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35155 Commits

Author SHA1 Message Date
Arun Isaac 94282358fd
gnu: m17n-db: Update to 1.8.0. 
* gnu/packages/emacs.scm (m17n-db): Update to 1.8.0.
 2018-09-24 17:46:18 +05:30
Ricardo Wurmus e72702475d
gnu: Add r-bseqsc. 
* gnu/packages/bioinformatics.scm (r-bseqsc): New variable.
 2018-09-24 13:31:20 +02:00
Ricardo Wurmus 28829c040f
gnu: Add r-cssam. 
* gnu/packages/bioinformatics.scm (r-cssam): New variable.
 2018-09-24 13:31:20 +02:00
Ricardo Wurmus a434730f2e
gnu: Add r-xbioc. 
* gnu/packages/bioinformatics.scm (r-xbioc): New variable.
 2018-09-24 13:31:20 +02:00
Pierre Neidhardt 5c8031ff73
gnu: Prefix all Emacs packages with "emacs-". 
* gnu/packages/emacs.scm: Prefix all Emacs packages with "emacs-".
This is to enforce consistency and so that `emacs-packages?' can reliably
detect Emacs packages based on the "emacs-" prefix.
 2018-09-24 12:56:04 +02:00
Tobias Geerinckx-Rice cd8aa06093
gnu: python-networkx: Use HTTPS home page. 
* gnu/packages/python.scm (python-networkx)[home-page]: Use HTTPS.
 2018-09-24 00:34:03 +02:00
Tobias Geerinckx-Rice dd29bd4ebc
gnu: python-networkx: Update to 2.2. 
* gnu/packages/python.scm (python-networkx): Update to 2.2.
 2018-09-24 00:34:02 +02:00
Tobias Geerinckx-Rice 68cbec027e
gnu: python-decorator: Update to 4.3.0. 
* gnu/packages/python.scm (python-decorator): Update to 4.3.0.
[arguments]: Run the test suite.
 2018-09-24 00:34:02 +02:00
Tobias Geerinckx-Rice 3715e79ec8
gnu: python-marshmallow: Update to 3.0.0b14. 
* gnu/packages/python.scm (python-marshmallow): Update to 3.0.0b14.
 2018-09-24 00:34:01 +02:00
Tobias Geerinckx-Rice a42b68480b
gnu: libiptcdata: Update to 1.0.5. 
* gnu/packages/image.scm (libiptcdata): Update to 1.0.5.
[home-page]: Follow Debian's maintained upstream.
 2018-09-24 00:34:01 +02:00
Tobias Geerinckx-Rice c30fd002c8
gnu: virtualgl: Update to 2.6. 
* gnu/packages/gl.scm (virtualgl): Update to 2.6.
[inputs]: Add libxtst.
 2018-09-24 00:34:01 +02:00
Tobias Geerinckx-Rice 2c36baa56f
gnu: parallel: Update to 20180922. 
* gnu/packages/parallel.scm (parallel): Update to 20180922.
 2018-09-24 00:34:00 +02:00
Tobias Geerinckx-Rice 2f7ad2a788
gnu: workrave: Use Guix's built-in bootstrap phase. 
* gnu/packages/gnome.scm (workrave)[arguments]: Remove
'autoconf' phase.
 2018-09-24 00:34:00 +02:00
Tobias Geerinckx-Rice 899e1974a6
gnu: python-gitdb: Update to 2.0.4. 
* gnu/packages/version-control.scm (python-gitdb): Update to 2.0.4.
[arguments]: Replace AND with equivalent but more 'accurate' BEGIN.
 2018-09-24 00:34:00 +02:00
Tobias Geerinckx-Rice 0604d3cfce
gnu: nano: Update to 3.1. 
* gnu/packages/nano.scm (nano): Update to 3.1.
 2018-09-24 00:33:59 +02:00
Tobias Geerinckx-Rice 25706b8fc9
gnu: fping: Use HTTPS home page. 
* gnu/packages/networking.scm (fping)[home-page]: Use HTTPS.
 2018-09-24 00:33:59 +02:00
Tobias Geerinckx-Rice 8fa361ce63
gnu: fping: Update to 4.1. 
* gnu/packages/networking.scm (fping): Update to 4.1.
 2018-09-24 00:33:59 +02:00
Ludovic Courtès fce2254711
vm: Use "cache=loose" for all 9p mounts. 
This significantly improves read throughput when running things like
"guix hash -r ...".

* gnu/system/vm.scm (%linux-vm-file-systems): Add 'flags' for "store".
Add "cache=loose" to every file system.
 2018-09-23 23:34:17 +02:00
Ludovic Courtès b5460d95e9
vm: Disable deduplication for 'guix system vm-image'. 
* gnu/system/vm.scm (qemu-image): Pass #:deduplicate? #f to
'root-partition-initializer'.
 2018-09-23 23:34:17 +02:00
Ludovic Courtès bb3b6ccb05
database: Register each store item only once. 
Fixes <https://bugs.gnu.org/32600>.
Reported by Leo Famulari.

