Merge branch 'master' into core-updates

34 files changed, 1291 insertions, 122 deletions

diff --git a/gnu/local.mk b/gnu/local.mk
index c62e6ea50e..c19d992874 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -584,6 +584,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/audacity-build-with-system-portaudio.patch \
   %D%/packages/patches/automake-skip-amhello-tests.patch	\
   %D%/packages/patches/avahi-localstatedir.patch		\
+  %D%/packages/patches/avogadro-boost148.patch			\
+  %D%/packages/patches/avogadro-eigen3-update.patch		\
+  %D%/packages/patches/avogadro-python-eigen-lib.patch		\
   %D%/packages/patches/avidemux-install-to-lib.patch		\
   %D%/packages/patches/awesome-reproducible-png.patch		\
   %D%/packages/patches/azr3.patch				\
@@ -768,6 +771,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/grep-timing-sensitive-test.patch		\
   %D%/packages/patches/groff-source-date-epoch.patch		\
   %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch	\
+  %D%/packages/patches/grub-check-error-efibootmgr.patch	\
   %D%/packages/patches/gsl-test-i686.patch			\
   %D%/packages/patches/gspell-dash-test.patch			\
   %D%/packages/patches/guile-1.8-cpp-4.5.patch			\
@@ -1082,7 +1086,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-mox3-python3.6-compat.patch	\
   %D%/packages/patches/python-paste-remove-website-test.patch	\
   %D%/packages/patches/python-paste-remove-timing-test.patch	\
-  %D%/packages/patches/python-pygit2-disable-network-tests.patch	\
   %D%/packages/patches/python-pycrypto-CVE-2013-7459.patch	\
   %D%/packages/patches/python2-pygobject-2-gi-info-type-error-domain.patch \
   %D%/packages/patches/python-pygpgme-fix-pinentry-tests.patch	\
diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index 727789a96e..e9abf399ab 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -85,7 +85,8 @@
              (uri (string-append "mirror://gnu/grub/grub-" version ".tar.xz"))
              (sha256
               (base32
-               "03vvdfhdmf16121v7xs8is2krwnv15wpkhkf16a4yf8nsfc3f2w1"))))
+               "03vvdfhdmf16121v7xs8is2krwnv15wpkhkf16a4yf8nsfc3f2w1"))
+             (patches (search-patches "grub-check-error-efibootmgr.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm
index d82db532aa..e6df1d23c7 100644
--- a/gnu/packages/c.scm
+++ b/gnu/packages/c.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 2d7cb7aad1..03120aaeee 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -23,16 +23,96 @@
   #:use-module (guix download)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages documentation)
+  #:use-module (gnu packages gl)
   #:use-module (gnu packages gv)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages qt)
   #:use-module (gnu packages xml)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python))
 
+(define-public avogadro
+  (package
+    (name "avogadro")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/cryos/avogadro/archive/"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "02v4h6hi1m7ilv0apdf74a8l1cm6dxnxyqp0rdaidrp3i9pf6lv4"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (patches
+               (search-patches "avogadro-eigen3-update.patch"
+                               "avogadro-python-eigen-lib.patch"
+                               "avogadro-boost148.patch"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:tests? #f
+       #:configure-flags
+       (list "-DENABLE_GLSL=ON"
+             (string-append "-DPYTHON_LIBRARIES="
+                            (assoc-ref %build-inputs "python")
+                            "/lib")
+             (string-append "-DPYTHON_INCLUDE_DIRS="
+                            (assoc-ref %build-inputs "python")
+                            "/include/python2.7"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-python-lib-path
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; This is necessary to install the Python module in the correct
+             ;; directory.
+             (substitute* "libavogadro/src/python/CMakeLists.txt"
+               (("^EXECUTE_PROCESS.*$") "")
+               (("^.*from sys import stdout.*$") "")
+               (("^.*OUTPUT_VARIABLE.*")
+                (string-append "set(PYTHON_LIB_PATH \""
+                               (assoc-ref outputs "out")
+                               "/lib/python2.7/site-packages\")")))
+             #t))
+         (add-after 'install 'wrap-program
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Make sure 'avogadro' runs with the correct PYTHONPATH.
+             (let* ((out (assoc-ref outputs "out")))
+               (setenv "PYTHONPATH"
+                       (string-append
+                        (assoc-ref outputs "out")
+                        "/lib/python2.7/site-packages:"
+                        (getenv "PYTHONPATH")))
+               (wrap-program (string-append out "/bin/avogadro")
+                 `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))))
+             #t)))))
+    (native-inputs
+     `(("doxygen" ,doxygen)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("boost" ,boost)
+       ("eigen" ,eigen)
+       ("glew" ,glew)
+       ("openbabel" ,openbabel)
+       ("python" ,python-2)
+       ("python-numpy" ,python2-numpy)
+       ("python-pyqt" ,python2-pyqt-4)
+       ("python-sip" ,python2-sip)
+       ("qt" ,qt-4)
+       ("zlib" ,zlib)))
+    (home-page "https://avogadro.cc")
+    (synopsis "Advanced molecule editor")
+    (description
+     "Avogadro is an advanced molecule editor and visualizer designed for use
+in computational chemistry, molecular modeling, bioinformatics, materials
+science, and related areas.  It offers flexible high quality rendering and a
+powerful plugin architecture.")
