gnu: Remove avogadro.

This package fails to build and has been superseded by avogadro2.

* gnu/packages/chemistry.scm (avogadro): Remove variable.
* gnu/packages/patches/avogadro-boost148.patch,
gnu/packages/patches/avogadro-eigen3-update.patch,
gnu/packages/patches/avogadro-python-eigen-lib.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.

3 files changed, 0 insertions, 833 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();