+{
-+  pinentry->close_button = 1;
-+  quit ();
-+}
-+
-+static void
-+changed_text_handler (void *data EINA_UNUSED,
-+                      Evas_Object *obj,
-+                      void *event EINA_UNUSED)
-+{
-+  const char *s;
-+  int length;
-+  int percent;
-+
-+  got_input = EINA_TRUE;
-+
-+  if (pinentry->repeat_passphrase && repeat_entry)
-+    {
-+      elm_object_text_set (repeat_entry, "");
-+      elm_object_text_set (error_label, "");
-+    }
-+
-+  if (!qualitybar || !pinentry->quality_bar)
-+    return;
-+
-+  s = elm_object_text_get (obj);
-+  if (!s)
-+    s = "";
-+  length = strlen (s);
-+  percent = length? pinentry_inq_quality (pinentry, s, length) : 0;
-+  evas_object_color_set(qualitybar,
-+                        255 - ( 2.55 * percent ),
-+                        2.55 * percent, 0, 255);
-+  elm_progressbar_value_set (qualitybar, (double) percent / 100.0);
-+}
-+
-+static void
-+on_check (void *data EINA_UNUSED, Evas_Object *obj, void *event EINA_UNUSED)
-+{
-+  if(elm_check_state_get(obj))
-+    {
-+        elm_entry_password_set(entry, EINA_FALSE);
-+        elm_object_text_set(check_label,ENTRY_HIDE);
-+    }
-+  else
-+    {
-+        elm_entry_password_set(entry, EINA_TRUE);
-+        elm_object_text_set(check_label,ENTRY_SHOW);
-+    }
-+  evas_object_size_hint_min_set(check_label,
-+                                ELM_SCALE_SIZE(BUTTON_WIDTH),
-+                                ELM_SCALE_SIZE(BUTTON_HEIGHT));
-+  evas_object_size_hint_align_set(check_label, 0, 1);
-+}
-+
-+static void
-+on_click (void *data, Evas_Object *obj EINA_UNUSED, void *event EINA_UNUSED)
-+{
-+  if (confirm_mode)
-+    {
-+      confirm_value = (confirm_value_t) data;
-+      quit ();
-+      return;
-+    }
-+
-+  if (data)
-+    {
-+      const char *s;
-+      const char *s2;
-+
-+      s = elm_entry_entry_get (entry);
-+      if (!s)
-+	s = "";
-+
-+      if (pinentry->repeat_passphrase && repeat_entry)
-+	{
-+	  s2 = elm_entry_entry_get (repeat_entry);
-+	  if (!s2)
-+	    s2 = "";
-+	  if (strcmp (s, s2))
-+	    {
-+              elm_object_text_set(error_label,
-+                                  pinentry->repeat_error_string?
-+                                  pinentry->repeat_error_string:
-+				   "not correctly repeated");
-+              elm_object_focus_set(entry,EINA_TRUE);
-+              return;
-+	    }
-+	  pinentry->repeat_okay = 1;
-+	}
-+
-+      passphrase_ok = 1;
-+      pinentry_setbufferlen (pinentry, strlen (s) + 1);
-+      if (pinentry->pin)
-+	strncpy (pinentry->pin, s, strlen(s) + 1);
-+    }
-+  quit ();
-+}
-+
-+static void
-+enter_callback (void *data, Evas_Object * obj, void *event_info EINA_UNUSED)
-+{
-+  if (data)
-+    elm_object_focus_set (data, 1);
-+  else
-+    on_click ((void *) CONFIRM_OK, obj, NULL);
-+}
-+
-+static Eina_Bool
-+timeout_cb (const void * data)
-+{
-+  pinentry_t pe = (pinentry_t)data;
-+  if (!got_input)
-+    {
-+      ecore_main_loop_quit();
-+      if (pe)
-+        pe->specific_err = gpg_error (GPG_ERR_TIMEOUT);
-+    }
-+
-+  timer = NULL;
-+  return ECORE_CALLBACK_DONE;
-+}
-+
-+static void
-+create_window (void)
-+{
-+  char *txt;
-+  Evas_Object *icon;
-+  Evas_Object *obj;
-+  Evas_Object *table;
-+  int btn_txt_len = 0;
-+  int row = 0;
-+  int ok_len = 0;
-+
-+  win = elm_win_util_dialog_add(NULL,"pinentry","enter pin");
-+  elm_win_autodel_set(win, EINA_TRUE);
-+  elm_win_center(win,EINA_TRUE,EINA_TRUE);
-+  evas_object_smart_callback_add(win, "delete,request", delete_event, NULL);
-+
-+  table = elm_table_add(win);
-+  elm_table_padding_set(table,ELM_SCALE_SIZE(PADDING),0);
-+  evas_object_size_hint_padding_set (table,
-+                                     ELM_SCALE_SIZE(PADDING),
-+                                     ELM_SCALE_SIZE(PADDING),
-+                                     ELM_SCALE_SIZE(PADDING),
-+                                     ELM_SCALE_SIZE(PADDING));
-+  evas_object_show(table);
-+
-+  if (pinentry->title)
-+    {
-+      txt = pinentry_utf8_to_local (pinentry->lc_ctype,
-+                                    pinentry->title);
-+      elm_win_title_set ( win, txt );
-+      free (txt);
-+    }
-+
-+  /* Description Label */
-+  if (pinentry->description)
-+    {
-+      char* aligned;
-+      int len;
-+
-+      obj = elm_label_add(table);
-+      elm_label_line_wrap_set (obj, ELM_WRAP_WORD);
-+      txt = pinentry_utf8_to_local (pinentry->lc_ctype, pinentry->description);
-+      len = strlen(txt)+20; // 20 chars for align tag
-+      aligned = calloc(len+1,sizeof(char));
-+      if(aligned)
-+        {
-+          snprintf(aligned,len, "<align=left>%s</align>",txt);
-+          elm_object_text_set(obj,aligned);
-+          free (aligned);
-+        } else
-+          elm_object_text_set(obj,txt);
-+      free (txt);
-+      evas_object_size_hint_weight_set(obj, EVAS_HINT_EXPAND, 0);
-+      evas_object_size_hint_align_set(obj, EVAS_HINT_FILL, 0);
-+      elm_table_pack(table, obj, 1, row, 5, 1);
-+      evas_object_show(obj);
-+      row++;
-+    }
-+  if (!confirm_mode && (pinentry->error || pinentry->repeat_passphrase))
-+    {
-+    /* Error Label */
-+    if (pinentry->error)
-+        txt = pinentry_utf8_to_local (pinentry->lc_ctype, pinentry->error);
-+      else
-+        txt = "";
-+      obj = elm_label_add(table);
-+      evas_object_color_set(obj, 255, 0, 0, 255);
-+      elm_object_text_set(obj,txt);
-+      elm_object_style_set(obj,"slide_bounce");