+    (license license:gpl2+)))
+
 (define-public domainfinder
   (package
     (name "domainfinder")
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index 599fd8cbbc..e26983da3b 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -185,8 +185,8 @@ their dependencies.")
       (license l:gpl3+))))
 
 (define-public cuirass
-  (let ((commit "4db99f647b3677086a2007763726d05a59b0cdcb")
-        (revision "18"))
+  (let ((commit "8d40c49170971ad7bbf8b97336934dbb3d949fc1")
+        (revision "19"))
     (package
       (name "cuirass")
       (version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -198,7 +198,7 @@ their dependencies.")
                 (file-name (string-append name "-" version))
                 (sha256
                  (base32
-                  "1lg3w0xjg6b806y8gfxj2dq1g0djm5pyk886j8g7n5n9ljlhjzxj"))))
+                  "0xxcapf9ag3zx6131v128vhin5m2j3w2gjbjbpdwr0qkaysh0gvf"))))
       (build-system gnu-build-system)
       (arguments
        '(#:modules ((guix build utils)
diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index ee7447b024..be178a5f99 100644
--- a/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@ -7,7 +7,7 @@
 ;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index ac8c1fdbc0..f2ed53f036 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -22,7 +22,7 @@
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index 34709b73fc..a095d0cd4f 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -12,7 +12,7 @@
 ;;; Copyright © 2018 Vasile Dumitrascu <va511e@yahoo.com>
 ;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 2322581a30..8665356f5c 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -34,7 +34,7 @@
 ;;; Copyright © 2017, 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2018 Sohom Bhattacharjee <soham.bhattacharjee15@gmail.com>
 ;;; Copyright © 2018 Mathieu Lirzin <mthl@gnu.org>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2018 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
 ;;; Copyright © 2018 Jack Hill <jackhill@jackhill.us>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
@@ -1179,16 +1179,18 @@ rather than the contents of files.")
 (define-public emacs-async
   (package
     (name "emacs-async")
+    (home-page "https://github.com/jwiegley/emacs-async")
     (version "1.9.3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://stable.melpa.org/packages/async-"
-                                  version ".tar"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url home-page)
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0xvi50y96y2qh81qkhj8p6ar1xnfasg58qvlsvgvvmdf4g8srlij"))))
+                "1zsnb6dy8p6y68xgidv3dfxaga4biramfw8fq7wac0sc50vc98vq"))))
     (build-system emacs-build-system)
-    (home-page "https://elpa.gnu.org/packages/async.html")
     (synopsis "Asynchronous processing in Emacs")
     (description
      "This package provides the ability to call asynchronous functions and
@@ -10025,8 +10027,8 @@ perform regression test for packages that provide font-lock rules.")
       (license license:gpl3+))))
 
 (define-public emacs-racket-mode
-  (let ((commit "1b78827d310b6d655782b7bba0f2360c9ef34ff6")
-        (revision "2"))
+  (let ((commit "add0190d3c9bdad25fee57f8efd0460c9a45c2ec")
+        (revision "1"))
     (package
       (name "emacs-racket-mode")
       (version (string-append "0.0.2" "-" revision "."
@@ -10040,7 +10042,7 @@ perform regression test for packages that provide font-lock rules.")
          (file-name (string-append name "-" version "-checkout"))
          (sha256
           (base32
-           "04mzxcg32av8p6v0pqb0si6qk5qxbrbllx6m3j16fp32bdz71sps"))))
+           "0bf6s4nqjfacij20x9vppdnq8fq1bf53cch6p4g8xqcqri3ms4jw"))))
       (build-system emacs-build-system)
       (arguments
        `(#:include '("\\.el$" "\\.rkt$")))
@@ -11374,8 +11376,8 @@ wiki.")
     (license license:expat)))
 
 (define-public emacs-recent-addresses
-  (let ((commit "d9da58db542089a1ceb5ef29e420dbfbc4a36373")
-        (revision "0"))
+  (let ((commit "afbbfdc43b81e620acf827ca20d297e0c517b6eb")
+        (revision "1"))
     (package
       (name "emacs-recent-addresses")
       (home-page "http://nschum.de/src/emacs/recent-addresses/")
@@ -11383,18 +11385,20 @@ wiki.")
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
-                      (url "https://github.com/nschum/recent-addresses.el")
+                      ;; Note: Use a branch that works with Helm.  Submitted
+                      ;; at <https://github.com/nschum/recent-addresses.el/pull/1>.