* guix/store/database.scm (register-items): Check whether TO-REGISTER is
in DB by calling 'path-id',  and skip the reset-timestamps,
registration, and deduplication phases when it is.
 2018-09-23 23:34:17 +02:00
Ludovic Courtès f0addd6461
database: 'register-items' shows a progress bar. 
* guix/store/database.scm (register-items): Add #:log-port.  Use
'progress-reporter/bar' to show a progress report.
(register-path): Pass #:log-port to 'register-items'.
 2018-09-23 23:34:16 +02:00
Ludovic Courtès a387b0bebb
store-copy: Display a progress bar when copying store items. 
* guix/build/store-copy.scm (populate-store): Add #:log-port parameter.
Use 'progress-reporter/bar' to report progress.
 2018-09-23 23:34:16 +02:00
Ludovic Courtès c122a2e509
serialization: Remove redundancy in 'write-file'. 
* guix/serialization.scm (write-file): Remove redundant 'member' call.
 2018-09-23 23:34:16 +02:00
Ludovic Courtès 88600acc93
system: Mention '--skip-checks' in initrd diagnostics. 
* gnu/system/mapped-devices.scm (check-device-initrd-modules): Add note
about '--skip-checks'.
 2018-09-23 23:34:16 +02:00
Pierre Neidhardt e10bf49668
gnu: Add emacs-synosaurus. 
* gnu/packages/emacs.scm (emacs-synosaurus): New variable.
 2018-09-23 17:19:56 +02:00
Rutger Helling 94676ded5f
gnu: xpra: Update to 2.3.4. 
* gnu/packages/xorg.scm (xpra): Update to 2.3.4.
 2018-09-23 13:15:38 +02:00
Mark H Weaver 84b334362e
gnu: eolie: Use webkitgtk-2.22. 
* gnu/packages/gnome.scm (eolie)[native-inputs]: Add gcc-7:lib.
[inputs]: Replace webkitgtk with webkitgtk-2.22.
[arguments]: Add "gcc:lib" to the list of libraries to add to
LD_LIBRARY_PATH.  Use invoke.
 2018-09-23 04:55:54 -04:00
Mark H Weaver 480d39a600
gnu: epiphany: Use webkitgtk-2.22. 
* gnu/packages/gnome.scm (epiphany)[native-inputs]: Add gcc-7.
[inputs]: Replace webkitgtk with webkitgtk-2.22.
 2018-09-23 01:25:21 -04:00
Mark H Weaver 844cc6f876
gnu: webkitgtk: Add version 2.22.2. 
* gnu/packages/webkit.scm (webkitgtk-2.22): New variable.
 2018-09-23 01:25:09 -04:00
Katherine Cox-Buday 21280a8cd8
gnu: Add Go 1.11. 
* gnu/packages/golang.scm (go-1.11): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-09-22 14:30:13 -04:00
Mark H Weaver ae71cd8ac9
gnu: icecat: Add fixes from upstream mozilla-esr60 [security fixes]. 
Includes fixes for CVE-2018-12383 and CVE-2018-12385.

* gnu/packages/patches/icecat-CVE-2018-12383.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/patches/icecat-avoid-bundled-libraries.patch: Adapt to apply
cleanly to IceCat 60.
* gnu/packages/gnuzilla.scm (mozilla-patch): Update to fetch from
mozilla-esr60.
(icecat): Add selected changesets from upstream mozilla-esr60.
 2018-09-22 13:48:32 -04:00
Danny Milosavljevic 91294b5361
Revert 'gnu: rust: Remove unused "ar" setting.'. 
Some versions of Rust do need it and others complain about it.
For now, revert the removal entirely.

