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63904 Commits

Author SHA1 Message Date
Tobias Geerinckx-Rice 2ffd1314cd
guix-install.sh: Make sure /etc/profile is sourced. 
New users regularly report missing newly-installed programmes and icons.

* etc/guix-install.scm (main): Tell users to log out & back in.
 2020-07-16 20:12:07 +02:00
Tobias Geerinckx-Rice 4089d7920f
guix-install.sh: Suggest running gpg as root. 
The original example regularly prevented new users from installing Guix
at all.

* etc/guix-install.scm (chk_gpg_keyring): Suggest ‘sudo -i gpg’.
 2020-07-16 20:12:07 +02:00
Tobias Geerinckx-Rice 7fc2ba2a2c
gnu: kyotocabinet: Use HTTPS. 
* gnu/packages/databases.scm (kyotocabinet)[source, home-page]:
Use HTTPS.
 2020-07-16 20:12:07 +02:00
Tobias Geerinckx-Rice c4944d6c81
gnu: java-xmlunit: Use HTTPS home page. 
* gnu/packages/java.scm (java-xmlunit)[home-page]: Use HTTPS.
 2020-07-16 20:12:07 +02:00
Tobias Geerinckx-Rice 69cfb72b38
gnu: libyaml: Use HTTPS. 
* gnu/packages/web.scm (libyaml)[source, home-page]: Use HTTPS.
 2020-07-16 20:12:06 +02:00
Tobias Geerinckx-Rice fe39c70195
gnu: Use HTTPS for mdc-berlin.de home pages. 
* gnu/packages/bioinformatics.scm (r-genomation, r-genomationdata, pigx-rnaseq)
(pigx-chipseq, pigx-bsseq, pigx-scrnaseq, pigx)[home-page]: Use HTTPS.
 2020-07-16 20:12:06 +02:00
Tobias Geerinckx-Rice c980589260
gnu: Use HTTPS for biojava.org home pages. 
* gnu/packages/bioinformatics.scm (java-biojava-core)
(java-biojava-phylo, java-biojava-alignment, java-biojava-phylo-4.0)
(java-biojava-alignment-4.0)[home-page]: Use HTTPS.
 2020-07-16 20:12:06 +02:00
Tobias Geerinckx-Rice 2ae03bf631
gnu: jack@0.125.0: Update URIs. 
gnu/packages/audio.scm (jack-1)[source]: Use a working mirror.
[home-page]: Use HTTPS.
 2020-07-16 20:12:06 +02:00
Tobias Geerinckx-Rice 00a34333bb
gnu: Use HTTPS for igraph.org. 
* gnu/packages/graph.scm (igraph, r-igraph)[home-page]: Use HTTPS.
 2020-07-16 20:12:06 +02:00
Tobias Geerinckx-Rice d48b5c8af7
gnu: ghc-pandoc-types: Use HTTPS home page. 
* gnu/packages/haskell-xyz.scm (ghc-pandoc-types)[home-page]: Use HTTPS.
 2020-07-16 20:12:06 +02:00
Tobias Geerinckx-Rice 1467ca6829
gnu: Use HTTPS for www.yesodweb.com. 
* gnu/packages/haskell-web.scm (ghc-css-text, ghc-yesod-persistent)
[home-page]: Use HTTPS.
 2020-07-16 20:12:06 +02:00
Tobias Geerinckx-Rice 702a101257
gnu: Use HTTPS for github.com (and subdomains) home pages. 
* gnu/packages/bioconductor.scm (r-qvalue)[home-page]: Use HTTPS and
follow permanent redirection.
* gnu/packages/check.scm (python-codecov, python-nosexcover)
[home-page]: Likewise.
* gnu/packages/cran.scm (r-ffbase, r-ggrepel, r-valr)
[home-page]: Likewise.
* gnu/packages/crates-io.scm (rust-block-0.1, rust-dispatch-0.1)
(rust-objc-0.2, rust-objc-exception-0.1)
(rust-objc-foundation-0.1, rust-objc-id-0.1, rust-objc-test-utils-0.0)
(rust-onig-5.0, rust-onig-sys-69.2, rust-vergen-3.1)
[home-page]: Likewise.
* gnu/packages/finance.scm (ledger-agent, keepkey-agent)
[home-page]: Likewise.
* gnu/packages/haskell-check.scm (ghc-tasty-expected-failure)
[home-page]: Likewise.
* gnu/packages/haskell-web.scm (ghc-bsb-http-chunked, ghc-warp)
(ghc-warp-tls)[home-page]: Likewise.
* gnu/packages/haskell-xyz.scm (ghc-configurator, ghc-hasktags)
(ghc-linear, ghc-newtype-generics, ghc-retry, ghc-xdg-basedir)
(ghc-pretty-show)[home-page]: Likewise.
* gnu/packages/java.scm (java-javax-inject)[home-page]: Likewise.