+                      (url "https://github.com/civodul/recent-addresses.el")
                       (commit commit)))
                 (sha256
                  (base32
-                  "175rvcwmkb5z7ss7q2y5178mvdvp5bhn39irz80qinlvaz8fm4nk"))
+                  "0ajrq0galjmdyjdjyxazykjyax3gh6hvfk4s7l657pi11g0q5zax"))
                 (file-name (git-file-name name version))))
       (build-system emacs-build-system)
       (synopsis "Record recently-used email addressed and auto-complete them")
       (description
-       "@code{recent-addresses} is an Emacs allows you to quickly look up
-previously used email addresses.  It can be used alongside the Gnus email
-client.")
+       "@code{recent-addresses} is an Emacs package that allows you to quickly
+look up previously used email addresses.  It can be used alongside the Gnus
+email client.")
       (license license:gpl2+))))
 
 (define-public emacs-fold-dwim
@@ -11643,3 +11647,30 @@ comments and Org files in the Magit status buffer.  Activating an item jumps
 to it in its file.  By default, it uses keywords from @code{hl-todo}, minus a
 few (like NOTE).")
       (license license:gpl3))))
+
+(define-public emacs-git-annex
+  ;; Unreleased version has a fontification fix.
+  (let ((commit "ebdb44aef1883f1b2b8058e05d30fb9315b03707")
+        (revision "1"))
+    (package
+      (name "emacs-git-annex")
+      (version (string-append "1.1-" revision "." (string-take commit 8)))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/jwiegley/git-annex-el")
+               (commit commit)))
+         (file-name (string-append name "-" version "-checkout"))
+         (sha256
+          (base32
+           "1mzv40gj7k10h7h5s43my8msgzjpj680qprqa9pp8nbyhl49v3wh"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/jwiegley/git-annex-el")
+      (synopsis "Emacs integration for git-annex")
+      (description "Enhances Dired and buffers visiting annex files with
+git-annex functionality.  In Dired, the names of annex files are shortened by
+hiding the symbolic links and fontified based on whether content is present.
+Commands for performing some common operations (e.g., unlocking and adding
+files) are provided.")
+      (license license:gpl2+))))
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index f11ce71f5a..3b433a1bfe 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -59,6 +59,7 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gperf)
+  #:use-module (gnu packages groff)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages image)
@@ -76,6 +77,7 @@
   #:use-module (gnu packages readline)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages tcl)
+  #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages tex)
   #:use-module (gnu packages wxwidgets)
@@ -224,6 +226,74 @@ tool to forward annotation from your schematic to layout using PCB; some minor
 utilities.")
     (license license:gpl2+)))
 
+(define-public lepton-eda
+  ;; This is a fork of gEDA/gaf started in late 2016.  One of its goal is to
+  ;; keep and to extend Guile support.
+  (package
+    (inherit geda-gaf)
+    (name "lepton-eda")
+    (version "1.9.5-20180820")
+    (home-page "https://github.com/lepton-eda/lepton-eda")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference (url home-page) (commit version)))
+              (sha256
+               (base32
+                "1ayaccvw18zh4g7a4x5jf6yxkphi5xafb0hpc732g59qkgwfcmlr"))
+              (file-name (git-file-name name version))))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("gettext" ,gnu-gettext)
+       ("texinfo" ,texinfo)
+       ("groff" ,groff)
+       ("which" ,which)
+       ,@(package-native-inputs geda-gaf)))
+    ;; For now it's Guile 2.0, not 2.2.
+    (arguments
+     (substitute-keyword-arguments (package-arguments geda-gaf)
+       ((#:configure-flags flags ''())
+        ;; When running "make", the POT files are built with the build time as
+        ;; their "POT-Creation-Date".  Later on, "make" notices that .pot
+        ;; files were updated and goes on to run "msgmerge"; as a result, the
+        ;; non-deterministic POT-Creation-Date finds its way into .po files,
+        ;; and then in .gmo files.  To avoid that, simply make sure 'msgmerge'
+        ;; never runs.  See <https://bugs.debian.org/792687>.
+        `(cons "ac_cv_path_MSGMERGE=true" ,flags))
+       ((#:phases phases '%standard-phases)
+        `(modify-phases ,phases
+           (add-before 'bootstrap 'prepare
+             (lambda _
+               ;; Some of the scripts there are invoked by autogen.sh.
+               (for-each patch-shebang (find-files "build-tools"))
+
+               ;; Make sure 'msgmerge' can modify the PO files.
+               (for-each (lambda (po)
+                           (chmod po #o666))
+                         (find-files "." "\\.po$"))
+
+               ;; This would normally be created by invoking 'git', but it
+               ;; doesn't work here.
+               (call-with-output-file "version.h"
+                 (lambda (port)
+                   (format port "#define PACKAGE_DATE_VERSION \"~a\"~%"
+                           ,(string-drop version
+                                         (+ 1 (string-index version #\-))))
+                   (format port "#define PACKAGE_DOTTED_VERSION \"~a\"~%"
+                           ,(string-take version
+                                         (string-index version #\-)))
+                   (format port "#define PACKAGE_GIT_COMMIT \"cabbag3\"~%")))
+               #t))))))
+    (description
+     "Lepton EDA ia an @dfn{electronic design automation} (EDA) tool set
+forked from gEDA/gaf in late 2016.  EDA tools are used for electrical circuit
+design, schematic capture, simulation, prototyping, and production.  Lepton
+EDA includes tools for schematic capture, attribute management, bill of
+materials (BOM) generation, netlisting into over 20 netlist formats, analog
+and digital simulation, and printed circuit board (PCB) layout, and many other
+features.")))