-+      elm_label_slide_duration_set(obj, 10);
-+      elm_label_slide_mode_set(obj, ELM_LABEL_SLIDE_MODE_ALWAYS);
-+      elm_label_slide_go(obj);
-+      evas_object_size_hint_weight_set(obj, EVAS_HINT_EXPAND, 0);
-+      evas_object_size_hint_align_set(obj, EVAS_HINT_FILL, 0);
-+      elm_table_pack(table, obj, 1, row, 5, 1);
-+      evas_object_show(obj);
-+      if (pinentry->error)
-+        free (txt);
-+      row++;
-+    }
-+
-+  qualitybar = NULL;
-+
-+  if (!confirm_mode)
-+    {
-+
-+    if (pinentry->prompt)
-+      {
-+        /* Entry/Prompt Label */
-+        obj = elm_label_add(table);
-+        txt = pinentry_utf8_to_local (pinentry->lc_ctype, pinentry->prompt);
-+        elm_object_text_set(obj,txt);
-+        free (txt);
-+        evas_object_size_hint_weight_set(obj, 0, EVAS_HINT_EXPAND);
-+        evas_object_size_hint_align_set(obj, 1, EVAS_HINT_FILL);
-+        elm_table_pack(table, obj, 1, row, 1, 1);
-+        evas_object_show(obj);
-+      }
-+
-+      entry = elm_entry_add(table);
-+      elm_entry_scrollable_set(entry, EINA_TRUE);
-+      elm_scroller_policy_set(entry,
-+                              ELM_SCROLLER_POLICY_OFF,
-+                              ELM_SCROLLER_POLICY_OFF);
-+      elm_entry_password_set(entry, EINA_TRUE);
-+      elm_entry_single_line_set(entry, EINA_TRUE);
-+      evas_object_size_hint_weight_set(entry, 0, 0);
-+      evas_object_size_hint_align_set(entry, EVAS_HINT_FILL, 0);
-+      elm_table_pack(table, entry, 2, row, 4, 1);
-+      evas_object_smart_callback_add(entry,
-+                                     "changed",
-+                                     changed_text_handler,
-+                                     NULL);
-+      evas_object_show(entry);
-+      row++;
-+
-+      /* Check box */
-+      obj = elm_check_add(table);
-+      evas_object_size_hint_align_set(obj, 1, EVAS_HINT_FILL);
-+      elm_table_pack(table, obj, 1, row, 1, 1);
-+      evas_object_smart_callback_add(obj, "changed", on_check, NULL);
-+      evas_object_show(obj);
-+
-+      /* Check Label */
-+      check_label = elm_label_add(table);
-+      on_check((void *)NULL, obj, (void *)NULL);
-+      elm_table_pack(table, check_label, 2, row, 4, 1);
-+      evas_object_show(check_label);
-+      row++;
-+
-+      if (pinentry->quality_bar)
-+	{
-+          /* Quality Bar Label */
-+	  obj = elm_label_add(table);
-+          txt = pinentry_utf8_to_local (pinentry->lc_ctype,
-+                                        pinentry->quality_bar);
-+          elm_object_text_set(obj,txt);
-+          free (txt);
-+          evas_object_size_hint_weight_set(obj, 0, EVAS_HINT_EXPAND);
-+          evas_object_size_hint_align_set(obj, 1, EVAS_HINT_FILL);
-+          elm_table_pack(table, obj, 1, row, 1, 1);
-+          evas_object_show(obj);
-+
-+	  qualitybar = elm_progressbar_add(table);
-+          evas_object_color_set(qualitybar, 255, 0, 0, 255);
-+          evas_object_show(qualitybar);
-+          if (pinentry->quality_bar_tt)
-+	    elm_object_tooltip_text_set (qualitybar,
-+					 pinentry->quality_bar_tt);
-+          evas_object_size_hint_weight_set(qualitybar, EVAS_HINT_EXPAND, 0);
-+          evas_object_size_hint_align_set(qualitybar, EVAS_HINT_FILL, 0);
-+          elm_table_pack(table, qualitybar, 2, row, 4, 1);
-+          row++;
-+	}
-+
-+      if (pinentry->repeat_passphrase)
-+        {
-+          /* Repeat Label */
-+	  obj = elm_label_add(table);
-+          txt = pinentry_utf8_to_local (pinentry->lc_ctype,
-+                                        pinentry->repeat_passphrase);
-+          elm_object_text_set(obj,txt);
-+          free (txt);
-+          evas_object_size_hint_weight_set(obj, 0, EVAS_HINT_EXPAND);
-+          evas_object_size_hint_align_set(obj, 1, EVAS_HINT_FILL);
-+          elm_table_pack(table, obj, 1, row, 1, 1);
-+          evas_object_show(obj);
-+
-+          repeat_entry = elm_entry_add(table);
-+          elm_entry_scrollable_set(repeat_entry, EINA_TRUE);
-+          elm_scroller_policy_set(repeat_entry,
-+                                  ELM_SCROLLER_POLICY_OFF,
-+                                  ELM_SCROLLER_POLICY_OFF);
-+          elm_entry_password_set(repeat_entry, EINA_TRUE);
-+          elm_entry_single_line_set(repeat_entry, EINA_TRUE);
-+          evas_object_size_hint_weight_set(repeat_entry, 0, 0);
-+          evas_object_size_hint_align_set(repeat_entry, EVAS_HINT_FILL, 0);
-+          elm_table_pack(table, repeat_entry, 2, row, 4, 1);
-+	  evas_object_smart_callback_add (repeat_entry, "activated",
-+					  enter_callback, NULL);
-+          evas_object_show(repeat_entry);
-+          evas_object_smart_callback_add (entry,
-+                                          "activated",
-+                                          enter_callback,
-+                                          repeat_entry);
-+          evas_object_smart_callback_add(repeat_entry,
-+                                         "activated",
-+                                         on_click,
-+                                         (void *) CONFIRM_OK);
-+          row++;
-+        }
-+      else
-+        evas_object_smart_callback_add(entry,
-+                                       "activated",
-+                                       on_click,
-+                                       (void *) CONFIRM_OK);
-+  }
-+
-+  /* Cancel Button */
-+  if (!pinentry->one_button)
-+    {
-+      obj = elm_button_add(table);
-+      icon = elm_icon_add (table);
