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01/01: Merge branch 'master' into core-updates
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From: |
Marius Bakke |
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Subject: |
01/01: Merge branch 'master' into core-updates |
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Date: |
Tue, 1 Aug 2017 17:46:43 -0400 (EDT) |
mbakke pushed a commit to branch core-updates
in repository guix.
commit aa9780daf92131dc9ee19868f9621fd2be56ab78
Merge: 6484e82 fc8f063
Author: Marius Bakke <address@hidden>
Date: Tue Aug 1 23:42:28 2017 +0200
Merge branch 'master' into core-updates
doc/guix.texi | 171 ++++++++++++++-
gnu/bootloader.scm | 3 +
gnu/bootloader/extlinux.scm | 19 +-
gnu/bootloader/grub.scm | 27 ++-
gnu/local.mk | 8 +-
gnu/packages/autotools.scm | 19 +-
gnu/packages/aux-files/emacs/guix-emacs.el | 9 +-
gnu/packages/bioinformatics.scm | 6 +-
gnu/packages/bootloaders.scm | 16 +-
gnu/packages/certs.scm | 19 +-
gnu/packages/databases.scm | 27 ++-
gnu/packages/disk.scm | 10 +-
gnu/packages/dns.scm | 4 +-
gnu/packages/emacs.scm | 147 ++++++++-----
gnu/packages/enlightenment.scm | 13 +-
gnu/packages/erlang.scm | 11 +-
gnu/packages/fpga.scm | 5 +-
gnu/packages/games.scm | 132 +++++++++++-
gnu/packages/gnome.scm | 14 +-
gnu/packages/gnunet.scm | 18 +-
gnu/packages/gnupg.scm | 4 +-
gnu/packages/gstreamer.scm | 14 +-
gnu/packages/guile.scm | 157 +++++++++-----
gnu/packages/linux.scm | 18 +-
gnu/packages/maths.scm | 35 +++
gnu/packages/mes.scm | 26 +--
gnu/packages/networking.scm | 28 ++-
gnu/packages/ocaml.scm | 238 +++++++++++++++++++++
gnu/packages/package-management.scm | 33 ++-
gnu/packages/patches/erlang-man-path.patch | 24 +++
.../patches/guile-ssh-channel-finalization.patch | 28 ---
gnu/packages/patches/guile-ssh-double-free.patch | 37 ----
gnu/packages/patches/guile-ssh-rexec-bug.patch | 16 --
gnu/packages/patches/libgit2-use-after-free.patch | 24 ---
.../patches/python-pbr-fix-man-page-support.patch | 28 ---
gnu/packages/python.scm | 5 +-
gnu/packages/regex.scm | 4 +-
gnu/packages/ruby.scm | 68 +++---
gnu/packages/ssh.scm | 16 +-
gnu/packages/sssd.scm | 7 +-
gnu/packages/statistics.scm | 22 +-
gnu/packages/tor.scm | 5 +-
gnu/packages/version-control.scm | 17 +-
gnu/packages/video.scm | 4 +-
gnu/packages/vim.scm | 31 +--
gnu/packages/virtualization.scm | 2 +-
gnu/packages/web.scm | 10 +-
gnu/packages/xdisorg.scm | 19 +-
gnu/packages/xorg.scm | 8 +-
gnu/services/admin.scm | 151 ++++++++++++-
gnu/services/cuirass.scm | 7 +
gnu/services/databases.scm | 73 +++++++
gnu/services/networking.scm | 11 +-
gnu/services/ssh.scm | 96 +++++++--
gnu/system.scm | 29 ++-
gnu/tests/admin.scm | 128 +++++++++++
gnu/tests/databases.scm | 121 +++++++++++
guix/git-download.scm | 7 +-
guix/graph.scm | 16 +-
guix/scripts/lint.scm | 41 ++--
guix/scripts/package.scm | 5 +
guix/scripts/substitute.scm | 2 +-
guix/scripts/system.scm | 13 +-
guix/ui.scm | 21 --
guix/utils.scm | 32 ++-
65 files changed, 1744 insertions(+), 615 deletions(-)
diff --cc gnu/local.mk
index 63894e8,db8be36..37ee7f7
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@@ -576,8 -580,11 +578,9 @@@ dist_patch_DATA =
%D%/packages/patches/emacs-fix-scheme-indent-function.patch \
%D%/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch \
%D%/packages/patches/emacs-source-date-epoch.patch \
+ %D%/packages/patches/erlang-man-path.patch \
%D%/packages/patches/eudev-rules-directory.patch \
- %D%/packages/patches/eudev-conflicting-declaration.patch \
%D%/packages/patches/evilwm-lost-focus-bug.patch \
- %D%/packages/patches/expat-CVE-2016-0718-fix-regression.patch \
%D%/packages/patches/exim-CVE-2017-1000369.patch \
%D%/packages/patches/fabric-tests.patch \
%D%/packages/patches/fastcap-mulGlobal.patch \
@@@ -750,8 -753,6 +750,7 @@@
%D%/packages/patches/libgit2-0.25.1-mtime-0.patch \
%D%/packages/patches/libgdata-fix-tests.patch \
%D%/packages/patches/libgdata-glib-duplicate-tests.patch \
- %D%/packages/patches/libgit2-use-after-free.patch \
+ %D%/packages/patches/libffi-3.2.1-complex-alpha.patch \
%D%/packages/patches/libjxr-fix-function-signature.patch \
%D%/packages/patches/libjxr-fix-typos.patch \
%D%/packages/patches/liboop-mips64-deplibs-fix.patch \
diff --cc gnu/packages/bioinformatics.scm
index 60beed8,909044f..6bbbe33
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@@ -3478,10 -3478,9 +3478,10 @@@ form of assemblies or reads."
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0ll00l81aflscgggs5nfhj12cbvdiz3gg7f7n5f537a3xhx60vn9"))
+ "0rws9r1ziv6way8cf49jg8bzj7x2131kfqkhj8byf0z5hnrq3bwv"))
(patches (search-patches "metabat-remove-compilation-date.patch"
- "metabat-fix-compilation.patch"))))
+ "metabat-fix-compilation.patch"
+ "metabat-fix-boost-issue.patch"))))
(build-system gnu-build-system)
(arguments
`(#:phases
diff --cc gnu/packages/package-management.scm
index b2e4a6a,5c0e5a9..506d1f9
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@@ -250,9 -261,10 +261,10 @@@
(base32
"1giy2aprjmn5fp9c4s9r125fljw4wv6ixy5739i5bffw4jgr0f9r"))))))
(propagated-inputs
- `(("gnutls" ,gnutls/guile-2.2) ;for 'guix download' & co.
+ `(("gnutls" ,gnutls)
("guile-json" ,guile-json)
- ("guile-ssh" ,guile-ssh)))
+ ("guile-ssh" ,guile-ssh)
+ ("guile-git" ,guile-git)))
(home-page "https://www.gnu.org/software/guix/";)
(synopsis "Functional package manager for installed software packages
and versions")
@@@ -276,9 -288,10 +288,10 @@@ the Nix package manager."
`(("guile" ,guile-2.0)
,@(alist-delete "guile" (package-inputs guix))))
(propagated-inputs
- `(("gnutls" ,gnutls)
+ `(("gnutls" ,gnutls/guile-2.0)
("guile-json" ,guile2.0-json)
- ("guile-ssh" ,guile2.0-ssh)))))
+ ("guile-ssh" ,guile2.0-ssh)
+ ("guile-git" ,guile2.0-git)))))
(define (source-file? file stat)
"Return true if FILE is likely a source file, false if it is a typical