* gnu/packages/libffi.scm (ruby-ffi)[home-page]: Likewise.
* gnu/packages/linux.scm (procenv)[home-page]: Likewise.
* gnu/packages/python-web.scm (python-aiodns, python-flask-htpasswd)
(python-pycares)[home-page]: Likewise.
* gnu/packages/python-xyz.scm (python-progressbar33, python-whatever)
(python-funcy)[home-page]: Likewise.
* gnu/packages/ruby.scm (ruby-rubyzip, ruby-spinach, ruby-gherkin-ruby)
(ruby-code-statistics, ruby-colorize, ruby-wwtd)[home-page]: Likewise.
 2020-07-16 20:12:06 +02:00
Tobias Geerinckx-Rice 228d290106
gnu: Update Haskell Wiki URIs. 
* gnu/packages/haskell-web.scm (ghc-hxt-regex-xmlschema)[home-page]:
Use HTTPS and follow permanent redirection.
* gnu/packages/haskell-xyz.scm (ghc-alsa-core, ghc-base-unicode-symbols)
(ghc-colour, ghc-data-accessor, ghc-data-accessor-transformers)
(ghc-gluraw, ghc-glut, ghc-gnuplot, ghc-haddock-test, ghc-opengl)
(ghc-openglraw, ghc-storablevector)[home-page]: Likewise.
 2020-07-16 20:12:06 +02:00
Tobias Geerinckx-Rice 70e1199c0d
gnu: bombadillo: Use HTTPS home page. 
* gnu/packages/web-browsers.scm (bombadillo)[home-page]: Use HTTPS.
 2020-07-16 20:12:05 +02:00
Tobias Geerinckx-Rice 3720a6f847
gnu: lsof: Use HTTPS home page. 
* gnu/packages/lsof.scm (lsof)[home-page]: Use HTTPS.
 2020-07-16 20:12:05 +02:00
Tobias Geerinckx-Rice c4ccf2db62
gnu: lirc: Use HTTPS home page. 
Also add a missing copyright line for an obvious nckx phase.

* gnu/packages/lirc.scm (lirc)[home-page]: Use HTTPS.
 2020-07-16 20:12:05 +02:00
Tobias Geerinckx-Rice 2c73599586
gnu: lv2: Use HTTPS. 
* gnu/packages/audio.scm (lv2)[source, home-page]: Use HTTPS.
 2020-07-16 20:12:05 +02:00
Guillaume Le Vaillant b736e9ba2c
gnu: Add cl-opticl. 
* gnu/packages/lisp-xyz.scm (sbcl-opticl, cl-opticl): New variables.
 2020-07-16 19:47:43 +02:00
Guillaume Le Vaillant b0e7bc35c4
gnu: Add cl-pngload. 
* gnu/packages/lisp-xyz.scm (sbcl-pngload, cl-pngload, ecl-pngload): New
  variables.
 2020-07-16 19:43:41 +02:00
Guillaume Le Vaillant 5dff9687c9
gnu: Add cl-zpb-exif. 
* gnu/packages/lisp-xyz.scm (sbcl-zpb-exif, cl-zpb-exif, ecl-zpb-exif): New
  variables.
 2020-07-16 19:13:17 +02:00
Guillaume Le Vaillant 242bd80793
gnu: Add cl-3bz. 
* gnu/packages/lisp-xyz.scm (sbcl-3bz, cl-3bz, ecl-3bz): New variables.
 2020-07-16 19:02:09 +02:00
Guillaume Le Vaillant 0f44f63ca2
gnu: Add cl-mmap. 
* gnu/packages/lisp-xyz.scm (sbcl-mmap, cl-mmap, ecl-mmap): New variables.
 2020-07-16 18:45:42 +02:00
Guillaume Le Vaillant 1c1b0532d1
gnu: Add cl-retrospectiff. 
* gnu/packages/lisp-xyz.scm (sbcl-retrospectiff, cl-retrospectiff,
  ecl-retrospectiff): New variables.
 2020-07-16 18:12:39 +02:00
Guillaume Le Vaillant fc748ff067
gnu: Add cl-opticl-core. 
* gnu/packages/lisp-xyz.scm (sbcl-opticl-core, cl-opticl-core,
  ecl-opticl-core): New variables.
 2020-07-16 17:58:21 +02:00
Guillaume Le Vaillant ec2c73b8ed
gnu: Add cl-freetype2. 
* gnu/packages/lisp-xyz.scm (sbcl-freetype2, cl-freetype2, ecl-freetype2): New
  variables.
 2020-07-16 17:48:57 +02:00
Guillaume Le Vaillant 7387c090b0
gnu: Add cl-skippy. 
* gnu/packages/lisp-xyz.scm (sbcl-skippy, cl-skippy, ecl-skippy): New
  variables.