-+      evas_object_size_hint_aspect_set (icon, EVAS_ASPECT_CONTROL_BOTH, 1, 1);
-+      if (elm_icon_standard_set (icon, "dialog-cancel") ||
-+          elm_icon_standard_set (icon, "window-close"))
-+        {
-+          evas_object_size_hint_min_set(icon,
-+                                        ELM_SCALE_SIZE(BUTTON_ICON_SIZE),
-+                                        ELM_SCALE_SIZE(BUTTON_ICON_SIZE));
-+          elm_object_part_content_set(obj, "icon", icon);
-+          evas_object_show (icon);
-+        }
-+      else
-+        evas_object_del(icon);
-+      if (pinentry->cancel || pinentry->default_cancel)
-+        {
-+          if(pinentry->cancel)
-+            txt = pinentry_utf8_to_local (pinentry->lc_ctype, pinentry->cancel);
-+          else
-+            txt = pinentry_utf8_to_local (pinentry->lc_ctype,
-+                                          pinentry->default_cancel);
-+          if(txt[0]=='_')
-+            elm_object_text_set(obj,txt+1);
-+          else
-+            elm_object_text_set(obj,txt);
-+          btn_txt_len = ELM_SCALE_SIZE(strlen(txt) * (PADDING * 1.5));
-+          free (txt);
-+        }
-+      else
-+        elm_object_text_set(obj, "Cancel"); //STOCK_CANCEL
-+      evas_object_size_hint_align_set(obj, 0, 0);
-+      if(btn_txt_len>ELM_SCALE_SIZE(BUTTON_WIDTH))
-+        evas_object_size_hint_min_set(obj,
-+                                      btn_txt_len,
-+                                      ELM_SCALE_SIZE(BUTTON_HEIGHT));
-+      else
-+        evas_object_size_hint_min_set(obj,
-+                                      ELM_SCALE_SIZE(BUTTON_WIDTH),
-+                                      ELM_SCALE_SIZE(BUTTON_HEIGHT));
-+      elm_table_pack(table, obj, 4, row, 1, 1);
-+      evas_object_smart_callback_add(obj,
-+                                     "clicked",
-+                                     on_click,
-+                                     (void *) CONFIRM_CANCEL);
-+      evas_object_show(obj);
-+    }
-+
-+  /* OK Button */
-+  obj = elm_button_add(table);
-+  icon = elm_icon_add (table);
-+  evas_object_size_hint_aspect_set (icon, EVAS_ASPECT_CONTROL_BOTH, 1, 1);
-+  if (elm_icon_standard_set (icon, "dialog-ok") ||
-+      elm_icon_standard_set (icon, "list-add"))
-+    {
-+      evas_object_size_hint_min_set(icon,
-+                                    ELM_SCALE_SIZE(BUTTON_ICON_SIZE),
-+                                    ELM_SCALE_SIZE(BUTTON_ICON_SIZE));
-+      elm_object_part_content_set(obj, "icon", icon);
-+      evas_object_show (icon);
-+    }
-+  else
-+    evas_object_del(icon);
-+  if (pinentry->ok || pinentry->default_ok)
-+    {
-+      if(pinentry->ok)
-+        txt = pinentry_utf8_to_local (pinentry->lc_ctype, pinentry->ok);
-+      else
-+        txt = pinentry_utf8_to_local (pinentry->lc_ctype, pinentry->default_ok);
-+      if(txt[0]=='_')
-+        elm_object_text_set(obj,txt+1);
-+      else
-+        elm_object_text_set(obj,txt);
-+      ok_len = ELM_SCALE_SIZE(strlen(txt) * (PADDING * 1.5));
-+      if(ok_len>btn_txt_len)
-+        btn_txt_len = ok_len;
-+      free (txt);
-+    }
-+  else
-+    elm_object_text_set(obj,"OK"); //STOCK_OK
-+  evas_object_size_hint_align_set(obj, 0, 0);
-+  if(btn_txt_len>ELM_SCALE_SIZE(BUTTON_WIDTH))
-+    evas_object_size_hint_min_set(obj,
-+                                  btn_txt_len,
-+                                  ELM_SCALE_SIZE(BUTTON_HEIGHT));
-+  else
-+    evas_object_size_hint_min_set(obj,
-+                                  ELM_SCALE_SIZE(BUTTON_WIDTH),
-+                                  ELM_SCALE_SIZE(BUTTON_HEIGHT));
-+  elm_table_pack(table, obj, 5, row, 1, 1);
-+  evas_object_smart_callback_add(obj, "clicked", on_click, (void *) CONFIRM_OK);
-+  evas_object_show(obj);
-+
-+  /* Key/Lock Icon */
-+  obj = elm_icon_add (win);
-+  evas_object_size_hint_aspect_set (obj, EVAS_ASPECT_CONTROL_BOTH, 1, 1);
-+  if (elm_icon_standard_set (obj, "dialog-password"))
-+    {
-+      double ic_size = WIDTH/5;
-+      if(row==0)
-+        ic_size = ic_size/3.5;
-+      else if(row<4)
-+        ic_size = ic_size - ic_size/row;
-+      evas_object_size_hint_min_set(obj,
-+                                    ELM_SCALE_SIZE(ic_size),
-+                                    ELM_SCALE_SIZE(ic_size));
-+      evas_object_size_hint_weight_set(obj, EVAS_HINT_EXPAND, EVAS_HINT_EXPAND);
-+      evas_object_size_hint_align_set(obj, EVAS_HINT_FILL, 0.5);
-+      elm_table_pack(table, obj, 0, 0, 1, row? row:1);
-+      evas_object_show (obj);
-+    }
-+  else
-+      evas_object_del(obj);
-+
-+  /* Box for padding */
-+  obj = elm_box_add (win);
-+  elm_box_pack_end (obj, table);
-+  evas_object_show (obj);
-+
-+  elm_win_resize_object_add(win,obj);
-+  evas_object_show(win);
-+
-+  if(entry)
-+    elm_object_focus_set (entry, EINA_TRUE);
-+
-+  if (pinentry->timeout > 0)
-+    timer = ecore_timer_add (pinentry->timeout,
-+                             (Ecore_Task_Cb)timeout_cb,
-+                             pinentry);
-+}
-+
-+static int
-+efl_cmd_handler (pinentry_t pe)
-+{
-+  int want_pass = !!pe->pin;
-+
-+  got_input = EINA_FALSE;
-+  pinentry = pe;
-+  confirm_value = CONFIRM_CANCEL;
-+  passphrase_ok = 0;
-+  confirm_mode = want_pass ? 0 : 1;
-+  /* init ecore-x explicitly using DISPLAY since this can launch
-+   * from console
-+   */
-+  if (pe->display)
-+    ecore_x_init (pe->display);
-+  elm_init (pargc, pargv);
-+  create_window ();
-+  ecore_main_loop_begin ();
