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-rw-r--r--gnu/packages/patches/avogadro-boost148.patch69
-rw-r--r--gnu/packages/patches/avogadro-eigen3-update.patch603
-rw-r--r--gnu/packages/patches/avogadro-python-eigen-lib.patch161
-rw-r--r--gnu/packages/patches/c++-gsl-find-system-gtest.patch96
-rw-r--r--gnu/packages/patches/freebayes-devendor-deps.patch2
-rw-r--r--gnu/packages/patches/icecat-makeicecat.patch4
-rw-r--r--gnu/packages/patches/mutt-CVE-2021-3181.patch45
-rw-r--r--gnu/packages/patches/pinentry-efl.patch798
8 files changed, 99 insertions, 1679 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(
+ ${name}
diff --git a/gnu/packages/patches/freebayes-devendor-deps.patch b/gnu/packages/patches/freebayes-devendor-deps.patch
index 7e84666b85..9886de11fb 100644
--- a/gnu/packages/patches/freebayes-devendor-deps.patch
+++ b/gnu/packages/patches/freebayes-devendor-deps.patch
@@ -23,7 +23,7 @@ index f6bf242..bded4af 100644
+tabixpp_dep = dependency('tabixpp', required : false)
+fastahack_dep = dependency('fastahack', required : false)
+smithwaterman_dep = dependency('smithwaterman', required : false)
-+vcflib_dep = dependency('libvcflib', required: false)
++vcflib_dep = dependency('vcflib', required: false)
thread_dep = dependency('threads')
if htslib_dep.found()
diff --git a/gnu/packages/patches/icecat-makeicecat.patch b/gnu/packages/patches/icecat-makeicecat.patch
index 3f16880260..edd1ced257 100644
--- a/gnu/packages/patches/icecat-makeicecat.patch
+++ b/gnu/packages/patches/icecat-makeicecat.patch
@@ -25,7 +25,7 @@ index 8be2362..48716f2 100755
-wget -N https://ftp.mozilla.org/pub/mozilla.org/firefox/releases/${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/mutt-CVE-2021-3181.patch b/gnu/packages/patches/mutt-CVE-2021-3181.patch
deleted file mode 100644
index df5214b052..0000000000
--- a/gnu/packages/patches/mutt-CVE-2021-3181.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-Fix CVE-2021-3181:
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2021-3181
-
-Patch copied from upstream source repository:
-
-https://gitlab.com/muttmua/mutt/-/commit/c059e20ea4c7cb3ee9ffd3500ffe313ae84b2545
-
-From c059e20ea4c7cb3ee9ffd3500ffe313ae84b2545 Mon Sep 17 00:00:00 2001
-From: Kevin McCarthy <kevin@8t8.us>
-Date: Sun, 17 Jan 2021 10:40:37 -0800
-Subject: [PATCH] Fix memory leak parsing group address.
-
-When there was a group address terminator with no previous addresses,
-an address would be allocated but not attached to the address list.
-
-Change this to only allocate when last exists.
-
-It would be more correct to not allocate at all unless we are inside a
-group list, but I will address that in a separate commit to master.
----
- rfc822.c | 5 ++---
- 1 file changed, 2 insertions(+), 3 deletions(-)
-
-diff --git a/rfc822.c b/rfc822.c
-index 7ff4eaa3..ced619f2 100644
---- a/rfc822.c
-+++ b/rfc822.c
-@@ -587,11 +587,10 @@ ADDRESS *rfc822_parse_adrlist (ADDRESS *top, const char *s)
- #endif
-
- /* add group terminator */
-- cur = rfc822_new_address ();
- if (last)
- {
-- last->next = cur;
-- last = cur;
-+ last->next = rfc822_new_address ();
-+ last = last->next;
- }
-
- phraselen = 0;
---
-GitLab
-
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
-
generated by cgit v1.2.3 (git 2.46.2) at 2024-12-25 07:33:42 +0000