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127954 Commits (34f0b66193f4aefde3ff6da2cc7c852ed0301fd1)

Author SHA1 Message Date
John Kehayias 97f292b47f
gnu: sdl2: Update to 2.28.5. 
* gnu/packages/sdl.scm (sdl2): Update to 2.28.5.

Change-Id: I853776bf82e84499486d32012a9b3a4636226668
 2023-11-05 22:11:30 -05:00
dan 50521348c8
gnu: sdl2: Add vulkan-loader to rpath. 
* gnu/packages/sdl.scm (sdl2)[arguments]: Append the path of libvulkan.so to
rpath.
[inputs]: Add vulkan-loader.

Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
Change-Id: I17c8388f5f7b3bb063b79fd4981263994da129c0
 2023-11-05 22:09:53 -05:00
宋文武 37fc2c99e0
gnu: libepoxy: Hardcode paths to GLES libraries. 
Fixes <https://issues.guix.gnu.org/64981>.

* gnu/packages/gl.scm (libepoxy)[arguments]<#:phases>: Hardcode paths to
libGLESv1_CM.so.1 and libGLESv2.so.2.

Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
Change-Id: I9d68a2b8f9c4ffee13ea63ea973970bf1d4c8a6d
 2023-11-05 22:09:51 -05:00
John Kehayias ed2c3143f3
gnu: mesa: Update to 23.2.1. 
* gnu/packages/gl.scm (mesa): Update to 23.2.1.

Change-Id: I9014c29696317eeda2c86170ef64d57dd02fe8f4
 2023-11-05 22:09:50 -05:00
John Kehayias d70f2b788e
gnu: curl: Run tests in parallel. 
* gnu/packages/curl.scm (curl)[arguments]: Respect PARALLEL-TESTS? in check
phase, by setting TFLAGS (curl's test flags).

Change-Id: I54dfe32b757824fd3d2b89d10b88315c7e8b8d2a
 2023-11-05 22:09:48 -05:00
John Kehayias 00442f15d4
gnu: curl: Ungraft. 
* gnu/packages/curl.scm (curl): Update to 8.4.0 from graft, preserving...
[arguments]<#:phases>: ... check phase to skip failing test on Hurd.
[replacement]: Remove.
(curl/fixed): Remove variable.

Change-Id: I9243d6b3a9084d9c24884e755f2f42ffafca4205
 2023-11-05 22:09:47 -05:00
John Kehayias b5915131ae
gnu: nghttp2: Update to 1.58.0 and ungraft. 
* gnu/packages/web.scm (nghttp2): Update to 1.58.0.
[replacement]: Remove.
(nghttp2-1.57): Remove variable.

Change-Id: I737253295d6b3a832156acc8736167ee1ab470eb
 2023-11-05 22:09:45 -05:00
Zheng Junjie bfbea553e7
gnu: libxkbcommon: Update to 1.6.0. 
* gnu/packages/xdisorg.scm (libxkbcommon): Update to 1.6.0.

Change-Id: I8e3c6852d5ba7a16605b508d00b98084254d593a
Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
 2023-11-05 22:09:44 -05:00
John Kehayias 3d51d19c85
gnu: libdrm: Update to 2.4.117. 
* gnu/packages/xdisorg.scm (libdrm): Update to 2.4.117.

Change-Id: I99b94bc4afeb8c0447d5ac0b08f6ade327af7cc3
 2023-11-05 22:09:42 -05:00
Hilton Chain 57375d8db7
gnu: pixman: Update to 0.42.2. 
* gnu/packages/xdisorg.scm (pixman): Update to 0.42.2.

Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
Change-Id: Ibfe2d23a115d19ad32ca8e39de69aae108ec66d4
 2023-11-05 22:09:40 -05:00
John Kehayias 4bcaa9b75b
gnu: libxpm: Ungraft. 
* gnu/packages/xorg.scm (libxpm): Update to 3.5.17.
[replacement]: Remove.
[source]: Update URL.
(libxpm/fixed): Remove variable.

Change-Id: If84b6093f90fdf7f751b1f25a32df5b478fd71cb
 2023-11-05 22:09:39 -05:00
John Kehayias 5dcbd9accf
gnu: libx11: Ungraft. 
* gnu/packages/xorg.scm (libx11): Update to 1.8.7.
[replacement]: Remove.
[source]: Update URL.
(libx11-fixed): Remove variable.