+
 (define-public pcb
   (package
     (name "pcb")
diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm
index 176eef5137..0b5a82e9e5 100644
--- a/gnu/packages/firmware.scm
+++ b/gnu/packages/firmware.scm
@@ -188,7 +188,7 @@ by the b43-open driver of Linux-libre.")
     (version "1.11.0")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://code.coreboot.org/p/seabios/downloads/get/"
+              (uri (string-append "https://www.seabios.org/downloads/"
                                   "seabios-" version ".tar.gz"))
               (sha256
                (base32
diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm
index 5352ea221b..ce67b6858b 100644
--- a/gnu/packages/freedesktop.scm
+++ b/gnu/packages/freedesktop.scm
@@ -12,7 +12,7 @@
 ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 Brendan Tildesley <brendan.tildesley@openmailbox.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -495,7 +495,7 @@ applications, X servers (rootless or fullscreen) or other display servers.")
 (define-public weston
   (package
     (name "weston")
-    (version "4.0.0")
+    (version "5.0.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -503,7 +503,7 @@ applications, X servers (rootless or fullscreen) or other display servers.")
                     "weston-" version ".tar.xz"))
               (sha256
                (base32
-                "0n2big8xw6g6n46zm1jyf00dv9r4d84visdz5b8vxpw3xzkhmz50"))))
+                "1bsc9ry566mpk6fdwkqpvwq2j7m79d9cvh7d3lgf6igsphik98hm"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 20b203aa6f..b4a088a051 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -11,7 +11,7 @@
 ;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
 ;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index b44db6a6bf..5c9f4d499c 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -1984,6 +1984,30 @@ Vicare Scheme and IronScheme.  Right now it contains:
 @end itemize\n")
     (license license:bsd-3)))
 
+(define-public guile-aa-tree
+  (package
+    (name "guile-aa-tree")
+    (version "3.1.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://savannah/guile-aa-tree/guile-aa-tree-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "0044c105r3q9vpl17pv3phl1b79kjm1llhkakqgiasixyav01blh"))))
+    (build-system guile-build-system)
+    (native-inputs `(("guile" ,guile-2.2)))
+    ;; https://savannah.nongnu.org/projects/guile-aa-tree
+    (home-page "https://qlfiles.net/guile-aa-tree/")
+    (synopsis "AA tree data structure for Guile")
+    (description
+     "This package provides an implementation of @dfn{AA trees}, a
+self-balancing binary tree data structure, for Guile.  It ensure @math{O(log
+n)} worst case performance for core operations.  The module provides
+non-mutating insert, delete, and search operations, with support for
+convenient nested tree operations.")
+    (license license:gpl3+)))
+
 (define-public guile-simple-zmq
   (let ((commit "1f3b7c0b9b249c6fde8e8a632b252d8a1b794424")
         (revision "1"))
diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 759ca6044e..7d7d85f951 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3268,7 +3268,7 @@ This is a better maintained fork of the \"temporary\" package.")
 (define-public ghc-smallcheck
   (package
     (name "ghc-smallcheck")
-    (version "1.1.1")
+    (version "1.1.5")
     (source
      (origin
        (method url-fetch)
@@ -3278,7 +3278,7 @@ This is a better maintained fork of the \"temporary\" package.")
              ".tar.gz"))
        (sha256
         (base32
-         "1ygrabxh40bym3grnzqyfqn96lirnxspb8cmwkkr213239y605sd"))))
+         "195fj7w3v03d1y1nm2ylavzrwxjcdbq0lb6zsw1dwyx5jmwfc84h"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-logict" ,ghc-logict)
@@ -4256,7 +4256,7 @@ simple general-purpose data structure\".")
 (define-public ghc-optparse-applicative
   (package
     (name "ghc-optparse-applicative")
-    (version "0.13.0.0")
+    (version "0.14.2.0")
     (source
      (origin
        (method url-fetch)
@@ -4265,15 +4265,8 @@ simple general-purpose data structure\".")
              "/optparse-applicative-" version ".tar.gz"))
        (sha256
         (base32
-         "1b0c5fdq8bd070g24vrjrwlq979r8dk8mys6aji9hy1l9pcv3inf"))))
+         "0c3z1mvynlyv1garjbdmdd3npm40dabgm75js4r07cf766c1wd71"))))
     (build-system haskell-build-system)
-    ;; These tests fail because the package doesn't come with all needed test
-    ;; files:
-    ;; - prop_drops_back_contexts
-    ;; - prop_context_carry
-    ;; - prop_help_on_empty
-    ;; - prop_help_on_empty_sub
-    (arguments `(#:tests? #f))
     (inputs
      `(("ghc-transformers-compat" ,ghc-transformers-compat)
        ("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint)))
@@ -5061,7 +5054,7 @@ occurrences of a substring (the first in case of overlaps) with another.")