 2020-07-16 17:20:13 +02:00
Guillaume Le Vaillant 556daf642a
gnu: Add cl-deflate. 
* gnu/packages/lisp-xyz.scm (sbcl-deflate, cl-deflate, ecl-deflate): New
  variables.
 2020-07-16 17:08:27 +02:00
Guillaume Le Vaillant 31c67a8525
gnu: Add cl-com.gigamonkeys.binary-data. 
* gnu/packages/lisp-xyz.scm (sbcl-com.gigamonkeys.binary-data,
  cl-com.gigamonkeys.binary-data, ecl-com.gigamonkeys.binary-data): New
  variables.
 2020-07-16 16:58:42 +02:00
Guillaume Le Vaillant 2020a0567b
gnu: Add cl-tga. 
* gnu/packages/lisp-xyz.scm (sbcl-tga, cl-tga, ecl-tga): New variables.
 2020-07-16 16:48:25 +02:00
Ricardo Wurmus d57ce2024b
gnu: r-quantreg: Update to 5.61. 
* gnu/packages/statistics.scm (r-quantreg): Update to 5.61.
[propagated-inputs]: Add r-conquer.
 2020-07-16 10:08:06 +02:00
Ricardo Wurmus c4dfd2bf62
gnu: r-r-rsp: Update to 0.44.0. 
* gnu/packages/statistics.scm (r-r-rsp): Update to 0.44.0.
 2020-07-16 10:08:06 +02:00
Ricardo Wurmus c85c85d67c
gnu: r-tibble: Update to 3.0.3. 
* gnu/packages/statistics.scm (r-tibble): Update to 3.0.3.
 2020-07-16 10:08:06 +02:00
Ricardo Wurmus 9fcf3d92a0
gnu: r-rlang: Update to 0.4.7. 
* gnu/packages/statistics.scm (r-rlang): Update to 0.4.7.
 2020-07-16 10:08:06 +02:00
Ricardo Wurmus 2d2b5d60f8
gnu: r-brms: Update to 2.13.3. 
* gnu/packages/cran.scm (r-brms): Update to 2.13.3.
 2020-07-16 10:08:06 +02:00
Ricardo Wurmus 22df7543b1
gnu: r-gamlss: Update to 5.1-7. 
* gnu/packages/cran.scm (r-gamlss): Update to 5.1-7.
 2020-07-16 10:08:06 +02:00
Ricardo Wurmus 88804120c3
gnu: r-gamlss-dist: Update to 5.1-7. 
* gnu/packages/cran.scm (r-gamlss-dist): Update to 5.1-7.
 2020-07-16 10:08:06 +02:00
Ricardo Wurmus 2762d722c5
gnu: r-pillar: Update to 1.4.6. 
* gnu/packages/cran.scm (r-pillar): Update to 1.4.6.
[propagated-inputs]: Add r-ellipsis and r-lifecycle.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus 4d639b61cf
gnu: r-mice: Update to 3.10.0. 
* gnu/packages/cran.scm (r-mice): Update to 3.10.0.
[propagated-inputs]: Add r-generics.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus df952ca338
gnu: r-broom: Update to 0.7.0. 
* gnu/packages/cran.scm (r-broom): Update to 0.7.0.
[propagated-inputs]: Remove r-nlme and r-reshape2; add r-ellipsis, r-glue, and
r-rlang.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus b7f051db14
gnu: r-rhdf5lib: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.1.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus 82eafe32a2
gnu: r-qtl2: Update to 0.22-11. 
* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-11.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus 16e16586d2
gnu: r-genomicfeatures: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.1.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus 02f3a622e2
gnu: r-summarizedexperiment: Update to 1.18.2. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.2.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus a9a912805a
gnu: r-activepathways: Update to 1.0.2. 
* gnu/packages/bioconductor.scm (r-activepathways): Update to 1.0.2.
[propagated-inputs]: Remove r-metap.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus 1a7d1c54d4
gnu: r-rsubread: Update to 2.2.4. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.2.4.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus ba663a331b
gnu: Add r-conquer. 
* gnu/packages/cran.scm (r-conquer): New variable.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus 021ad446fc
gnu: r-cairo: Update to 1.5-12.2. 
* gnu/packages/statistics.scm (r-cairo): Update to 1.5-12.2.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus 79f7cd99da
gnu: r-gplots: Update to 3.0.4. 
* gnu/packages/statistics.scm (r-gplots): Update to 3.0.4.
[native-inputs]: Add r-knitr.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus f12fd76912
gnu: r-xml: Update to 3.99-0.4. 
* gnu/packages/statistics.scm (r-xml): Update to 3.99-0.4.
 2020-07-16 10:08:04 +02:00
Ricardo Wurmus f7b05fb978
gnu: r-tibble: Update to 3.0.2. 
* gnu/packages/statistics.scm (r-tibble): Update to 3.0.2.
 2020-07-16 10:08:04 +02:00