-+
-+  if (timer)
-+    {
-+      ecore_timer_del (timer);
-+      timer = NULL;
-+    }
-+
-+  if (confirm_value == CONFIRM_CANCEL || grab_failed)
-+    pe->canceled = 1;
-+
-+  pinentry = NULL;
-+  if (want_pass)
-+    {
-+      if (passphrase_ok && pe->pin)
-+	return strlen (pe->pin);
-+      else
-+	return -1;
-+    }
-+  else
-+    return (confirm_value == CONFIRM_OK) ? 1 : 0;
-+}
-+
-+int
-+main (int argc, char *argv[])
-+{
-+  pinentry_init (PGMNAME);
-+
-+#ifdef FALLBACK_CURSES
-+  if (pinentry_have_display (argc, argv))
-+    {
-+#endif
-+
-+  pinentry_cmd_handler = efl_cmd_handler;
-+  pargc = argc;
-+  pargv = argv;
-+
-+#ifdef FALLBACK_CURSES
-+    }
-+  else
-+    {
-+      pinentry_cmd_handler = curses_cmd_handler;
-+    }
-+#endif
-+
-+  pinentry_parse_opts (argc, argv);
-+  if (pinentry_loop ())
-+    return 1;
-+
-+  return 0;
-+}
--- 
-2.8.0.rc3
-
diff --git a/gnu/packages/patches/podofo-cmake-3.12.patch b/gnu/packages/patches/podofo-cmake-3.12.patch
deleted file mode 100644
index 0a3c19b21a..0000000000
--- a/gnu/packages/patches/podofo-cmake-3.12.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-The build fails with cmake 3.12.0.  This patch will be obsolete with the next
-release.
-
-https://sourceforge.net/p/podofo/tickets/24/attachment/podofo-cmake-3.12.patch
-
-
---- a/test/TokenizerTest/CMakeLists.txt	2018-07-20 18:26:02.921494293 +0200
-+++ b/test/TokenizerTest/CMakeLists.txt	2018-07-20 18:34:53.727136443 +0200
-@@ -2,10 +2,3 @@
- TARGET_LINK_LIBRARIES(TokenizerTest ${PODOFO_LIB} ${PODOFO_LIB_DEPENDS})
- SET_TARGET_PROPERTIES(TokenizerTest PROPERTIES COMPILE_FLAGS "${PODOFO_CFLAGS}")
- ADD_DEPENDENCIES(TokenizerTest ${PODOFO_DEPEND_TARGET})
--
--# Copy the test samples over to the build tree
--ADD_CUSTOM_COMMAND(
--    TARGET TokenizerTest
--    POST_BUILD
--    COMMAND "${CMAKE_COMMAND}" -E copy_directory "${CMAKE_CURRENT_SOURCE_DIR}/objects" "${CMAKE_CURRENT_BINARY_DIR}/objects"
--    )
diff --git a/gnu/packages/patches/python-mediafile-wavpack.patch b/gnu/packages/patches/python-mediafile-wavpack.patch
new file mode 100644
index 0000000000..9839fe87b5
--- /dev/null
+++ b/gnu/packages/patches/python-mediafile-wavpack.patch
@@ -0,0 +1,57 @@
+This patch has already been applied upstream, but is not included in the
+current release 0.6.0.
+
+From d2fc3b59f77c515b02dfe7ad936f89264375d2b4 Mon Sep 17 00:00:00 2001
+From: Adrian Sampson <adrian@radbox.org>
+Date: Wed, 29 Jul 2020 19:42:57 -0400
+Subject: [PATCH] Fix test for WavPack bitrate
+
+Fixes #34.
+---
+ docs/index.rst         | 5 +++++
+ mediafile.py           | 2 +-
+ test/test_mediafile.py | 2 +-
+ 3 files changed, 7 insertions(+), 2 deletions(-)
+
+diff --git a/docs/index.rst b/docs/index.rst
+index 7b622df..1465405 100644
+--- a/docs/index.rst
++++ b/docs/index.rst
+@@ -100,6 +100,11 @@ Internals
+ Changelog
+ ---------
+ 
++v0.7.0
++''''''
++
++- Mutagen 1.45.0 or later is now required.
++
+ v0.6.0
+ ''''''
+ 
+diff --git a/mediafile.py b/mediafile.py
+index 23fadaf..9e9d063 100644
+--- a/mediafile.py
++++ b/mediafile.py
+@@ -56,7 +56,7 @@
+ import six
+ 
+ 
+-__version__ = '0.6.0'
++__version__ = '0.7.0'
+ __all__ = ['UnreadableFileError', 'FileTypeError', 'MediaFile']
+ 
+ log = logging.getLogger(__name__)
+diff --git a/test/test_mediafile.py b/test/test_mediafile.py
+index e9e1850..7f17f44 100644
+--- a/test/test_mediafile.py
++++ b/test/test_mediafile.py
+@@ -907,7 +907,7 @@ class WavpackTest(ReadWriteTestBase, unittest.TestCase):
+         'bitrate': 109312,
+         'format': u'WavPack',
+         'samplerate': 44100,
+-        'bitdepth': 0,
++        'bitdepth': 16,
+         'channels': 1,
+     }
+ 
diff --git a/gnu/packages/patches/r-httpuv-1.5.4-unvendor-libuv.patch b/gnu/packages/patches/r-httpuv-1.5.5-unvendor-libuv.patch
index 0947718059..0947718059 100644
--- a/gnu/packages/patches/r-httpuv-1.5.4-unvendor-libuv.patch
+++ b/gnu/packages/patches/r-httpuv-1.5.5-unvendor-libuv.patch
diff --git a/gnu/packages/patches/tipp10-disable-downloader.patch b/gnu/packages/patches/tipp10-disable-downloader.patch
new file mode 100644
index 0000000000..4917a927f9
--- /dev/null
+++ b/gnu/packages/patches/tipp10-disable-downloader.patch
@@ -0,0 +1,165 @@
+https://salsa.debian.org/debian/tipp10/-/raw/debian/2.1.0-5/debian/patches/disable_downloaders.patch
+
+Author: Reiner Herrmann <reiner@reiner-h.de>
+Description: Disable downloaders
+ This makes porting to Qt5 much easier, as QHttp is no longer available.
+ But the functionality was not enabled anyway or is no longer useful.
+ .
+ - checkversion.h/.cpp:
+   At startup (while loading settings), Tipp10 "phones home" to do an
+   update check (www.tipp10.com/update/version.tipp10v210).
+   For a packaged software and one that is no longer being developed,
+   this does not make much sense.
+ - updatedialog.h/.cpp:
+   Can download newer sqlite database (www.tipp10.com/update/sql.tipp10v210.utf),
+   but this file is no longer available on the server (404).
+   The update action has also not been enabled in the menu, so the update
+   functionality was currently not active:
+     widget/mainwindow.cpp:143:  //fileMenu->addAction(updateAction);
+ - downloaddialog.h/.cpp:
+   Allows downloading lessons from user-specified location.
+   But the action (widget/startwidget.cpp -> lessonDownload) has not been part
+   of any menu, so it was also not in use.
+
+--- a/tipp10.pro
++++ b/tipp10.pro
+@@ -15,7 +15,6 @@
+ INCLUDEPATH     += 	.