 (define-public ghc-integer-logarithms
   (package
     (name "ghc-integer-logarithms")
-    (version "1.0.2")
+    (version "1.0.2.1")
     (source
      (origin
        (method url-fetch)
@@ -5070,16 +5063,16 @@ occurrences of a substring (the first in case of overlaps) with another.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0w5mhak181zi6qr5h2zbcs9ymaqacisp9jwk99naz6s8zz5rq1ii"))))
+         "1wj8kgjg5bn2yrs4zh9qfjv85cx6w998j9pi39yrbv305944mb9j"))))
     (build-system haskell-build-system)
-    (inputs
-     `(("ghc-tasty" ,ghc-tasty)
-       ("ghc-tasty-smallcheck" ,ghc-tasty-smallcheck)
-       ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)
+    (native-inputs
+     `(("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-smallcheck" ,ghc-smallcheck)
+       ("ghc-tasty" ,ghc-tasty)
        ("ghc-tasty-hunit" ,ghc-tasty-hunit)
-       ("ghc-quickcheck" ,ghc-quickcheck)
-       ("ghc-smallcheck" ,ghc-smallcheck)))
-    (home-page "https://github.com/phadej/integer-logarithms")
+       ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)
+       ("ghc-tasty-smallcheck" ,ghc-tasty-smallcheck)))
+    (home-page "https://github.com/Bodigrim/integer-logarithms")
     (synopsis "Integer logarithms")
     (description
      "This package provides the following modules:
@@ -5093,7 +5086,7 @@ in migrated modules.")
 (define-public ghc-scientific
   (package
     (name "ghc-scientific")
-    (version "0.3.5.2")
+    (version "0.3.6.2")
     (source
      (origin
        (method url-fetch)
@@ -5103,14 +5096,15 @@ in migrated modules.")
              ".tar.gz"))
        (sha256
         (base32
-         "0msnjz7ml0zycw9bssslxbg0nigziw7vs5km4q3vjbs8jpzpkr2w"))))
+         "03ql2f0ac8bsl524idy9xxa3kxisb2sj3avflzw580j5hzy0m397"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-integer-logarithms" ,ghc-integer-logarithms)
        ("ghc-text" ,ghc-text)
        ("ghc-hashable" ,ghc-hashable)
-       ("ghc-primitive" ,ghc-primitive)
-       ("ghc-tasty" ,ghc-tasty)
+       ("ghc-primitive" ,ghc-primitive)))
+    (native-inputs
+     `(("ghc-tasty" ,ghc-tasty)
        ("ghc-tasty-ant-xml" ,ghc-tasty-ant-xml)
        ("ghc-tasty-hunit" ,ghc-tasty-hunit)
        ("ghc-tasty-smallcheck" ,ghc-tasty-smallcheck)
diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm
index 3410880a67..87546045a6 100644
--- a/gnu/packages/image-viewers.scm
+++ b/gnu/packages/image-viewers.scm
@@ -74,12 +74,14 @@
      '(#:phases (modify-phases %standard-phases (delete 'configure))
        #:test-target "test"
        #:make-flags
-       (list "CC=gcc" (string-append "PREFIX=" (assoc-ref %outputs "out")))))
+       (list "CC=gcc" (string-append "PREFIX=" (assoc-ref %outputs "out"))
+             "exif=1")))
     (native-inputs
      `(("perl" ,perl)
        ("perl-test-command" ,perl-test-command)))
     (inputs `(("imlib2" ,imlib2)
               ("curl" ,curl)
+              ("libexif" ,libexif)
               ("libpng" ,libpng)
               ("libxt" ,libxt)
               ("libx11" ,libx11)
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index d70811bccf..c6010f1f56 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -18,7 +18,7 @@
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 8bb0162a47..696544c368 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -398,8 +398,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.18.4")
-(define %linux-libre-hash "1q3bndhwxwcrlyi0qcgxjsp5fl92wkfgk4y41qwrrywfv9xj3sl7")
+(define %linux-libre-version "4.18.5")
+(define %linux-libre-hash "1y52ns34vh9p4pfj08xsycv8p0xywm6dbpdi0wwpkll1xgpqikvf")
 
 (define %linux-libre-4.18-patches
   (list %boot-logo-patch
@@ -429,8 +429,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:patches %linux-libre-4.18-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.66")
-(define %linux-libre-4.14-hash "1sf18m6xjyg535yviz3yjbislf57s180y67z7mzbcl5pq9352bg9")
+(define %linux-libre-4.14-version "4.14.67")
+(define %linux-libre-4.14-hash "050zvdxjy6sc64q75pr1gxsmh49chwav2pwxz8xlif39bvahnrpg")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
@@ -439,14 +439,14 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.123"
-                    "1rljdp3vzhmdc6qha6b9dq0d1a3xz06rn51pb4ad3a2y61mph9sv"
+  (make-linux-libre "4.9.124"
+                    "0p78gx5jiqvaf2cadf5jp40lzgarrg0m0ybf9w2499v28vjsp30q"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.151"
-                    "0irzdq4p8a6dxyx5basgrc7af7w48hmyjwbk5hff8wn8jy71p9zm"
+  (make-linux-libre "4.4.152"
+                    "082aajyr363ca95pxlg9iascf5d7k2gbw9ggsbsa1hj6nhspsxw6"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index af2dcf8eaf..edffcfce96 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -16,7 +16,7 @@
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 nee <nee.git@hidamari.blue>
 ;;; Copyright © 2018 Stefan Reichör <stefan@xsteve.at>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 95cdd5c513..943bcecb86 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -25,7 +25,7 @@
 ;;; Copyright © 2018 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index a63fd9bb36..e09bbea5cc 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -19,7 +19,7 @@
 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
 ;;; Copyright © 2018 Thomas Sigurdsen <tonton@riseup.net>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
 ;;;
 ;;; This file is part of GNU Guix.
