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Author SHA1 Message Date
Jack Hill
be00aec4e4 gnu: webkitgtk: Update to 2.42.2. 
* gnu/packages/webkit.scm (webkitgtk): Update to 2.42.2.

Change-Id: Id2a0cd7ec512a088ba6faf1a0eb7e7b500d95f7e
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2023-11-17 20:30:14 +01:00
Liliana Marie Prikler
3c2f4ae417 gnu: libadwaita: Update to 1.4.0. 
* gnu/packages/gnome.scm (libadwaita): Update to 1.4.0.

Change-Id: I322caffb65a2b19f87e4c03a267a85c155d65124
 2023-11-17 20:30:14 +01:00
Liliana Marie Prikler
4963d4c6bb gnu: appstream: Update to 0.16.4. 
* gnu/packages/freedesktop.scm (appstream): Update to 0.16.4.
[arguments]<#:configure-flags>: Add “-Dsystemd=false”.
<#:phases>: Adjust accordingly.

Change-Id: I9c22cbd10681666c20e848dbc1e52ca08431d984
 2023-11-11 01:38:07 +01:00
Liliana Marie Prikler
02555467ce gnu: libxmlb: Update to 0.3.14. 
* gnu/packages/xml.scm (libxmlb): Update to 0.3.14.

Change-Id: I8571b3f46a5528d04cc2ea013ff2ab0ef4ba19da
 2023-11-11 01:37:59 +01:00
Liliana Marie Prikler
a7e831a556 gnu: gtk: Update to 4.12.3. 
* gnu/packages/gtk.scm (gtk): Update to 4.12.3.
[source]: Remove snippet.
[arguments]<#:configure-flags>: Add “--no-suite=headless”.
<#:phases>: Also patch text-color tests in gsk/nodeparser.

Change-Id: Iedabfd12ae4f60f02ea21f427b85aeb6b17d03d6
 2023-11-11 01:19:20 +01:00
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
Ricardo Wurmus
4ccceb31b9 gnu: r-biomvcclass: Update to 1.70.0. 
* gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.70.0.

Change-Id: I0c6214669ec284d314eb7dc90270558934070e4b
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
b4e803a8a9 gnu: r-mvcclass: Update to 1.76.0. 
* gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.76.0.

Change-Id: I6e7fa851c804009ae41a955b117d95b33fd1b2f0
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
c91a1a8bc8 gnu: r-biomformat: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.30.0.

Change-Id: I661d11f81a0dedbc8381b5ba1806643b5ff52aa6
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
2b4dcd4a7b gnu: r-biodb: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-biodb): Update to 1.10.0.

Change-Id: If1d14855b2bf134741c54c0a51daefdf2b80a49f
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
9480ea5046 gnu: r-biocthis: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.12.0.

Change-Id: I8400ebfd178f916488e022152e75db59f05994e6
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
327c9bd7c8 gnu: r-basilisk: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.14.0.

Change-Id: I86f5306de138eb1fedffbae65c14f9acd504c86c
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
b5527cc3c6 gnu: r-basilisk-utils: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.14.0.

Change-Id: I6113042a10770ee50e4ef997ee41fe109f917885
 2023-11-03 22:49:27 +01:00