+ CONFIG          += 	qt

+ QT              += 	sql

+-QT              += 	network

+ RC_FILE         += 	tipp10.rc

+ RESOURCES       += 	tipp10.qrc

+ HEADERS         += 	def/defines.h \

+@@ -36,15 +35,12 @@
+                     widget/settingspages.h \

+                     widget/lessondialog.h \

+                     widget/regexpdialog.h \

+-                    widget/downloaddialog.h \

+                     widget/lessonprintdialog.h \

+                     widget/lessonresult.h \

+-                    widget/updatedialog.h \

+                     widget/helpbrowser.h \

+                     widget/companylogo.h \

+                     widget/errormessage.h \

+                     widget/txtmessagedialog.h \

+-                    widget/checkversion.h \

+                     sql/connection.h \

+                     sql/lessontablesql.h \

+                     sql/chartablesql.h \

+@@ -70,15 +66,12 @@
+                     widget/settingspages.cpp \

+                     widget/lessondialog.cpp \

+                     widget/regexpdialog.cpp \

+-                    widget/downloaddialog.cpp \

+                     widget/lessonprintdialog.cpp \

+                     widget/lessonresult.cpp \

+-                    widget/updatedialog.cpp \

+                     widget/helpbrowser.cpp \

+                     widget/companylogo.cpp \

+                     widget/errormessage.cpp \

+                     widget/txtmessagedialog.cpp \

+-                    widget/checkversion.cpp \

+                     sql/lessontablesql.cpp \

+                     sql/chartablesql.cpp \

+                     sql/trainingsql.cpp \

+--- a/widget/mainwindow.cpp
++++ b/widget/mainwindow.cpp
+@@ -41,11 +41,9 @@
+ 

+ #include "mainwindow.h"