diff --git a/gnu/packages/patches/avogadro-boost148.patch b/gnu/packages/patches/avogadro-boost148.patch
new file mode 100644
index 0000000000..f244f14674
--- /dev/null
+++ b/gnu/packages/patches/avogadro-boost148.patch
@@ -0,0 +1,69 @@
+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
new file mode 100644
index 0000000000..a5f669292f
--- /dev/null
+++ b/gnu/packages/patches/avogadro-eigen3-update.patch
@@ -0,0 +1,603 @@
+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
new file mode 100644
index 0000000000..ac9f2e30af
--- /dev/null
+++ b/gnu/packages/patches/avogadro-python-eigen-lib.patch
@@ -0,0 +1,161 @@
+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/grub-check-error-efibootmgr.patch b/gnu/packages/patches/grub-check-error-efibootmgr.patch
new file mode 100644
index 0000000000..b2fd160c9a
--- /dev/null
+++ b/gnu/packages/patches/grub-check-error-efibootmgr.patch
@@ -0,0 +1,176 @@
+Without this patch, GRUB may proceed to wipe all firmware boot entries
+and report a successful installation, even if efibootmgr hit an error.
+
+Origin URL:
+https://git.sv.gnu.org/cgit/grub.git/commit/?id=6400613ad0b463abc93362086a491cd2a5e99b0d
+
+From 6400613ad0b463abc93362086a491cd2a5e99b0d Mon Sep 17 00:00:00 2001
+From: Steve McIntyre <steve@einval.com>
+Date: Wed, 31 Jan 2018 21:49:36 +0000
+Subject: Make grub-install check for errors from efibootmgr
+
+Code is currently ignoring errors from efibootmgr, giving users
+clearly bogus output like:
+
+        Setting up grub-efi-amd64 (2.02~beta3-4) ...
+        Installing for x86_64-efi platform.
+        Could not delete variable: No space left on device
+        Could not prepare Boot variable: No space left on device
+        Installation finished. No error reported.
+
+and then potentially unbootable systems. If efibootmgr fails, grub-install
+should know that and report it!
+
+We've been using similar patch in Debian now for some time, with no ill effects.
+
+diff --git a/grub-core/osdep/unix/platform.c b/grub-core/osdep/unix/platform.c
+index a3fcfca..ca448bc 100644
+--- a/grub-core/osdep/unix/platform.c
++++ b/grub-core/osdep/unix/platform.c
+@@ -78,19 +78,20 @@ get_ofpathname (const char *dev)
+ 		   dev);
+ }
+ 
+-static void
++static int
+ grub_install_remove_efi_entries_by_distributor (const char *efi_distributor)
+ {
+   int fd;
+   pid_t pid = grub_util_exec_pipe ((const char * []){ "efibootmgr", NULL }, &fd);
+   char *line = NULL;
+   size_t len = 0;
++  int rc;
+ 
+   if (!pid)
+     {
+       grub_util_warn (_("Unable to open stream from %s: %s"),
+ 		      "efibootmgr", strerror (errno));
+-      return;
++      return errno;
+     }
+ 
+   FILE *fp = fdopen (fd, "r");
+@@ -98,7 +99,7 @@ grub_install_remove_efi_entries_by_distributor (const char *efi_distributor)
+     {
+       grub_util_warn (_("Unable to open stream from %s: %s"),
+ 		      "efibootmgr", strerror (errno));
+-      return;
++      return errno;
+     }
+ 
+   line = xmalloc (80);
+@@ -119,23 +120,25 @@ grub_install_remove_efi_entries_by_distributor (const char *efi_distributor)
+       bootnum = line + sizeof ("Boot") - 1;
+       bootnum[4] = '\0';
+       if (!verbosity)
+-	grub_util_exec ((const char * []){ "efibootmgr", "-q",
++	rc = grub_util_exec ((const char * []){ "efibootmgr", "-q",
+ 	      "-b", bootnum,  "-B", NULL });
+       else
+-	grub_util_exec ((const char * []){ "efibootmgr",
++	rc = grub_util_exec ((const char * []){ "efibootmgr",
+ 	      "-b", bootnum, "-B", NULL });
+     }
+ 
+   free (line);
++  return rc;
+ }
+ 
+-void
++int
+ grub_install_register_efi (grub_device_t efidir_grub_dev,
+ 			   const char *efifile_path,
