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Author SHA1 Message Date
Marius Bakke
1f8838d1f6
gnu: libgc: Fix replacement inheritance. 
* gnu/packages/bdw-gc.scm (libgc-8.0): Do not use PACKAGE/INHERIT, because it
does not make sense to inherit any replacements of LIBGC.
(libgc/back-pointers): Use PACKAGE/INHERIT.
 2020-03-02 23:39:44 +01:00
Ricardo Wurmus
1e07875b57
gnu: Add r-zseq. 
* gnu/packages/cran.scm (r-zseq): New variable.
 2020-03-02 23:05:49 +01:00
Ricardo Wurmus
02366a12d0
gnu: Add r-ztype. 
* gnu/packages/cran.scm (r-ztype): New variable.
 2020-03-02 23:05:49 +01:00
Ricardo Wurmus
11ab52888d
gnu: Add r-zvcv. 
* gnu/packages/cran.scm (r-zvcv): New variable.
 2020-03-02 23:05:49 +01:00
Ricardo Wurmus
505d6716d0
gnu: Add r-zyp. 
* gnu/packages/cran.scm (r-zyp): New variable.
 2020-03-02 23:05:49 +01:00
Ricardo Wurmus
7316f137dc
gnu: Add r-kendall. 
* gnu/packages/cran.scm (r-kendall): New variable.
 2020-03-02 23:05:49 +01:00
Maxim Cournoyer
1639e0b7b6
gnu: python-smmap: Update to version 3.0.1, deprecate python-smmap2. 
* gnu/packages/python-xyz.scm (python-smmap): Rename from python-smmap2, and
update to version 3.0.1.
(python-smmap2, python2-smmap2): Preserve original bindings, marked as
deprecated.
* gnu/packages/version-control.scm (python-gitdb)[propagated-inputs]: Depend
on the new python-smmap package.
 2020-03-02 17:03:03 -05:00
Maxim Cournoyer
166dbbb012
gnu: python-gitpython: Update to 3.1.0. 
* gnu/packages/version-control.scm (python-gitpython): Update to 3.1.0.
 2020-03-02 17:03:03 -05:00
Maxim Cournoyer
cbe4272e6f
gnu: python-gitdb: Update to 4.0.2. 
* gnu/packages/version-control.scm (python-gitdb): Update to 4.0.2.
[source]: Correct the PyPI URL to refer to the actual gitdb package, not a
mirror.  This mirror had a problematic setup.py install requirement that
required gitdb>=4.0.1, which would cause run time errors when using snakemake.
 2020-03-02 17:03:03 -05:00
Maxim Cournoyer
357af7f283
gnu: python-pyyaml: Update to 5.3. 
* gnu/packages/python-xyz.scm (python-pyyaml): Update to 5.3.
 2020-03-02 17:03:02 -05:00
Maxim Cournoyer
8c06d6d8ce
gnu: python-xenon: Update to 0.7.0. 
* gnu/packages/python-xyz.scm (python-xenon): Update to 0.7.0.
[arguments]: Set #:tests? to #f to disable test suite.
 2020-03-02 17:03:02 -05:00
Maxim Cournoyer
f675ab4faf
gnu: python-radon: Update to 4.1.0. 
* gnu/packages/python-xyz.scm (python-radon): Update to 4.1.0.
 2020-03-02 17:03:02 -05:00
Maxim Cournoyer
bd13705540
gnu: python-colorama: Update to 0.4.3. 
* gnu/packages/python-xyz.scm (python-colorama): Update to 0.4.3.
 2020-03-02 17:03:02 -05:00
Maxim Cournoyer
9c9704a9d7
gnu: Add python-wget. 
* gnu/packages/python-xyz.scm (python-wget): New variable.
 2020-03-02 17:03:02 -05:00
Nicolas Goaziou
1eee899617
gnu: emacs-windower: Fix description. 
* gnu/packages/emacs-xyz.scm (emacs-windower): Fix Texinfo code for lists in
description.
 2020-03-02 22:59:57 +01:00
Ricardo Wurmus
7a4b2da48f
gnu: r-forcats: Update to 0.5.0. 