+ #include "settingsdialog.h"

+-#include "updatedialog.h"

+ #include "def/defines.h"

+ #include "def/errordefines.h"

+ #include "errormessage.h"

+-#include "checkversion.h"

+ 

+ MainWindow::MainWindow() {

+ 	trainingStarted = false;

+@@ -214,8 +212,8 @@
+ }

+ 

+ void MainWindow::showUpdate() {

+-	UpdateDialog updateDialog(this);

+-	updateDialog.exec();

++	//UpdateDialog updateDialog(this);

++	//updateDialog.exec();

+ 	// Fill lesson list after online update

+ 	startWidget->fillLessonList(false);

+ }

+@@ -486,6 +484,7 @@
+ 	settings.endGroup();

+ 

+     settings.beginGroup("general");

++#if 0

+     if (settings.value("check_new_version", true).toBool()) {

+ 

+         QDate lastVersionCheck = settings.value("last_version_check").toDate();

+@@ -499,6 +498,7 @@
+         }

+         settings.setValue("last_version_check", today);

+     }

++#endif

+     settings.endGroup();

+ }

+ 

+--- a/widget/settingspages.cpp
++++ b/widget/settingspages.cpp
+@@ -581,7 +581,7 @@
+ 

+ 	// Layout of group box vertical

+ 	QVBoxLayout *layout = new QVBoxLayout;

+-    layout->addWidget(checkNewVersion);

++    //layout->addWidget(checkNewVersion);

+     layout->addSpacing(1);

+     layout->addWidget(checkNativeStyle);

+     layout->setMargin(16);

+@@ -610,7 +610,6 @@
+     checkIntelligence->setChecked(settings.value("check_toggle_intelligence", true).toBool());

+ 	checkLimitLesson->setChecked(settings.value("check_limit_lesson", true).toBool());

+ 	checkLessonPublish->setChecked(settings.value("check_lesson_publish", true).toBool());

+-    checkNewVersion->setChecked(settings.value("check_new_version", true).toBool());

+     checkNativeStyle->setChecked(settings.value("check_native_style", false).toBool());

+ 	settings.endGroup();

+ }

+@@ -636,7 +635,6 @@
+ 	settings.setValue("check_limit_lesson", checkLimitLesson->isChecked());

+ 	settings.setValue("check_lesson_publish", checkLessonPublish->isChecked());

+ 	settings.setValue("check_native_style", checkNativeStyle->isChecked());

+-    settings.setValue("check_new_version", checkNewVersion->isChecked());

+     settings.endGroup();

+ 

+ 	return requireRestart;

+--- a/widget/startwidget.cpp
++++ b/widget/startwidget.cpp
+@@ -43,12 +43,10 @@
+ 

+ #include "startwidget.h"

+ #include "sql/startsql.h"

+-#include "updatedialog.h"

+ #include "def/defines.h"

+ #include "def/errordefines.h"

+ #include "errormessage.h"

+ #include "lessondialog.h"

+-#include "downloaddialog.h"

+ #include "illustrationdialog.h"

+ #include "txtmessagedialog.h"

+ 

+@@ -1048,7 +1046,7 @@
+ }

+ 

+ void StartWidget::clickDownloadLesson() {

+-

++#if 0

+ 	QStringList lessonData;

+ 

+ 	DownloadDialog downloadDialog(&lessonData, this);

+@@ -1083,6 +1081,7 @@
+ 			}

+ 		}

+ 	}

++#endif

+ }

+ 

+ void StartWidget::clickEditLesson() {

diff --git a/gnu/packages/patches/tipp10-qt5.patch b/gnu/packages/patches/tipp10-qt5.patch
new file mode 100644
index 0000000000..34ad5cd708
--- /dev/null
+++ b/gnu/packages/patches/tipp10-qt5.patch
@@ -0,0 +1,69 @@
+https://salsa.debian.org/debian/tipp10/-/raw/debian/2.1.0-5/debian/patches/qt5.patch
+
+Author: Reiner Herrmann <reiner@reiner-h.de>
+Description: Port to Qt5
+Bug-Debian: https://bugs.debian.org/875207
+
+--- a/tipp10.pro
++++ b/tipp10.pro
+@@ -14,6 +14,7 @@
+ DEPENDPATH      += 	.

+ INCLUDEPATH     += 	.

