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171839 Commits

Author SHA1 Message Date
Ricardo Wurmus
dd9414f646 gnu: r-metafor: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/cran.scm (r-metafor)[arguments]: Remove phase
'delete-bad-tests; supply SKIPPED-TESTS argument instead.

Change-Id: I084e975dc3cebe5e1a5a7e1c09d6896bc7d056cc
 2026-04-02 07:37:09 +02:00
Ricardo Wurmus
8ade45da35 gnu: r-calculus: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/cran.scm (r-calculus)[arguments]: Remove phase
'delete-bad-tests; supply SKIPPED-TESTS argument instead.

Change-Id: Iaeb02ed0de4fb43f45f300b19abb9486b0548ad2
 2026-04-02 07:37:09 +02:00
Ricardo Wurmus
84a23fbbb0 gnu: r-lgr: Enable all tests. 
* gnu/packages/cran.scm (r-lgr)[arguments]: Remove phase 'delete-bad-tests.

Change-Id: Ie5fd4c214fd1d9e56560c23c988897d6557ea3c9
 2026-04-02 07:37:09 +02:00
Ricardo Wurmus
3a54283d12 gnu: r-zzlite: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/cran.scm (r-zzlite)[arguments]: Remove phase
'delete-bad-tests; supply TEST-DIRECTORY and SKIPPED-TESTS arguments instead.

Change-Id: I26401971d1a778c33e585dc1bd6294be2ad71cce
 2026-04-02 07:37:09 +02:00
Ricardo Wurmus
a3e0d40c9d gnu: r-paws-common: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/cran.scm (r-paws-common)[arguments]: Remove phase
'delete-bad-tests; supply TEST-DIRECTORY and SKIPPED-TESTS arguments instead.

Change-Id: I9910f74f9096c5c0e1a8dd4fc027385132ea231d
 2026-04-02 07:37:08 +02:00
Ricardo Wurmus
244146fe1d gnu: r-ggh4x: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/cran.scm (r-ggh4x)[arguments]: Remove phase
'delete-bad-tests; supply TEST-DIRECTORY and SKIPPED-TESTS arguments instead.

Change-Id: I888f7a62a74037fc2b8ec4894452043c8e195d6a
 2026-04-02 07:37:08 +02:00
Ricardo Wurmus
f10a9a4f19 gnu: r-forestplot: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/cran.scm (r-forestplot)[arguments]: Remove phase
'delete-bad-tests; supply TEST-DIRECTORY and SKIPPED-TESTS arguments instead.

Change-Id: I785bd439887f016c4863b89c947292e357f65c75
 2026-04-02 07:37:08 +02:00
Ricardo Wurmus
d563d8c242 gnu: r-rliger: Update to 2.2.1. 
* gnu/packages/cran.scm (r-rliger, r-liger): Move variable definitions from here...
* gnu/packages/bioconductor.scm (r-rliger, r-liger): ...to here; update to 2.2.1.
[source]: Update source URL; remove obsolete snippet.
[arguments]: Remove phases 'strip-jar-timestamps and 'build-java-part.
[native-inputs]: Remove icedtea, optimizer-src, unzip, and zip; add
r-circlize, r-complexheatmap, r-testthat, and r-viridis.
[propagated-inputs]: Remove r-cowplot, r-dosnow, r-fnn, r-foreach, r-ggrepel,
r-hmisc, r-ica, r-irlba, r-mclust, r-plyr, r-rann-l1, r-riverplot, and
r-rtsne; add r-cli, r-delayedarray, r-hdf5array, r-hdf5r, r-leidenalg, r-lifecycle,
r-magrittr, r-rann, r-rcppplanc, r-rcppprogress, r-rlang, r-s4vectors,
r-scales, and r-uwot.

Change-Id: I35bcdd94954f6fdf5aa641f9756c65a0efe1008e
 2026-04-02 07:37:08 +02:00
Ricardo Wurmus
eb3fce3a00 gnu: Remove r-swne. 
This package has been abandoned years ago.  It depends on liger, which has
been removed from CRAN on 2024-06-14.  It is unlikely to work with the newer
version of rliger.

* gnu/packages/statistics.scm (r-swne): Remove variable.

Change-Id: Ie7d7b3c9e1726b8219ad816c4b8db7621708c3b2
 2026-04-02 07:37:08 +02:00
Ricardo Wurmus
10a1b8079d gnu: r-bpcells: Do not build bundled highway library. 
* gnu/packages/bioinformatics.scm (r-bpcells)[source]: Remove bundled highway
sources.
[arguments]: Fix check.
[inputs]: Add google-highway.

Change-Id: Ib70e7f9f64053b9e840c8c5f04e966beb4cf2869
 2026-04-02 07:37:08 +02:00
Ricardo Wurmus
999ae6d830 gnu: Add r-rcppplanc. 
* gnu/packages/cran.scm (r-rcppplanc): New variable.