+ 			   const char *efi_distributor)
+ {
+   const char * efidir_disk;
+   int efidir_part;
++  int ret;
+   efidir_disk = grub_util_biosdisk_get_osdev (efidir_grub_dev->disk);
+   efidir_part = efidir_grub_dev->disk->partition ? efidir_grub_dev->disk->partition->number + 1 : 1;
+ 
+@@ -151,23 +154,26 @@ grub_install_register_efi (grub_device_t efidir_grub_dev,
+   grub_util_exec ((const char * []){ "modprobe", "-q", "efivars", NULL });
+ #endif
+   /* Delete old entries from the same distributor.  */
+-  grub_install_remove_efi_entries_by_distributor (efi_distributor);
++  ret = grub_install_remove_efi_entries_by_distributor (efi_distributor);
++  if (ret)
++    return ret;
+ 
+   char *efidir_part_str = xasprintf ("%d", efidir_part);
+ 
+   if (!verbosity)
+-    grub_util_exec ((const char * []){ "efibootmgr", "-q",
++    ret = grub_util_exec ((const char * []){ "efibootmgr", "-q",
+ 	  "-c", "-d", efidir_disk,
+ 	  "-p", efidir_part_str, "-w",
+ 	  "-L", efi_distributor, "-l", 
+ 	  efifile_path, NULL });
+   else
+-    grub_util_exec ((const char * []){ "efibootmgr",
++    ret = grub_util_exec ((const char * []){ "efibootmgr",
+ 	  "-c", "-d", efidir_disk,
+ 	  "-p", efidir_part_str, "-w",
+ 	  "-L", efi_distributor, "-l", 
+ 	  efifile_path, NULL });
+   free (efidir_part_str);
++  return ret;
+ }
+ 
+ void
+diff --git a/include/grub/util/install.h b/include/grub/util/install.h
+index 5910b0c..0dba8b6 100644
+--- a/include/grub/util/install.h
++++ b/include/grub/util/install.h
+@@ -210,7 +210,7 @@ grub_install_create_envblk_file (const char *name);
+ const char *
+ grub_install_get_default_x86_platform (void);
+ 
+-void
++int
+ grub_install_register_efi (grub_device_t efidir_grub_dev,
+ 			   const char *efifile_path,
+ 			   const char *efi_distributor);
+diff --git a/util/grub-install.c b/util/grub-install.c
+index 5e4cdfd..690f180 100644
+--- a/util/grub-install.c
++++ b/util/grub-install.c
+@@ -1848,9 +1848,13 @@ main (int argc, char *argv[])
+ 	  if (!removable && update_nvram)
+ 	    {
+ 	      /* Try to make this image bootable using the EFI Boot Manager, if available.  */
+-	      grub_install_register_efi (efidir_grub_dev,
+-					 "\\System\\Library\\CoreServices",
+-					 efi_distributor);
++	      int ret;
++	      ret = grub_install_register_efi (efidir_grub_dev,
++					       "\\System\\Library\\CoreServices",
++					       efi_distributor);
++	      if (ret)
++	        grub_util_error (_("efibootmgr failed to register the boot entry: %s"),
++				 strerror (ret));
+ 	    }
+ 
+ 	  grub_device_close (ins_dev);
+@@ -1871,6 +1875,7 @@ main (int argc, char *argv[])
+ 	{
+ 	  char * efifile_path;
+ 	  char * part;
++	  int ret;
+ 
+ 	  /* Try to make this image bootable using the EFI Boot Manager, if available.  */
+ 	  if (!efi_distributor || efi_distributor[0] == '\0')
+@@ -1887,8 +1892,11 @@ main (int argc, char *argv[])
+ 			  efidir_grub_dev->disk->name,
+ 			  (part ? ",": ""), (part ? : ""));
+ 	  grub_free (part);
+-	  grub_install_register_efi (efidir_grub_dev,
+-				     efifile_path, efi_distributor);
++	  ret = grub_install_register_efi (efidir_grub_dev,
++					   efifile_path, efi_distributor);
++	  if (ret)
++	    grub_util_error (_("efibootmgr failed to register the boot entry: %s"),
++			     strerror (ret));
+ 	}
+       break;
+ 
diff --git a/gnu/packages/patches/python-pygit2-disable-network-tests.patch b/gnu/packages/patches/python-pygit2-disable-network-tests.patch
deleted file mode 100644
index 5578e4c375..0000000000
--- a/gnu/packages/patches/python-pygit2-disable-network-tests.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-Disable tests trying to look up remote servers.