+ CONFIG          += 	qt

++QT              += 	widgets multimedia printsupport

+ QT              += 	sql

+ RC_FILE         += 	tipp10.rc

+ RESOURCES       += 	tipp10.qrc

+--- a/main.cpp
++++ b/main.cpp
+@@ -24,7 +24,6 @@
+ ****************************************************************/

+ 

+ #include <QApplication>

+-#include <QPlastiqueStyle>

+ #include <QString>

+ #include <QSettings>

+ #include <QCoreApplication>

+@@ -212,7 +211,7 @@
+ 

+     // Set windows style

+ 	if (!useNativeStyle) {

+-	    app.setStyle("plastique");

++	    app.setStyle("fusion");

+     }

+ 

+ 	// Translation

+--- a/games/abcrainwidget.cpp
++++ b/games/abcrainwidget.cpp
+@@ -235,8 +235,7 @@
+ 		charballs.last()->wind = (qrand() % 8) + 2;

+ 		charballs.last()->rad = 0;

+ 

+-		chartext.append(new QGraphicsTextItem(QString(characterTemp),

+-			charballs.last(), scene));

++		chartext.append(new QGraphicsTextItem(QString(characterTemp), charballs.last()));

+ 		chartext.last()->setFont(QFont("Courier", 16, 100));

+ 		chartext.last()->setPos(-(chartext.last()->boundingRect().width() / 2), -(chartext.last()->boundingRect().height() / 2));

+ 

+--- a/sql/chartablesql.cpp
++++ b/sql/chartablesql.cpp
+@@ -137,7 +137,7 @@
+ 	sortColumn(4);

+ 

+ 	headerview->setStretchLastSection(true);

+-	headerview->setResizeMode(QHeaderView::Interactive);

++	headerview->setSectionResizeMode(QHeaderView::Interactive);

+ 	headerview->setSortIndicatorShown(true);

+ 

+ 	// Resize the columns

+--- a/sql/lessontablesql.cpp
++++ b/sql/lessontablesql.cpp
+@@ -202,7 +202,7 @@
+ 	sortColumn(-1);

+ 

+ 	headerview->setStretchLastSection(true);

+-	headerview->setResizeMode(QHeaderView::Interactive);

++	headerview->setSectionResizeMode(QHeaderView::Interactive);

+ 	headerview->setSortIndicatorShown(true);