Change-Id: Iea5a920cf93e17a8067dce4ca84e31962acf76d6
 2026-04-02 07:37:08 +02:00
Ricardo Wurmus
665a4bb53c gnu: Add r-hdf5r-extra. 
* gnu/packages/cran.scm (r-hdf5r-extra): New variable.

Change-Id: I40287d71ed7230de84257f69f35c64515bb1d0d4
 2026-04-02 07:37:08 +02:00
Ricardo Wurmus
66f0fbab6f gnu: Add r-easy-utils. 
* gnu/packages/cran.scm (r-easy-utils): New variable.

Change-Id: I311f043a02fe13bda64a9e3679e20d72aa001b2d
 2026-04-02 07:37:08 +02:00
Ricardo Wurmus
03e46fcf61 gnu: Add r-highfive. 
* gnu/packages/cran.scm (r-highfive): New variable.

Change-Id: I67010dec8965cc5c80420f58d461f83456a29243
 2026-04-02 07:37:07 +02:00
Ricardo Wurmus
831e2c3570 gnu: r-xgboost: Enable all tests. 
* gnu/packages/cran.scm (r-xgboost)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: If226037e79cd12e2156ba8fd7e3ca623814b18bc
 2026-04-02 07:37:07 +02:00
Ricardo Wurmus
19a7acba62 gnu: r-spam: Use SKIPPED-TESTS argument. 
* gnu/packages/cran.scm (r-spam)[arguments]: Remove phase
'delete-bad-tests; replace it with SKIPPED-TESTS argument.

Change-Id: I7b94239df462f5575dbd9beeea8e830b522b8cdd
 2026-04-02 07:37:07 +02:00
Ricardo Wurmus
6eebaaa4db gnu: r-assertive-properties: Disable only one test. 
* gnu/packages/cran.scm (r-assertive-properties)[arguments]: Remove phase
'delete-bad-tests; replace it with SKIPPED-TESTS argument.

Change-Id: I697b4a812d377c5bcce636f406ed65e70f30b98f
 2026-04-02 07:37:07 +02:00
Ricardo Wurmus
410b0cdb1a gnu: r-pander: Be more explicit about disabling tests. 
* gnu/packages/cran.scm (r-pander)[native-inputs]: Add r-descr,
r-microbenchmark, r-nlme, r-randomforest, r-rms, r-survival, r-tables, and
r-zoo.
[arguments]: Remove phase 'delete-bad-tests; replace it with TEST-DIRECTORY
and SKIPPED-TESTS arguments; add phase 'testthat-compatibility.
[properties]: Record more extra inputs.

Change-Id: I480b905df23420be6a3c9d9547ee43abcb9fec24
 2026-04-02 07:37:07 +02:00
Ricardo Wurmus
4b1eeff1d7 gnu: r-sessioninfo: Replace custom phase with test arguments. 
* gnu/packages/cran.scm (r-sessioninfo)[arguments]: Remove phase
'delete-bad-tests; provide SKIPPED-TESTS argument instead.

Change-Id: I1103be5957f08f81ca0a82cfad232c76aa13db18
 2026-04-02 07:37:07 +02:00
Ricardo Wurmus
dd67937e23 gnu: r-usethis: Replace custom phase with test arguments. 
* gnu/packages/cran.scm (r-usethis)[arguments]: Remove phase
'delete-bad-tests; provide SKIPPED-TESTS argument instead.

Change-Id: I2514272e09dae46183a250c66b5c097689b54467
 2026-04-02 07:37:07 +02:00
Ricardo Wurmus
1f40f7f9aa gnu: r-libcoin: Replace custom phase with test arguments. 
* gnu/packages/cran.scm (r-libcoin)[arguments]: Remove phase
'delete-bad-tests; provide TEST-DIRECTORY and SKIPPED-TESTS arguments instead.

Change-Id: Ia8b2765472a1883862c70a3887514c1e5c1cd57b
 2026-04-02 07:37:07 +02:00
Ricardo Wurmus
4a0e418e42 gnu: r-ggformula: Replace custom phase with test arguments. 
* gnu/packages/cran.scm (r-ggformula)[arguments]: Remove phase
'delete-bad-tests; provide SKIPPED-TESTS argument instead.

Change-Id: Id64f18c83b7a8168bd83c6ccf3e2aaa61db92687
 2026-04-02 07:37:07 +02:00
Ricardo Wurmus
300a4609de gnu: r-reformulas: Replace custom phase with test arguments. 
* gnu/packages/cran.scm (r-reformulas)[arguments]: Remove phase
'delete-bad-tests; provide TEST-DIRECTORY and SKIPPED-TESTS arguments instead.