-
-diff --git a/test/test_credentials.py b/test/test_credentials.py
---- a/test/test_credentials.py
-+++ b/test/test_credentials.py
-@@ -68,6 +68,7 @@ class CredentialCreateTest(utils.NoRepoTestCase):
-         self.assertEqual((username, None, None, None), cred.credential_tuple)
- 
- 
-+@unittest.skipIf(True, "network tests are not supported in Guix")
- class CredentialCallback(utils.RepoTestCase):
-     def test_callback(self):
-         class MyCallbacks(pygit2.RemoteCallbacks):
-@@ -92,6 +93,7 @@ class CredentialCallback(utils.RepoTestCase):
-         remote = self.repo.create_remote("github", url)
-         self.assertRaises(TypeError, lambda: remote.fetch(callbacks=MyCallbacks()))
- 
-+@unittest.skipIf(True, "network tests are not supported in Guix")
- class CallableCredentialTest(utils.RepoTestCase):
- 
-     def test_user_pass(self):
-diff --git a/test/test_repository.py b/test/test_repository.py
---- a/test/test_repository.py
-+++ b/test/test_repository.py
-@@ -573,6 +573,7 @@ class CloneRepositoryTest(utils.NoRepoTestCase):
-         self.assertTrue('refs/remotes/custom_remote/master' in repo.listall_references())
-         self.assertIsNotNone(repo.remotes["custom_remote"])
- 
-+    @unittest.skipIf(True, "network tests are not supported in Guix")
-     def test_clone_with_credentials(self):
-         repo = clone_repository(
-             "https://bitbucket.org/libgit2/testgitrepository.git",
-diff --git a/test/test_submodule.py b/test/test_submodule.py
---- a/test/test_submodule.py
-+++ b/test/test_submodule.py
-@@ -42,6 +42,7 @@ SUBM_PATH = 'submodule'
- SUBM_URL = 'https://github.com/libgit2/pygit2'
- SUBM_HEAD_SHA = '819cbff552e46ac4b8d10925cc422a30aa04e78e'
- 
-+@unittest.skipIf(True, "network tests are not supported in Guix")
- class SubmoduleTest(utils.SubmoduleRepoTestCase):
- 
-     def test_lookup_submodule(self):
diff --git a/gnu/packages/perl-check.scm b/gnu/packages/perl-check.scm
index a2900c34c0..16010b441f 100644
--- a/gnu/packages/perl-check.scm
+++ b/gnu/packages/perl-check.scm
@@ -12,7 +12,7 @@
 ;;; Copyright © 2017 Petter <petter@mykolab.ch>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 8bdd221a53..47d5d8bbb2 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -19,7 +19,7 @@
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm
index 5b5ec89fc2..3fd3d0854b 100644
--- a/gnu/packages/photo.scm
+++ b/gnu/packages/photo.scm
@@ -109,7 +109,7 @@ cameras (CRW/CR2, NEF, RAF, DNG, and others).")
                (base32
                 "06nlsibr3ylfwp28w8f5466l6drgrnydgxrm4jmxzrmk5svaxk8n"))))
     (build-system gnu-build-system)
-    (home-page "http://libexif.sourceforge.net/")
+    (home-page "https://libexif.github.io/")
     (synopsis "Read and manipulate EXIF data in digital photographs")
     (description
      "The libexif C library allows applications to read, edit, and save EXIF
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 15f6d33121..dd33ba8e0c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3172,16 +3172,14 @@ association studies (GWAS) on extremely large data sets.")
 (define-public python-pygit2
   (package
     (name "python-pygit2")
-    (version "0.26.0")
+    (version "0.26.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pygit2" version))
        (sha256
         (base32
-         "1cbc488ra3kg7r3qky17ms0szi3cda2d96qfkv1l9djsy9hnvw57"))
-       (patches
-        (search-patches "python-pygit2-disable-network-tests.patch"))))
+         "145k3fsd21274swia7mcc7n3kzlbd47xmg55mxsjdb5d9b7fr858"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-six" ,python-six)
diff --git a/gnu/packages/slang.scm b/gnu/packages/slang.scm
index f9956d0113..24eb5fa137 100644
--- a/gnu/packages/slang.scm
+++ b/gnu/packages/slang.scm
@@ -37,14 +37,14 @@
 (define-public slang
   (package
     (name "slang")
-    (version "2.3.1a")
+    (version "2.3.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://www.jedsoft.org/releases/slang/slang-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "0dlcy0hn0j6cj9qj5x6hpb0axifnvzzmv5jqq0wq14fygw0c7w2l"))
+                "06p379fqn6w38rdpqi98irxi2bf4llb0rja3dlgkqz7nqh7kp7pw"))
               (modules '((guix build utils)))
               (snippet
                '(begin
diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 355683df8a..ce34423713 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -14,7 +14,7 @@
 ;;; Copyright © 2017 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 01e41b1914..6825cd7d2d 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -24,7 +24,7 @@
 ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2018 Brendan Tildesley <brendan.tildesley@openmailbox.org>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index ffd9e252e8..2e64ce35ad 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -23,7 +23,7 @@
 ;;; Copyright © 2017 Mike Gerwitz <mtg@gnu.org>
 ;;; Copyright © 2018 Thomas Sigurdsen <tonton@riseup.net>
 ;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;