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17405 Commits

Author SHA1 Message Date
Roel Janssen 4644644ace
gnu: Add r-bioccheck. 
* gnu/packages/bioinformatics.scm (r-bioccheck): New variable.
 2016-10-20 09:53:02 +02:00
Leo Famulari c645cef7da
gnu: openssh: Fix CVE-2016-8858. 
* gnu/packages/patches/openssh-memory-exhaustion.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/ssh.scm (openssh)[source]: Use it.
 2016-10-19 18:02:39 -04:00
Rene Saavedra 3ad7dce1d9
gnu: Add gucharmap. 
* gnu/packages/gnome.scm (gucharmap): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-10-19 23:20:19 +02:00
Carlos Sánchez de La Lama 80c9164fd7
gnu: %static-inputs: Use bash from PATH in bootstrap tar. 
gnu/packages/make-bootstrap.scm (%static-inputs): Use bash from PATH.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-10-19 23:20:19 +02:00
Leo Famulari c21b1a1fbb
gnu: borg: Install more documentation. 
* gnu/packages/backup.scm (borg)[arguments]: Install more documentation in
'install-doc' phase. Use (srfi srfi-26).
 2016-10-19 16:00:26 -04:00
Leo Famulari 7ffa5d4a2d
gnu: python-file: Work around "double encoding" bug in file@5.28. 
* gnu/packages/patches/python-file-double-encoding-bug.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/python.scm (python-file)[source]: Use it.
(python2-file)[source]: Use the source of FILE directly, without the
patch.
 2016-10-19 14:36:51 -04:00
Leo Famulari 00bf74be05
gnu: python-file: Don't create a compressed egg. 
* gnu/packages/python.scm (python-file, python2-file)[arguments]: Pass
"--single-version-externally-managed" "--root=/" to #:configure-flags.
 2016-10-19 14:36:48 -04:00
Tobias Geerinckx-Rice b332c823b7
gnu: gparted: Update to 0.27.0. 
* gnu/packages/disk.scm (gparted): Update to 0.27.0.
 2016-10-19 19:34:17 +02:00
Tobias Geerinckx-Rice f5d3773268
gnu: ncftp: Use ‘modify-phases’. 
* gnu/packages/ftp.scm (ncftp): Use the ‘modify-phases’ syntax.
 2016-10-19 19:34:17 +02:00
Tobias Geerinckx-Rice c17b5986f2
gnu: mcelog: Update to 143. 
* gnu/packages/linux.scm (mcelog): Update to 143.
 2016-10-19 19:34:17 +02:00
Tobias Geerinckx-Rice 5e270e8e8f
gnu: lftp: Update to 4.7.3. 
* gnu/packages/ftp.scm (lftp): Update to 4.7.3.
[source]: Use HTTPS. Remove patch.
[arguments]: Add ‘disable-impure-tests’ phase. Add #:configure-flags with
explicit location of readline headers.
[home-page]: Use HTTPS.
* gnu/packages/patches/lftp-dont-save-unknown-host-fingerprint.patch: Delete
file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2016-10-19 19:34:17 +02:00
Leo Famulari d5ccf71ec6
gnu: awscli: Update to 1.11.5. 
* gnu/packages/python.scm (awscli): Update to 1.11.5.
[source]: Use pypi-uri.
[inputs]: Add python-s3transfer.
 2016-10-19 13:12:48 -04:00
Leo Famulari 94cffc6386
gnu: Add python-s3transfer. 
* gnu/packages/python.scm (python-s3transfer, python2-s3transfer): New
variable.
 2016-10-19 13:12:48 -04:00
Leo Famulari e09f952d9f
gnu: python-botocore: Update to 1.4.62. 
* gnu/packages/python.scm (python-botocore, python2-botocore): Update to 1.4.62.
 2016-10-19 13:12:47 -04:00
Leo Famulari ecd68c53a6
gnu: python-rsa: Update to 3.4.2. 
* gnu/packages/python.scm (python-rsa, python2-rsa): Update to 3.4.2.
 2016-10-19 13:12:47 -04:00
Leo Famulari def6213f65
gnu: Add libseccomp. 
* gnu/packages/linux.scm (libseccomp): New variable.
 2016-10-19 13:01:31 -04:00
Marius Bakke 6de9dfce80
gnu: xapian: Update to 1.4.0. 
* gnu/packages/search.scm (xapian): Update to 1.4.0.
[source]: Use https URL.
[home-page]: Use https URL.
[arguments]: Remove 'patch-remotetcp-harness' phase. Replace 'check'
phase with a list of custom test targets.
 2016-10-19 17:00:51 +01:00
Marius Bakke 16a23d4ad2
gnu: xapian: Use 'modify-phases' syntax. 
* gnu/packages/search.scm (xapian)[arguments]: Use 'modify-phases'. Fix
'/bin/sh' substitution to use (which "sh") instead of (which "bash").
 2016-10-19 17:00:43 +01:00
Marius Bakke 6cf27c89a5
gnu: notmuch: Enable tests. 
* gnu/packages/patches/notmuch-emacs-25-compatibility-fix.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/mail.scm (notmuch)[source]: Use patch.
[arguments]: Add verbose make flags. Add phase 'patch-notmuch-lib.el' to
fix hard-coded /bin/sh. Add 'prepare-test-environment' phase to patch
test shebangs and set environment.
[native-inputs]: Change from 'emacs-minimal' to 'emacs-no-x'. Add dtach,
gnupg, man, perl and which.
 2016-10-19 17:00:37 +01:00
Marius Bakke 540d6cc711
gnu: notmuch: Update to 0.23. 
* gnu/packages/mail.scm (notmuch): Update to 0.23.
[home-page]: Use https URL.
(python-notmuch)[version]: Inherit from notmuch.
[home-page]: Ditto.
 2016-10-19 17:00:24 +01:00
Mark H Weaver b09e0cd154
gnu: chez-scheme: Remove use of 'ghostscript-gs' wrapper. 
This is a followup to commit d2478b4cdd.

