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Author SHA1 Message Date
Efraim Flashner
e4b91f10c8
gnu: python-scipy: Adjust phases. 
* gnu/packages/python-science.scm (python-scipy)[arguments]: Replace
'check with custom 'check phase.
 2022-03-17 14:51:38 +02:00
jgart
bae2201a8d
gnu: sicp: Update to 20180718-2.bda03f7. 
* gnu/packages/scheme.scm (sicp): Update to 20180718-2.bda03f7.
  [version]: Use git-version function.
  [source]: Use git-file-name function.
  [arguments]: Remove trailing `#t`.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-03-17 10:02:23 +01:00
jgart
a7b40dff2f
gnu: cl-3bmd: Update to 0.0.0-3.4e08d82. 
* gnu/packages/lisp-xyz.scm (sbcl-3bmd): Update to 0.0.0-3.4e08d82.
  [native-inputs]: Add sbcl-fiasco.
  [inputs]: Add python, python-pygments, and use newer inputs guix style.
  [arguments]: Add 'fix-python3-path' phase.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-03-17 10:01:59 +01:00
jgart
b999ce74ba
gnu: cl-envy: Update to 26a7faa. 
* gnu/packages/lisp-xyz.scm (sbcl-envy): Update to 26a7faa.
  [native-inputs]: Uncomment test inputs and use new style.
  [arguments]: Add 'asd-systems' parameter, Remove 'fix-tests' phase.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-03-17 09:32:39 +01:00
Ricardo Wurmus
24f7c64bb2
gnu: Add r-ggtern. 
* gnu/packages/cran.scm (r-ggtern): New variable.
 2022-03-17 07:46:19 +01:00
Carl Dong
34e9eae68c
gnu: cross-base: Don't specify mingw --with-newlib 
Previous to this commit, we added a --with-newlib configure flag to
cross-gcc when cross-newlib?, but cross-newlib? is true only when
target-mingw?.

It turns out that specifying --with-newlib disables the
GLIBCXX_CROSSCONFIG check, which is used to detect
_GLIBCXX_HAVE__WFOPEN, which is required in C++17 std::filesystem for
mingw-w64 systems.

Additional context: In gnu/packages/embedded.scm, --with-newlib is
specified explicitly when we're actually using newlib, which seems like
the correct way of handling it.

Situation in other distros:
- Debian's gcc-mingw-w64 doesn't specify --with-newlib
- Fedora's mingw64-gcc-c++ explicitly specifies --without-newlib

Chesterton's fence: Chatting with janneke, who originally added this
mechanism, reveals that this flag is not only no longer required, but
also that removing it doesn't break his guile-mingw builds. See IRC logs
of #guix for 2022-02-15.

* gnu/packages/cross-base.scm (cross-gcc-arguments): Don't check for and
specify --with-newlib.
(cross-libc): Check for mingw and use mingw-w64 directly.
(cross-newlib?): Remove, unexport.
(native-libc): Remove.
 2022-03-16 22:13:48 -04:00
Tobias Geerinckx-Rice
0c6c957a01
gnu: knot: Update to 3.1.6. 
* gnu/packages/dns.scm (knot): Update to 3.1.6.
 2022-03-13 01:00:00 +01:00
Leo Famulari
69d3896c0f
gnu: expat: Update to 2.4.7. 
This fixes some regressions in 2.4.5 and 2.4.6:

https://www.xml.com/news/2022-02-expat-246/
https://www.xml.com/news/2022-03-expat-247/

* gnu/packages/xml.scm (expat/fixed): Update to 2.4.7.
 2022-03-16 17:14:19 -04:00
Leo Famulari
62ea3d510f
gnu: OpenSSL 3: Update to 3.0.2 [fixes CVE-2022-0778]. 
For more information about this vulnerability:

https://www.openssl.org/news/secadv/20220315.txt

* gnu/packages/tls.scm (openssl-3.0): Update to 3.0.2.
 2022-03-16 17:14:19 -04:00
Leo Famulari
139a5cab04
gnu: OpenSSL: Update to 1.1.1n [fixes CVE-2022-0778]. 
For more information about this vulnerability:

https://www.openssl.org/news/secadv/20220315.txt

* gnu/packages/tls.scm (openssl/fixed): Update to 1.1.1n.
 2022-03-16 17:14:08 -04:00
Tobias Geerinckx-Rice
3076e69577
gnu: isc-dhcp: Update bundled BIND to 9.11.37. 
* gnu/packages/admin.scm (isc-dhcp)[inputs]:
Update bind-source-tarball to 9.11.37.
 2022-03-13 01:00:37 +01:00
Tobias Geerinckx-Rice
880e70e8b6
gnu: bind: Update to 9.16.27 [fixes CVE-2022-0396]. 
* gnu/packages/dns.scm (isc-bind): Update to 9.16.27.
 2022-03-13 01:00:00 +01:00
Tobias Geerinckx-Rice
1ef6203630
gnu: cdrtools: Don't return #t from snippet. 
* gnu/packages/cdrom.scm (cdrtools)[source]: Don't return #t from snippet.
 2022-03-13 01:00:01 +01:00
Tobias Geerinckx-Rice
0ac0f43a90
gnu: cdrtools: Use G-expressions. 
* gnu/packages/cdrom.scm (cdrtools)[arguments]:
Rewrite as G-expressions.  Don't return #t from phases.
 2022-03-13 01:00:00 +01:00
Tobias Geerinckx-Rice
b97a8b8941
gnu: cdrtools: Link dynamically. 
* gnu/packages/cdrom.scm (cdrtools)[arguments]: Add "LINKMODE=dynamic" to
the #:configure-flags.
 2022-03-13 01:00:00 +01:00
Tobias Geerinckx-Rice
53ac77389c
gnu: cdrtools: Prepare for cross-compilation. 
* gnu/packages/cdrom.scm (cdrtools)[arguments]: Use CC-FOR-TARGET.
 2022-03-13 01:00:00 +01:00
Efraim Flashner
21457fb31e
gnu: ruby-stackprof: Adjust skipped test on powerpc-linux. 
* gnu/packages/ruby.scm (ruby-stackprof)[arguments]: On powerpc-linux
adjust the 'skip-dubious-test phase.
 2022-03-16 20:24:52 +02:00
Andrew Tropin
d74d18437e
gnu: i2pd: Update to 2.41.0. 
* gnu/packages/i2p.scm (i2pd): Update to 2.41.0.
  [arguments]: Remove trailing slash to match all libi2pd entries.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-03-16 16:48:11 +01:00
jgart
4637b6952c
gnu: cl-mito: Update to 47ba486. 
* gnu/packages/lisp-xyz.scm (sbcl-mito): Update to 47ba486.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-03-16 16:48:11 +01:00
Guillaume Le Vaillant
2da3c84ab7
gnu: opencpn: Update to 5.6.0. 
* gnu/packages/geo.scm (opencpn): Update to 5.6.0.
  [inputs]: Add alsa-utils, eudev, jasper, libjpeg-turbo and libusb.
 2022-03-16 16:48:11 +01:00
Tanguy Le Carrour
797e308047
gnu: Add tessen. 
* gnu/packages/password-utils.scm (tessen): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-03-16 15:48:53 +01:00
Denis 'GNUtoo' Carikli
d7a30c6e1d
gnu: matterbridge: update to 1.24.0 
* gnu/packages/messaging.scm (matterbridge): Update to 1.24.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-03-16 15:48:52 +01:00
Pradana AUMARS
fee68a93d8
gnu: Add python-mathlibtools. 
* gnu/packages/lean.scm (python-mathlibtools): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-03-16 15:48:52 +01:00
Jai Vetrivelan
f1aa1f3412
gnu: dunst: Update to 1.8.1. 
* gnu/packages/dunst.scm (dunst): Update to 1.8.1.
* gnu/packages/patches/dunst-1.7.3-fix-crash.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-03-16 15:48:52 +01:00
Denis 'GNUtoo' Carikli
4ba792fa15
gnu: python-gitlab: update to 3.2.0 
* gnu/packages/python-web.scm (python-gitlab): Update to 3.2.0

Signed-off-by: Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-03-16 15:48:52 +01:00
Ludovic Courtès
47960b5526
system: Improve 'read-boot-parameters' incompatibility diagnostic. 
Previously, when reading an incompatible "parameters" file, 'guix
system' would print a warning and then crash with a wrong-type-arg
backtrace because code expects 'read-boot-parameters' to always return a
<boot-parameters> record.

* gnu/system.scm (read-boot-parameters): Upon incompatibility, raise an
error instead of returning #f.  Also raise a '&fix-hint' condition.
* tests/boot-parameters.scm ("read, construction, mandatory fields"):
Define 'test-read-boot-parameters' as a macro; expect
'formatted-message?' exceptions rather than #f returns.
 2022-03-16 15:48:52 +01:00
Brendan Tildesley
5d4af22ef2
gnu: cryfs: Update to 0.11.2. 
* gnu/packages/crypto.scm (cryfs): Update to 0.11.2.
[arguments]: Fix build with boost 1.77

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-03-16 15:48:52 +01:00
Ludovic Courtès
00dfff84c6
packages: 'modify-inputs' preserves outputs in 'replace' clauses. 
Fixes <https://issues.guix.gnu.org/53915>.
Reported by Gordon Quad <gordon@niflheim.info>.

