Make repo compile against a recent guix

8 files changed, 11 insertions, 3 deletions

diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm
index 1e2c86e..a609905 100644
--- a/gn/packages/bnw.scm
+++ b/gn/packages/bnw.scm
@@ -8,6 +8,7 @@
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages statistics)
   #:use-module (gn packages javascript)
   #:use-module (gn packages web))
diff --git a/gn/packages/cran.scm b/gn/packages/cran.scm
index 6a2a4ea..f93aa77 100644
--- a/gn/packages/cran.scm
+++ b/gn/packages/cran.scm
@@ -4,6 +4,7 @@
   #:use-module (guix download)
   #:use-module (guix build-system r)
   #:use-module (gnu packages)
+  #:use-module (gnu packages cran)
   #:use-module (gnu packages statistics))
 
 (define-public r-tictoc
diff --git a/gn/packages/edash.scm b/gn/packages/edash.scm
index ac88e22..eda4da3 100644
--- a/gn/packages/edash.scm
+++ b/gn/packages/edash.scm
@@ -271,7 +271,7 @@ necessary.")
        ("python-pyyaml" ,python-pyyaml)
        ("python-pytest-cov" ,python-pytest-cov)
        ("python-jsonschema" ,python-jsonschema)
-       ("python-pytest-pep8" ,python-pytest-pep8)
+       ;; ("python-pytest-pep8" ,python-pytest-pep8) no longer upstream
        ("python-pytest-cache" ,python-pytest-cache)
 ;;       ("python-pytest-flakes" ,python-pytest-flakes)
        ))
@@ -303,7 +303,7 @@ with the Specification.")
        ("python-pyflakes" ,python-pyflakes)
        ("python-flake8" ,python-flake8)
        ("python-pytest-cov" ,python-pytest-cov)
-       ("python-pytest-pep8" ,python-pytest-pep8)
+       ;; ("python-pytest-pep8" ,python-pytest-pep8) no longer upstream
        ("python-pytest-cache" ,python-pytest-cache)
 ;;       ("python-pytest-flakes" ,python-pytest-flakes)
        ))
diff --git a/gn/packages/emacs-xyz.scm b/gn/packages/emacs-xyz.scm
index 6d1e525..2543ea2 100644
--- a/gn/packages/emacs-xyz.scm
+++ b/gn/packages/emacs-xyz.scm
@@ -8,6 +8,7 @@
   #:use-module (guix build emacs-utils)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages)
+  #:use-module (gnu packages emacs-build)
   #:use-module (gnu packages emacs-xyz)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages rust-apps)
diff --git a/gn/packages/jupyterhub.scm b/gn/packages/jupyterhub.scm
index 322999b..6828329 100644
--- a/gn/packages/jupyterhub.scm
+++ b/gn/packages/jupyterhub.scm
@@ -7,6 +7,7 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages docker)
+  #:use-module (gnu packages jupyter)
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages monitoring)
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 7cb5d77..38a2290 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -3,11 +3,13 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages cran)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages jupyter)
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages maths)
diff --git a/gn/packages/ruby.scm b/gn/packages/ruby.scm
index befb550..6870d60 100644
--- a/gn/packages/ruby.scm
+++ b/gn/packages/ruby.scm
@@ -30,6 +30,8 @@
   #:use-module (gnu packages ragel)
   #:use-module (gnu packages rails)
   #:use-module (gnu packages ruby)
+  #:use-module (gnu packages ruby-check)
+  #:use-module (gnu packages ruby-xyz)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages version-control)
   #:use-module (guix packages)
diff --git a/gn/packages/sambamba.scm b/gn/packages/sambamba.scm
index dd8fbfa..e5623d4 100644
--- a/gn/packages/sambamba.scm
+++ b/gn/packages/sambamba.scm
@@ -89,7 +89,7 @@ data.  It also provides the @command{bgzip}, @command{htsfile}, and
        ))
       (native-inputs
        `(("ldc" ,ldc)
-         ("shunit2-old" ,shunit2-old)
+         ;; ("shunit2-old" ,shunit2-old) disable for a bit
          ("coreutils" ,coreutils) ; for env
          ("perl" ,perl) ; Needed for building htslib
          ("ruby" ,ruby) ; Needed for building htslib