* gnu/packages/chez.scm (chez-scheme)[native-inputs]: Replace
'ghostscript-gs' with 'ghostscript'.
 2016-10-19 11:26:51 -04:00
Mark H Weaver d2478b4cdd
Merge branch 'master' into core-updates 2016-10-19 10:54:36 -04:00
ng0 152ffe7cb6
gnu: Add opensmtpd-extras. 
* gnu/packages/mail.scm (opensmtpd-extras): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-10-19 17:37:16 +03:00
ng0 8b53366c63
gnu: Add opensmtpd. 
* gnu/packages/mail.scm (opensmtpd): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-10-19 17:32:49 +03:00
ng0 71f048c624
gnu: Add libasr. 
* gnu/packages/dns.scm (libasr): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-10-19 17:28:06 +03:00
Efraim Flashner c11933c920
gnu: zile: Use 'modify-phases' syntax. 
* gnu/packages/zile.scm (zile)[arguments]: Use 'modify-phases' syntax.
 2016-10-19 17:10:17 +03:00
Efraim Flashner fa216a4d01
gnu: zile: Update to 2.4.13. 
* gnu/packages/zile.scm (zile): Update to 2.4.13.
[home-page]: Use https.
 2016-10-19 17:10:17 +03:00
Ludovic Courtès fe9bdb581e
tests: Make sure child process of 'pivot-root' test exits. 
* tests/syscalls.scm ("pivot-root"): Use 'test-equal'.  Wrap child body
in 'dynamic-wind'.
 2016-10-19 15:54:11 +02:00
Ludovic Courtès 0d7034ca4f
tests: Fix typo in 'with-graft' transformation test. 
This is a followup to 645b9df858.

* tests/scripts-build.scm ("options->transformation, with-graft"): Use
'with-graft', not 'with-input'.
 2016-10-19 15:54:10 +02:00
Ludovic Courtès 2535635f18
Use (ice-9 binary-ports) instead of (rnrs io ports). 
This reduces the closure of (guix ui) from 123 to 106 modules.

* guix/derivations.scm: Use (ice-9 binary-ports) instead of (rnrs io
ports).
(map-derivation)[substitute-file]: Use 'read-string' instead of
'get-string-all'.
* guix/ftp-client.scm: Likewise.
* guix/hash.scm: Likewise.
* guix/http-client.scm: Likewise.
* guix/pki.scm (ensure-acl, current-acl): Likewise.
* guix/scripts/archive.scm (authorize-key)[read-key]: Likewise.
* guix/scripts/authenticate.scm (read-canonical-sexp)
(read-hash-data): Likewise.
* guix/scripts/download.scm: Likewise.
* guix/scripts/offload.scm (register-gc-root, remove-gc-roots)
(send-files): Likewise.
* guix/scripts/publish.scm (lazy-read-file-sexp): Likewise.
* guix/scripts/refresh.scm: Likewise.
* guix/scripts/substitute.scm (check-acl-initialized): Likewise.
* guix/serialization.scm (read-maybe-utf8-string): Likewise.
* guix/scripts/hash.scm (guix-hash): Use 'force-output' instead of
'flush-output-port'.
* guix/store.scm (process-stderr): Likewise.
* guix/tests.scm: Likewise.
* guix/utils.scm: Use (ice-9 binary-ports) and autoload (rnrs io ports)
for 'make-custom-binary-input-port'.
 2016-10-19 15:54:10 +02:00
Ludovic Courtès 4bb54cc42f
lint: Suggest @code instead of quotes. 
* guix/scripts/lint.scm (%quoted-identifier-rx): New variable.
(check-description-style)[check-quotes]: New procedure.
Use it.
* tests/lint.scm ("description: suggest ornament instead of quotes"):
New test.
 2016-10-19 15:54:10 +02:00
Ludovic Courtès 4534d85e70
gnu: Add Ao. 
* gnu/packages/engineering.scm (ao): New variable.
 2016-10-19 15:54:10 +02:00
Ludovic Courtès a966281f2d
gnu: glfw: Propagate the relevant inputs. 
* gnu/packages/gl.scm (glfw)[inputs]: Rename to...
[propagated-inputs]: ... this.  Add LIBXXF86VM.
 2016-10-19 15:54:10 +02:00
Ludovic Courtès 7fee5b5397
container: Allow 'container-excursion' to the same namespaces. 
Before that, 'container-excursion' would call 'setns' even when the
target namespace is the one the caller is already in, which would fail.