* guix/packages.scm (replace-input): Preserve the outputs of INPUT by
default.
* tests/packages.scm ("modify-inputs, replace, extra output"): New test.
 2022-03-16 15:48:51 +01:00
Ludovic Courtès
e3801126a9
tests: Exercise 'modify-inputs' with a 'replace' clause. 
* tests/packages.scm ("modify-inputs, replace")
("modify-inputs, replace, change output"): New tests.
 2022-03-16 15:48:51 +01:00
Fatima Toothpaste
66a4a5ecb2
gnu : nicotine+: Update to 3.2.1. 
* gnu/packages/nicotine.scm (nicotine+): Update to 3.2.1.
  [source]: Delete network requried tests in snippet.
  [arguments]: Remove trailing #t.
  Replae 'check phase to run proper test.
  [inputs]: Add bash-minimal, gspell, libappindicator.
  [native-inputs]: Remove python-pytest. Add xvfb-run.
  [home-page]: Update URL.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-03-16 15:48:51 +01:00
Efraim Flashner
53d986215f
Revert "gnu: %boot3-inputs: Add missing input." 
This reverts commit ed2ca2dcb5.

This is no longer needed after the gcc STARTFILE_PREFIX_SPEC commit.
 2022-03-16 12:17:09 +02:00
Efraim Flashner
030900747b
Revert "gnu: Add %final-inputs-riscv64." 
This reverts commit 0444be8689.

This is no longer necessary after the gcc STARTFILE_PREFIX_SPEC commit.
 2022-03-16 12:16:15 +02:00
Efraim Flashner
32f52f82b3
gnu: gcc: For riscv64-linux remove STARTFILE_PREFIX_SPEC. 
* gnu/packages/gcc.scm (gcc-4.7)[arguments]: When building for
riscv64-linux and the 'gcc/configure/riscv' directory exists adjust the
STARTFILE_PREFIX_SPEC so it doesn't do anything.
 2022-03-16 12:09:42 +02:00
kiasoc5
53370c7b03
gnu: httpie: Update to 3.1.0 [security fixes]. 
Fixes CVE-2022-24737 and CVE-2022-0430.

* gnu/packages/python-web.scm (httpie): Update to 3.1.0.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2022-03-15 20:01:33 -04:00
zimoun
8a0713aef2
gnu: Add r-diffcyt. 
* gnu/packages/bioconductor.scm (r-diffcyt): New variable.
 2022-03-15 22:55:37 +01:00
zimoun
69af58e9a1
gnu: Add r-ga. 
* gnu/packages/cran.scm (r-ga): New variable.
 2022-03-15 22:55:01 +01:00
zimoun
76f96c891c
gnu: Add r-carrier. 
* gnu/packages/cran.scm (r-carrier): New variable.
 2022-03-15 22:54:14 +01:00
zimoun
71ec67ef3f
gnu: Add r-babelwhale. 
* gnu/packages/cran.scm (r-babelwhale): New variable.
 2022-03-15 22:53:09 +01:00
zimoun
59978546fe
gnu: Add r-polychrome. 
* gnu/packages/cran.scm (r-polychrome): New variable.
 2022-03-15 22:52:37 +01:00
zimoun
fdbc472bd1
gnu: Add r-scannotatr. 
* gnu/packages/bioconductor.scm (r-scannotatr): New variable.
 2022-03-15 22:50:42 +01:00
Ricardo Wurmus
bec806e2fc
gnu: r-sn: Update to 2.0.2. 
* gnu/packages/statistics.scm (r-sn): Update to 2.0.2.
 2022-03-15 22:14:47 +01:00
Ricardo Wurmus
b3dbb32bb3
gnu: r-dt: Update to 0.21. 
* gnu/packages/statistics.scm (r-dt): Update to 0.21.
 2022-03-15 22:14:47 +01:00
Ricardo Wurmus
b6a1cc89d4
gnu: r-simr: Update to 1.0.6. 
* gnu/packages/statistics.scm (r-simr): Update to 1.0.6.
[propagated-inputs]: Add r-lmertest.
[synopsis]: Change case and spelling.
[description]: Use complete sentences.
 2022-03-15 22:14:47 +01:00
Ricardo Wurmus
6c30609f23
gnu: r-rmarkdown: Update to 2.13. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.13.
[propagated-inputs]: Add r-bslib.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus
be72c056f6
gnu: r-withr: Update to 2.5.0. 
* gnu/packages/statistics.scm (r-withr): Update to 2.5.0.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus
f077fa0fd0
gnu: r-openssl: Update to 2.0.0. 
* gnu/packages/statistics.scm (r-openssl): Update to 2.0.0.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus
2af90fa53e
gnu: r-commonmark: Update to 1.8.0. 
* gnu/packages/statistics.scm (r-commonmark): Update to 1.8.0.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus
46a1b44782
gnu: r-desc: Update to 1.4.1. 
* gnu/packages/statistics.scm (r-desc): Update to 1.4.1.
[propagated-inputs]: Remove r-crayon; add r-cli.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus
f2386cafcf
gnu: r-bbmisc: Update to 1.12. 
* gnu/packages/statistics.scm (r-bbmisc): Update to 1.12.
[propagated-inputs]: Add r-data-table.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus
4bc8d24e16
gnu: r-locfit: Update to 1.5-9.5. 
* gnu/packages/statistics.scm (r-locfit): Update to 1.5-9.5.
 2022-03-15 22:14:46 +01:00