Change-Id: I945c5d15ca7ef3ed9f5de348815f9644028b1c9a
 2023-11-05 22:09:36 -05:00
Liliana Marie Prikler 72e886328c
Merge branch 'master' into gnome-team 
Change-Id: I88d3789460d1a89917451d80405d89a2824006ac
 2023-11-04 07:43:44 +01:00
Clément Lassieur f54f36b363
gnu: passff-host: Add explicit references to inputs and remove some. 
This removes ‘coreutils’, ‘grep’, ‘sed’, ‘which’, ‘bash-minimal’ and
‘gnu-make’ inputs, which were only used by the Makefile and
install_host_app.sh.  Instead of running install_host_app.sh (through
‘make’) which does a few text substitutions, do the text substitutions with
Scheme code.  This simplifies things and avoids unnecessary native inputs.

* gnu/packages/browser-extensions.scm (passff-host)[build-system]: Change to
copy-build-system.
[arguments]: Copy passff.json and passff.py.  Do text substitutions on
them rather than running make.  Refer to ‘password-store’ and ‘python’ through
inputs rather than directly.
[inputs]: Add PASSWORD-STORE and PYTHON.

Change-Id: I8fdb757516a7c30eae36b15f2a8d91e1445b19a5
 2023-11-04 00:52:39 +01:00
Clément Lassieur 625cfb4c4c
gnu: password-store: Add missing ‘tail’ input. 
* gnu/packages/password-utils.scm (password-store)[arguments]: Add “tail” to
the list of requisites.
[inputs]: Add COREUTILS.

Change-Id: I7f59e6c0abfb5396b9548edaec08d3b0a7c0eb23
 2023-11-04 00:52:38 +01:00
Afkhami, Navid 10d728139d
gnu: Add r-ggbreak. 
* gnu/packages/cran.scm (r-ggbreak): New variable.

Change-Id: I27d62d0110fb56e77dc8cf82581adb6259317c2d
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-03 23:39:57 +01:00
Vinicius Monego 479fdc8451
gnu: python-pymc: Update to 5.9.1. 
* gnu/packages/statistics.scm (python-pymc): Update to 5.9.1.

Change-Id: I3d7927e7173f36ba4edeab06bd930c285432c29f
 2023-11-03 19:25:36 -03:00
Vinicius Monego 43d9fa0802
gnu: python-pytensor: Update to 2.17.3. 
* gnu/packages/python-science.scm (python-pytensor): Update to 2.17.3.

Change-Id: I2843aca1df4d43883bf643e6e363bd3700202c45
 2023-11-03 19:25:36 -03:00
Vinicius Monego 1879bfd88f
gnu: python-deepxde: Update to 1.10.0. 
* gnu/packages/machine-learning.scm (python-deepxde): Update to 1.10.0.

Change-Id: Ibc37f9e7df45c49f590beb1dda87236e853b88c1
 2023-11-03 19:25:36 -03:00
Vinicius Monego 96e8502faa
gnu: Add python-emcee. 
* gnu/packages/statistics.scm (python-emcee): New variable.
 2023-11-03 19:25:35 -03:00
Vinicius Monego a7d56852e3
gnu: Add python-salib. 
* gnu/packages/python-science.scm (python-salib): New variable.
 2023-11-03 19:25:35 -03:00
Vinicius Monego 9642b1c7af
gnu: python-openturns: Update to 1.21.1. 
* gnu/packages/statistics.scm (python-openturns): Update to 1.21.1.
 2023-11-03 19:25:35 -03:00
Vinicius Monego a55c3110be
gnu: python-opentsne: Update to 1.0.0. 
* gnu/packages/machine-learning.scm (python-opentsne): Update to 1.0.0.
 2023-11-03 19:25:35 -03:00
Vinicius Monego ef473d3422
gnu: symengine: Update to 0.11.1. 
* gnu/packages/algebra.scm (symengine): Update to 0.11.1.
 2023-11-03 19:25:31 -03:00
Ricardo Wurmus eb93ab2d14
gnu: r-gdata: Remove Excel from description. 
gdata 3.0.0 has removed support for reading Excel files.

* gnu/packages/statistics.scm (r-gdata)[description]: Update it.

Change-Id: Ic4090bc765d330d38136bf1b1dbbb6bb136edd39
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 8be2f44765
gnu: Remove r-sigpathway. 
This package has been removed with the release of Bioconductor 3.18.

* gnu/packages/bioconductor.scm (r-sigpathway): Remove variable.

Change-Id: I5cb9d938f370aa28b196f9cea95fb6024c2e6e37
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 38b5777ec8
gnu: r-rhdf5filters: Simplify. 
* gnu/packages/bioconductor.scm (r-rhdf5filters)[arguments]: Remove
'use-system-libraries phase and pass configure flags to disable bundled
libraries.

Change-Id: I2fb115e7b3df00cccb3f8d6659d465075d21f19b
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 78641cf9da
gnu: r-spams: Build with C++11. 
* gnu/packages/statistics.scm (r-spams)[arguments]: Add phase 'use-c++11.

Change-Id: Ie477af6afe8993919090f6c81e071cee542e69bc
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 142313cf0c
gnu: Remove r-genomegraphs. 
This package had been removed from Bioconductor with release 3.11.