* gnu/packages/statistics.scm (r-forcats): Update to 0.5.0.
 2020-03-02 21:53:49 +01:00
Ricardo Wurmus
3f809fe875
gnu: r-testthat: Update to 2.3.2. 
* gnu/packages/statistics.scm (r-testthat): Update to 2.3.2.
 2020-03-02 21:53:48 +01:00
Ricardo Wurmus
d82a17ebaa
gnu: r-openmx: Update to 2.17.3. 
* gnu/packages/cran.scm (r-openmx): Update to 2.17.3.
 2020-03-02 21:53:48 +01:00
Ricardo Wurmus
2d063d4535
gnu: r-summarytools: Update to 0.9.6. 
* gnu/packages/cran.scm (r-summarytools): Update to 0.9.6.
 2020-03-02 21:53:48 +01:00
Ricardo Wurmus
bbba65e269
gnu: r-officer: Update to 0.3.7. 
* gnu/packages/cran.scm (r-officer): Update to 0.3.7.
[propagated-inputs]: Remove r-base64enc, r-htmltools, r-rcpp, and r-rlang.
 2020-03-02 21:53:48 +01:00
Ricardo Wurmus
1284df4ef6
gnu: r-seqminer: Update to 8.0. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0.
 2020-03-02 21:53:48 +01:00
Tobias Geerinckx-Rice
b4034d1bc4
gnu: ecl-clunit: Use HTTPS home page. 
* gnu/packages/lisp-xyz.scm (ecl-clunit)[home-page]: Use HTTPS.
 2020-03-02 21:46:27 +01:00
Tobias Geerinckx-Rice
711ebe771e
gnu: mapnik: Use HTTPS home page. 
* gnu/packages/geo.scm (mapnik)[home-page]: Use HTTPS.
 2020-03-02 21:46:27 +01:00
Tobias Geerinckx-Rice
4e5ad79e4d
gnu: python-rq: Use HTTPS home page. 
* gnu/packages/databases.scm (python-rq)[home-page]: Use HTTPS.
 2020-03-02 21:46:27 +01:00
Tobias Geerinckx-Rice
35e74723b5
gnu: java-plexus-interpolation: Use HTTPS home page. 
* gnu/packages/java.scm (java-plexus-interpolation)[home-page]: Use HTTPS.
 2020-03-02 21:46:27 +01:00
Tobias Geerinckx-Rice
c99f0e5780
gnu: amsynth: Use HTTPS home page. 
* gnu/packages/music.scm (amsynth)[home-page]: Use HTTPS.
 2020-03-02 21:46:27 +01:00
Tobias Geerinckx-Rice
a369682826
gnu: pootle: Use HTTPS home page. 
* gnu/packages/django.scm (pootle)[home-page]: Use HTTPS.
 2020-03-02 21:46:27 +01:00
Tobias Geerinckx-Rice
9bbb492042
gnu: muse-sequencer: Update home page. 
* gnu/packages/music.scm (muse-sequencer)[home-page]: Follow (HTTPS)
redirection.
 2020-03-02 21:46:27 +01:00
Tobias Geerinckx-Rice
ba6b48b84f
gnu: opensmtpd: Support ECDSA certificates. 
The required libressl version is now stable and more featureful than
openssl.

* gnu/packages/mail.scm (opensmtpd)[inputs]: Replace openssl with libressl.
 2020-03-02 21:46:27 +01:00
Tobias Geerinckx-Rice
0250672b97
gnu: libressl: Update to 3.0.2. 
* gnu/packages/tls.scm (libressl): Update to 3.0.2.
 2020-03-02 21:46:27 +01:00
Tobias Geerinckx-Rice
b69c770305
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.10.0. 
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): Update to 3.10.0.
 2020-03-02 21:46:27 +01:00
Nicolas Goaziou
45a2636a0b
gnu: emacs-modus-themes: Update to 0.6.0. 
* gnu/packages/emacs-xyz.scm (emacs-modus-themes): Update to 0.6.0.