This reverts commit ec944a1de9.
 2018-09-22 10:09:47 +02:00
Ben Woodcroft 05fb1e0017
gnu: hmmer: Update to 3.2.1. 
* gnu/packages/bioinformatics.scm (hmmer): Update to 3.2.1.
[origin]: Remove patch.
[license]: Change to BSD-3.
[supported-systems]: New field.
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-09-22 09:16:47 +10:00
Nicolas Goaziou 78b7b9dbe9
gnu: snap: Update to 4.2.1.4. 
* gnu/packages/education.scm (snap): Update to 4.2.1.4.
 2018-09-21 22:22:09 +02:00
Nicolas Goaziou a255142af3
gnu: emacs-org: Update to 9.1.14. 
* gnu/packages/emacs.scm (emacs-org): Update to 9.1.14.
 2018-09-21 21:55:28 +02:00
Tobias Geerinckx-Rice 1302837f6b
gnu: workrave: Update to 1.10.21. 
* gnu/packages/gnome.scm (workrave): Update to 1.10.21.
[source]: Use GIT-FILE-NAME.
 2018-09-21 20:32:27 +02:00
Tobias Geerinckx-Rice 43726c522f
gnu: emacs-password-store: Update to 1.7.3. 
* gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.3.
 2018-09-21 20:32:27 +02:00
Tobias Geerinckx-Rice 10fadd1e3d
gnu: filezilla: Update to 3.37.1. 
* gnu/packages/ftp.scm (filezilla): Update to 3.37.1.
 2018-09-21 19:52:27 +02:00
Tobias Geerinckx-Rice 9a32bdf8a9
gnu: wxwidgets: Update to 3.0.4. 
* gnu/packages/wxwidgets.scm (wxwidgets): Update to 3.0.4.
 2018-09-21 19:52:26 +02:00
Tobias Geerinckx-Rice 199d72e327
gnu: python-pyparsing: Update to 2.2.1. 
* gnu/packages/python.scm (python-pyparsing): Update to 2.2.1.
[source]: Use PYPI-URI.
 2018-09-21 19:52:26 +02:00
Danny Milosavljevic ec944a1de9
gnu: rust: Remove unused "ar" setting. 
* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Remove
unused "ar" setting.
 2018-09-21 17:59:09 +02:00
Ludovic Courtès 92a9f14b9d
doc: Add section about inferiors. 
* doc/guix.texi (Inferiors): New node.
(Channels): Add xref to "Inferiors".
 2018-09-21 17:04:38 +02:00
Ludovic Courtès 2dad031375
inferior: Add 'inferior-for-channels'. 
* guix/inferior.scm (%inferior-cache-directory): New variable.
(inferior-for-channels): New procedure.
 2018-09-21 17:04:38 +02:00
Ludovic Courtès c37f38bde6
channels: Add 'channel-instances->derivation'. 
* guix/channels.scm (channel-instances->derivation): New procedure.
(latest-channel-derivation): Use it.
(channel-instance-derivations): Make private.
 2018-09-21 17:04:38 +02:00
Ludovic Courtès 811b21fb15
profiles: 'packages->manifest' now accepts inferior packages. 
* guix/profiles.scm (packages->manifest)[inferiors-loaded?]: New
variable.
[inferior->entry]: New procedure.
Accept inferior packages when INFERIORS-LOADED? is true.
* tests/guix-package.sh: Add test using a manifest with an inferior.
* tests/inferior.scm ("packages->manifest"): New test.
 2018-09-21 17:04:37 +02:00
Ludovic Courtès 2e6d64e122
inferior: Add 'inferior-package->manifest-entry'. 
* guix/inferior.scm (inferior-package->manifest-entry): New procedure.
* tests/inferior.scm (manifest-entry->list): New procedure.
("inferior-package->manifest-entry"): New test.
 2018-09-21 17:04:37 +02:00
Ludovic Courtès eee8b303f6
inferior: Add 'inferior-package-search-paths' & co. 
* guix/inferior.scm (%inferior-package-search-paths)
(inferior-package-native-search-paths)
(inferior-package-search-paths)
(inferior-package-transitive-native-search-paths): New procedures.
* tests/inferior.scm ("inferior-package-search-paths"): New test.
 2018-09-21 17:04:37 +02:00
Ludovic Courtès 6030396aec
inferior: Add 'inferior-package-inputs' & co. 
* guix/inferior.scm (open-inferior): Use (ice-9 match).
(inferior-package-input-field, inferior-package-inputs):
(inferior-package-native-inputs)
(inferior-package-propagated-inputs)
(inferior-package-transitive-propagated-inputs): New procedures.
* tests/inferior.scm ("inferior-package-inputs"): New test.

inputs fixlet
 2018-09-21 17:04:37 +02:00
Ludovic Courtès e1a4ffdab5
inferior: Add 'lookup-inferior-packages'. 
* guix/inferior.scm (<inferior>)[packages, table]: New fields.
(open-inferior): Initialize these new fields.
(inferior-packages): Rename to...
(%inferior-packages): ... this.
(inferior-packages): New procedure; force the promise.
(%inferior-package-table, lookup-inferior-packages): New procedures.
* tests/inferior.scm ("lookup-inferior-packages")
("lookup-inferior-packages and eq?-ness"): New tests.
 2018-09-21 17:04:37 +02:00
Ludovic Courtès 9daf046c5d
inferior: Add 'inferior-package-derivation'. 
* guix/inferior.scm (read-inferior-response)
(send-inferior-request): New procedures.
(inferior-eval): Rewrite in terms of these.
(proxy, inferior-package-derivation, inferior-package->derivation)
(package-compiler): New procedures.
* tests/inferior.scm ("inferior-package-derivation"): New test.
 2018-09-21 17:04:37 +02:00