* gnu/packages/bioconductor.scm (r-genomegraphs): Remove variable.

Change-Id: I73cc8cc8546089d91212176939b8c0c0a7afc309
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 0150529188
gnu: Remove r-wavetiling. 
This package had been removed from Bioconductor since release 3.12.

* gnu/packages/bioconductor.scm (r-wavetiling): Remove variable.

Change-Id: I5eb624d975f0eb170b263266b144eacf11944580
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus abaca151b2
gnu: r-mpo-db: Include HPO sqlite database. 
* gnu/packages/bioconductor.scm (r-mpo-db)[arguments]: Bypass fetching of the
database from the internet when in build environment.
[native-inputs]: Add MPO.sqlite.

Change-Id: Ic7228322b89ce78a85a9bd5ffbd985ccd906d268
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus b30127052e
gnu: r-readwriter: Update to 0.3.2-1.12d32cb. 
* gnu/packages/bioinformatics.scm (r-readwriter): Update to 0.3.2-1.12d32cb.

Change-Id: I412190ce94bee4e7b5fce27db7ef8a72188e74f4
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus c66c66ee3f
gnu: r-hpo-db: Include HPO sqlite database. 
* gnu/packages/bioconductor.scm (r-hpo-db)[arguments]: Bypass fetching of the
database from the internet when in build environment.
[native-inputs]: Add HPO.sqlite.

Change-Id: Ie01605ef2531d992fb85c07bae5cfaabda626ea6
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus a938342899
gnu: r-rhdf5lib: Adjust modifications to Makevars. 
* gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Adjust patch.

Change-Id: Iaef3d2d80c22de1c2a0b64e7c13f5fa3b8e5719d
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus c82c9c8090
gnu: r-phyloseq: Update to 1.46.0. 
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.46.0.

Change-Id: Id11b5e913529ac8efce0d046168f4a9dbe0dbabd
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 1c3e8ab395
gnu: r-tximeta: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.20.0.

Change-Id: I8d9c5d01efc8f6c64290cdfdd193d95cd1da9152
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 270d7e1079
gnu: r-tricycle: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-tricycle): Update to 1.10.0.

Change-Id: I72a9e1140c17ce8605bfe6e83cc290eb1ae2fad2
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 9ee38f4ee6
gnu: r-tcgabiolinks: Update to 2.30.0. 
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.30.0.

Change-Id: If7e571bfa6454bfa94dd395606575391dc506ecd
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 28480926a5
gnu: r-biscuiteer: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.16.0.

Change-Id: Ib6cffbbeedfe87932acfcbfb2b789b4c92a9bf81
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 53ebbff56c
gnu: r-omnipathr: Update to 3.10.1. 
* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.10.1.
[propagated-inputs]: Add r-lubridate and r-stringi.

Change-Id: Ia18b66848cd6996dfdc551bf4b182bb5ac3e17a8
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 41a4f01473
gnu: r-omicade4: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-omicade4): Update to 1.42.0.

Change-Id: I4369e5721116bf73f096ee39a516ada94c348872
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 73efb254d8
gnu: r-dmrseq: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.22.0.

Change-Id: I738c2fb7e0fa3e816d3767f854b8f9ed77425591
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus f6e56299e7
gnu: r-dada2: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-dada2): Update to 1.30.0.

Change-Id: I0955c3a61b4d81cd6809e2eb287d8acfcccfb789
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 407e9b2710
gnu: r-bsseq: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-bsseq): Update to 1.38.0.

Change-Id: Ie31f0b5c726da98a0caa4c658a5c62c1a5f40eaa
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 69d7d7a6db
gnu: r-biotmle: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-biotmle): Update to 1.26.0.

Change-Id: Ied1d1e649fba277aa724040af31334f664d2debd
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 9f2c8b711b
gnu: r-biotip: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-biotip): Update to 1.16.0.

Change-Id: I73503554b0271e5fe950c6da367b4893972f27e9
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus a7d1b8832a
gnu: r-bioqc: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-bioqc): Update to 1.30.0.

Change-Id: I0b5fd7cac1283a7f12a1221ad453eb56767e8b90
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus ee259a9ad9
gnu: r-bionetstat: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.22.0.

Change-Id: I92f2ebef0b65b947a719bdd1008f07ce279263a4
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus b0190a7d5c
gnu: r-bionet: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-bionet): Update to 1.62.0.

Change-Id: I0712a4ba67c27b32d6666e91d9515f0299e61848
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus 63f3a845ea
gnu: r-bionero: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-bionero): Update to 1.10.0.

Change-Id: I396a37dd28571a471b45d4d8aca6ce40a1cbd384
 2023-11-03 22:49:27 +01:00