+ 

+ 	// Resize the columns

diff --git a/gnu/packages/patches/vcflib-use-shared-libraries.patch b/gnu/packages/patches/vcflib-use-shared-libraries.patch
deleted file mode 100644
index e198ec663c..0000000000
--- a/gnu/packages/patches/vcflib-use-shared-libraries.patch
+++ /dev/null
@@ -1,135 +0,0 @@
-This patch is a combination of many of the patches from Debian:
-https://sources.debian.org/src/libvcflib/1.0.1+dfsg-3/debian/patches/
-
----
- Makefile | 63 +++++++++++---------------------------------------------
- 1 file changed, 12 insertions(+), 51 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 6b13350..be85f22 100644
---- a/Makefile
-+++ b/Makefile
-@@ -114,43 +114,25 @@ BIN_SOURCES = src/vcfecho.cpp \
- 			  src/vcfnull2ref.cpp \
- 			  src/vcfinfosummarize.cpp
- 
--# when we can figure out how to build on mac
--# src/vcfsom.cpp
--
- #BINS = $(BIN_SOURCES:.cpp=)
- BINS = $(addprefix $(BIN_DIR)/,$(notdir $(BIN_SOURCES:.cpp=)))
- SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
- 
--TABIX = tabixpp/tabix.o
--FASTAHACK = fastahack/Fasta.o
--SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
--REPEATS = smithwaterman/Repeats.o
--INDELALLELE = smithwaterman/IndelAllele.o
--DISORDER = smithwaterman/disorder.o
--LEFTALIGN = smithwaterman/LeftAlign.o
--FSOM = fsom/fsom.o
- FILEVERCMP = filevercmp/filevercmp.o
- 
--# Work out how to find htslib
--# Use the one we ship in tabixpp unless told otherwise by the environment
--HTS_LIB ?= $(VCF_LIB_LOCAL)/tabixpp/htslib/libhts.a
--HTS_INCLUDES ?= -I$(VCF_LIB_LOCAL)/tabixpp/htslib
--HTS_LDFLAGS ?= -L$(VCF_LIB_LOCAL)/tabixpp/htslib -lhts -lbz2 -lm -lz -llzma -pthread
--
--
--INCLUDES = $(HTS_INCLUDES) -I$(INC_DIR) 
--LDFLAGS = -L$(LIB_DIR) -lvcflib $(HTS_LDFLAGS) -lpthread -lz -lm -llzma -lbz2
-+INCLUDES = -I$(INC_DIR) $(shell pkg-config --cflags htslib fastahack smithwaterman tabixpp)
-+LDFLAGS = -L$(LIB_DIR) -lvcflib -lpthread -lz -lstdc++ -lm -llzma -lbz2 $(shell pkg-config --libs htslib fastahack smithwaterman tabixpp)
- 
- 
- 
--all: $(OBJECTS) $(BINS) scriptToBin
-+all: $(OBJECTS) $(BINS) scriptToBin libvcflib.a
- 
- scriptToBin: $(BINS)
- 	$(CP) scripts/* $(BIN_DIR)
- 
- GIT_VERSION += $(shell git describe --abbrev=4 --dirty --always)
- 
--CXXFLAGS = -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x
-+CXXFLAGS = -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -fPIC
- #CXXFLAGS = -O2
- #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
- 
-@@ -168,7 +150,7 @@ profiling:
- gprof:
- 	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
- 
--$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
-+$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(FILEVERCMP)
- 	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && $(CP) src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
- 
- multichoose: pre
-@@ -177,39 +159,22 @@ multichoose: pre
- intervaltree: pre
- 	cd intervaltree && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
- 
--$(TABIX): pre
--	cd tabixpp && INCLUDES="$(HTS_INCLUDES)" LIBPATH="-L. $(HTS_LDFLAGS)" HTSLIB="$(HTS_LIB)" $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
--
--$(SMITHWATERMAN): pre
--	cd smithwaterman && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
--
--$(DISORDER): $(SMITHWATERMAN)
--
--$(REPEATS): $(SMITHWATERMAN)
--
--$(LEFTALIGN): $(SMITHWATERMAN)
--
--$(INDELALLELE): $(SMITHWATERMAN)
--
--$(FASTAHACK): pre
--	cd fastahack && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) Fasta.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
--
--#$(FSOM):
--#	cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
--
- $(FILEVERCMP): pre
- 	cd filevercmp && make && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) *.o $(VCF_LIB_LOCAL)/$(INC_DIR)/
- 
- $(SHORTBINS): pre
- 	$(MAKE) $(BIN_DIR)/$@
- 
--$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
-+$(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SSW) $(FILEVERCMP) pre intervaltree
- 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
- 
--libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre
--	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
-+libvcflib.a: $(OBJECTS) $(SSW) $(FILEVERCMP) pre
-+	ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP)
- 	$(CP) libvcflib.a $(LIB_DIR)
- 
-+libvcflib.so: $(OBJECTS) $(SSW) $(FILEVERCMP) pre
-+	$(CXX) -shared -o libvcflib.so $(OBJECTS) $(SSW) $(FILEVERCMP)
-+	$(CP) libvcflib.so $(LIB_DIR)
- 
- test: $(BINS)
- 	@prove -Itests/lib -w tests/*.t
-@@ -230,16 +195,12 @@ clean:
- 	$(RM) $(BINS) $(OBJECTS)
- 	$(RM) ssw_cpp.o ssw.o
- 	$(RM) libvcflib.a
-+	$(RM) libvcflib.so
- 	$(RM) -r $(BIN_DIR)
- 	$(RM) -r $(LIB_DIR)
- 	$(RM) -r $(INC_DIR)
- 	$(RM) -r $(OBJ_DIR)
--	$(MAKE) clean -C tabixpp
--	$(MAKE) clean -C smithwaterman
--	$(MAKE) clean -C fastahack
- 	$(MAKE) clean -C multichoose
--	$(MAKE) clean -C fsom
--	$(MAKE) clean -C libVCFH
- 	$(MAKE) clean -C test
- 	$(MAKE) clean -C filevercmp
- 	$(MAKE) clean -C intervaltree
--- 
-2.28.0
-
diff --git a/gnu/packages/patches/vlc-qt-5.15.patch b/gnu/packages/patches/vlc-qt-5.15.patch
deleted file mode 100644
index e986a99861..0000000000
--- a/gnu/packages/patches/vlc-qt-5.15.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-Fix build of VLC with Qt 5.15. Otherwise it fails like this:
-
-------
-In file included from gui/qt/util/timetooltip.moc.cpp:10:0:
-gui/qt/util/timetooltip.hpp:49:18: error: field ‘mPainterPath’ has incomplete type ‘QPainterPath’
-     QPainterPath mPainterPath;
-                  ^~~~~~~~~~~~
-In file included from /gnu/store/jsxxnsdvij5mrrv6c0kj0261k0f44xlz-qtbase-5.15.2/include/qt5/QtGui/qbrush.h:49:0,
-                 from /gnu/store/jsxxnsdvij5mrrv6c0kj0261k0f44xlz-qtbase-5.15.2/include/qt5/QtGui/qpalette.h:46,
-                 from /gnu/store/jsxxnsdvij5mrrv6c0kj0261k0f44xlz-qtbase-5.15.2/include/qt5/QtWidgets/qwidget.h:48,
-                 from /gnu/store/jsxxnsdvij5mrrv6c0kj0261k0f44xlz-qtbase-5.15.2/include/qt5/QtWidgets/QWidget:1,
-                 from gui/qt/util/timetooltip.hpp:27,
-                 from gui/qt/util/timetooltip.moc.cpp:10:
-/gnu/store/jsxxnsdvij5mrrv6c0kj0261k0f44xlz-qtbase-5.15.2/include/qt5/QtGui/qmatrix.h:54:7: note: forward declaration of ‘class QPainterPath’
- class QPainterPath;
-       ^~~~~~~~~~~~
-make[4]: *** [Makefile:25852: gui/qt/util/libqt_plugin_la-timetooltip.moc.lo] Error 1
-------
-
-diff --git a/modules/gui/qt/components/playlist/views.cpp b/modules/gui/qt/components/playlist/views.cpp
-index 24db9d9..73c1779 100644
---- a/modules/gui/qt/components/playlist/views.cpp
-+++ b/modules/gui/qt/components/playlist/views.cpp
-@@ -27,6 +27,7 @@
- #include "input_manager.hpp"                      /* THEMIM */
- 
- #include <QPainter>
-+#include <QPainterPath>
- #include <QRect>
- #include <QStyleOptionViewItem>
- #include <QFontMetrics>
-diff --git a/modules/gui/qt/dialogs/plugins.cpp b/modules/gui/qt/dialogs/plugins.cpp
-index d233382..69728eb 100644
---- a/modules/gui/qt/dialogs/plugins.cpp
-+++ b/modules/gui/qt/dialogs/plugins.cpp
-@@ -53,6 +53,7 @@
- #include <QListView>
- #include <QListWidget>
- #include <QPainter>
-+#include <QPainterPath>
- #include <QStyleOptionViewItem>
- #include <QKeyEvent>
- #include <QPushButton>
-diff --git a/modules/gui/qt/util/timetooltip.hpp b/modules/gui/qt/util/timetooltip.hpp
-index 6a1329e..9f50b18 100644
---- a/modules/gui/qt/util/timetooltip.hpp
-+++ b/modules/gui/qt/util/timetooltip.hpp
-@@ -25,6 +25,7 @@
- #include "qt.hpp"
- 
- #include <QWidget>
-+#include <QPainterPath>
- 
- class TimeTooltip : public QWidget
- {
-