* gnu/build/linux-container.scm (container-excursion): Introduce
'source' and 'target'.  Compare the result of 'readlink' on these
instead of comparing file descriptors to decide whether to call
'setns'.
* tests/containers.scm ("container-excursion, same namespace"): New test.
 2016-10-19 15:54:10 +02:00
Roel Janssen 99df12cd19
gnu: Add r-biocstyle. 
* gnu/packages/bioinformatics.scm (r-biocstyle): New variable.
 2016-10-19 15:22:06 +02:00
Roel Janssen 207ce8fbe5
gnu: Add r-biocviews. 
* gnu/packages/bioinformatics.scm (r-biocviews): New variable.
 2016-10-19 15:09:55 +02:00
Benz Schenk b747718e23
gnu: Add iperf. 
* gnu/packages/networking.scm (iperf): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2016-10-19 13:19:07 +01:00
Hartmut Goebel b5a5fb1927
gnu: python-dateutil, python-dateutil-2: Update to new home-page. 
* gnu/packages/python.scm (python-dateutil, python2-dateutil,
  python-dateutil-2, python2-dateutil-2)[home-page]: Update URL.
 2016-10-19 11:52:54 +02:00
Roel Janssen c79ad57a8d
gnu: Add r-optparse. 
* gnu/packages/bioinformatics.scm (r-optparse): New variable.
 2016-10-19 10:48:56 +02:00
Roel Janssen 2acaaee550
gnu: Add r-getopt. 
* gnu/packages/bioinformatics.scm (r-getopt): New variable.
 2016-10-19 09:55:45 +02:00
Federico Beffa 7d95c0006a
gnu: Add GHC 8.0.1. 
* gnu/packages/haskell.scm (ghc-8): New variable.
 2016-10-19 08:44:11 +02:00
Federico Beffa 1bd00f1737
gnu: Add ghc-hashtables. 
* gnu/packages/haskell.scm (ghc-hashtables): New variable.
 2016-10-19 08:44:11 +02:00
Federico Beffa db61a00971
gnu: Add ghc-easyplot. 
* gnu/packages/haskell.scm (ghc-easyplot): New variable.
 2016-10-19 08:44:11 +02:00
Federico Beffa 4225c7116d
gnu: Add ghc-hmatrix-gsl-stats. 
* gnu/packages/haskell.scm (ghc-hmatrix-gsl-stats): New variable.
 2016-10-19 08:44:11 +02:00
Federico Beffa 271a5365aa
gnu: Add ghc-hmatrix-special. 
* gnu/packages/haskell.scm (ghc-hmatrix-special): New variable.
 2016-10-19 08:44:11 +02:00
Federico Beffa 932104abce
gnu: Add ghc-hmatrix-gsl. 
* gnu/packages/haskell.scm (ghc-hmatrix-gsl): New variable.
 2016-10-19 08:44:11 +02:00
Federico Beffa 95595618b1
gnu: Add ghc-hmatrix. 
* gnu/packages/haskell.scm (ghc-hmatrix): New variable.
 2016-10-19 08:44:11 +02:00
Federico Beffa 725dddd7fb
gnu: Add ghc-storable-complex. 
* gnu/packages/haskell.scm (ghc-storable-complex): New variable.
 2016-10-19 08:44:11 +02:00
Federico Beffa fb6d2d75f3
gnu: Add chez-fmt. 
* gnu/packages/chez.scm (chez-fmt): New variable.
 2016-10-19 08:44:11 +02:00
Federico Beffa 87d6c9ef8a
gnu: Add chez-irregex. 
* gnu/packages/chez.scm (chez-irregex): New variable.
 2016-10-19 08:44:11 +02:00