 2020-03-02 21:37:15 +01:00
Leo Famulari
8e1f5aaba2
gnu: Syncthing: Fix installation of the 'util' package output. 
* gnu/packages/syncthing.scm (syncthing)[arguments]: Adjust the 'install' phase.
 2020-03-02 15:36:21 -05:00
Efraim Flashner
7b1ba1e4fc
gnu: librsvg-next: Fix cargo dependency. 
* gnu/packages/gnome.scm (librsvg-next-source): Don't hardcode patch
version of cargo inputs.
 2020-03-02 22:11:16 +02:00
Efraim Flashner
597f41ca49
gnu: rust-diff-0.1: Update to 0.1.12. 
* gnu/packages/crates-io.scm (rust-diff-0.1): Update to 0.1.12.
[arguments]: Replace rust-quickcheck-0.8 with 0.9 in
cargo-development-inputs.
 2020-03-02 22:09:04 +02:00
Efraim Flashner
4b309aad04
gnu: rust-defmac-0.2: Don't skip build. 
* gnu/packages/crates-io.scm (rust-defmac-0.2)[arguments]: Don't skip
build.
 2020-03-02 21:58:22 +02:00
Efraim Flashner
64a28fd6e1
gnu: rust-datetime-0.4: Don't skip build. 
* gnu/packages/crates-io.scm (rust-datetime-0.4)[arguments]: Don't skip
build. Add rust-regex-0.1 to cargo-development-inputs.
 2020-03-02 21:56:54 +02:00
Efraim Flashner
49877d9fd6
gnu: rust-constant-time-eq-0.1: Don't skip build. 
* gnu/packages/crates-io.scm (rust-constant-time-eq-0.1)[arguments]:
Don't skip build.
 2020-03-02 21:48:02 +02:00
Vincent Legoll
bdcec7028c
gnu: debootstrap: Update to 1.0.119. 
* gnu/packages/debian.scm (debootstrap): Update to 1.0.119.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2020-03-02 21:33:28 +02:00
Efraim Flashner
c1febbbf94
gnu: vim: Update to 8.2.0343. 
* gnu/packages/vim.scm (vim): Update to 8.2.0343.
 2020-03-02 10:40:34 +02:00
Ricardo Wurmus
5f5e0830f6
gnu: r-multiassayexperiment: Update to 1.12.3. 
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.12.3.
 2020-03-01 23:38:33 +01:00
Ricardo Wurmus
e766ba9a52
gnu: r-cicero: Update to 1.4.2. 
* gnu/packages/bioconductor.scm (r-cicero): Update to 1.4.2.
 2020-03-01 23:38:26 +01:00
Ricardo Wurmus
0a30342def
gnu: r-mlinterfaces: Update to 1.66.4. 
* gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.66.4.
 2020-03-01 23:38:19 +01:00
Ricardo Wurmus
aece78fe2f
gnu: r-biocneighbors: Update to 1.4.2. 
* gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.4.2.
 2020-03-01 23:38:12 +01:00
Ricardo Wurmus
8351faae8a
gnu: r-chippeakanno: Update to 3.20.1. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.20.1.
 2020-03-01 23:38:06 +01:00
Ricardo Wurmus
f73b75e00c
gnu: r-hdf5array: Update to 1.14.3. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3.
 2020-03-01 23:37:58 +01:00
Ricardo Wurmus
6c1f5a1b7e
gnu: r-rsamtools: Update to 2.2.3. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3.
 2020-03-01 23:37:52 +01:00
Ricardo Wurmus
9bbf3f9de2
gnu: r-edger: Update to 3.28.1. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1.
 2020-03-01 23:37:40 +01:00
Ricardo Wurmus
efb98dd09d
gnu: gwl: Update to 0.2.1. 
* gnu/packages/package-management.scm (gwl): Update to 0.2.1.
[arguments]: Add phase "fix-tests".
 2020-03-01 23:21:18 +01:00
Ricardo Wurmus
42c7f6e748
gnu: r-nloptr: Update to 1.2.2. 
* gnu/packages/statistics.scm (r-nloptr): Update to 1.2.2.
 2020-03-01 23:21:18 +01:00