Change-Id: Ic6e25632ba131543d59b69ee9776d46c385329c1
 2026-04-02 07:37:06 +02:00
Ricardo Wurmus
18aa6965f2 gnu: r-network: Enable all tests. 
* gnu/packages/cran.scm (r-network)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: Ie1f6a9c0cb521b217a5c65e16acbb26eeacfc3b9
 2026-04-02 07:37:06 +02:00
Ricardo Wurmus
1aaeadfc5e gnu: r-shinytree: Replace custom phase with test arguments. 
* gnu/packages/cran.scm (r-shinytree)[arguments]: Remove phase
'delete-bad-tests; provide SKIPPED-TESTS argument instead.

Change-Id: I176882b178735503b08cad1989b7e9e94f67b5ce
 2026-04-02 07:37:06 +02:00
Ricardo Wurmus
36a628f71f gnu: r-httptest2: Replace custom phase with test arguments. 
* gnu/packages/cran.scm (r-httptest2)[arguments]: Remove phase
'delete-bad-tests; provide SKIPPED-TESTS argument instead.

Change-Id: I5716ae7a024dff64e287c75b04dfa6c07a3c4d1e
 2026-04-02 07:37:06 +02:00
Ricardo Wurmus
aa1940e124 gnu: r-zoo: Replace custom phase with test arguments. 
* gnu/packages/cran.scm (r-zoo)[arguments]: Remove phase
'delete-bad-tests; provide SKIPPED-TESTS argument instead.

Change-Id: Ia50dff58e20faa9be118d4648b3aa2b08cb0461c
 2026-04-02 07:37:06 +02:00
Ricardo Wurmus
6e0c466751 gnu: r-mosaiccore: Replace custom phase with test arguments. 
* gnu/packages/cran.scm (r-mosaiccore)[arguments]: Remove phase
'delete-bad-tests; provide SKIPPED-TESTS argument instead.

Change-Id: Ibbe98827c995a92e9a7aadcc0085422973990ee5
 2026-04-02 07:37:06 +02:00
Ricardo Wurmus
fffc3c0da0 gnu: r-dendextend: Enable all but one test. 
* gnu/packages/cran.scm (r-dendextend)[arguments]: Remove phase
'delete-bad-tests; supply SKIPPED-TESTS argument instead.

Change-Id: I7dd31bedd66fa9fe8b57c6e4e13f2c952231fe0e
 2026-04-02 07:37:06 +02:00
Ricardo Wurmus
694359fbcb gnu: r-fitdistrplus: Enable all tests. 
* gnu/packages/cran.scm (r-fitdistrplus)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I2b5468d168ac4f73b2343e54c5d27f1d0f0cec2c
 2026-04-02 07:37:06 +02:00
Ricardo Wurmus
c0c26f5aaf gnu: Add r-tables. 
* gnu/packages/cran.scm (r-tables): New variable.

Change-Id: Ic247e02577ce0dfadc4f8628f34f0ab454f621b0
 2026-04-02 07:37:06 +02:00
Ricardo Wurmus
105f255702 gnu: Add r-descr. 
* gnu/packages/cran.scm (r-descr): New variable.

Change-Id: I5de2304cb863325e6f16059492f53d45a585edf4
 2026-04-02 07:37:06 +02:00
Ricardo Wurmus
02f4332dc0 gnu: Add r-merderiv. 
* gnu/packages/cran.scm (r-merderiv): New variable.

Change-Id: I7eba9b8c0ab6f3c034bd7b9fe17bd61926fcef18
 2026-04-02 07:37:05 +02:00
Ricardo Wurmus
e87e15ba2d gnu: r-lme4: Skip one test. 
* gnu/packages/cran.scm (r-lme4)[arguments]: Skip one test.

Change-Id: I6662e45cebfc42678f7893ea66890b98db0091e5
 2026-04-02 07:37:05 +02:00
Ricardo Wurmus
d67c6db5d2 gnu: r-rcppml: Update to 0.3.7.1. 
* gnu/packages/cran.scm (r-rcppml): Update to 0.3.7.1.
[arguments]: Delete phase 'disable-bad-tests.
[native-inputs]: Add r-nnlm.

Change-Id: I508da20cfc16cd5655f0d01712f9970b3630e326
 2026-04-02 07:37:05 +02:00
Ricardo Wurmus
02e6a8fd5d gnu: r-robustbase: Replace custom phase with test arguments. 
* gnu/packages/cran.scm (r-robustbase)[arguments]: Remove phase
'delete-bad-tests; provide TEST-DIRECTORY and SKIPPED-TESTS arguments.

Change-Id: Icfbb16c47a50acbc5df14ccaa319064ee84b1a77
 2026-04-02 07:37:05 +02:00
Ricardo Wurmus
373064a976 gnu: r-with-tests, r-minimal: Update to 4.5.3. 
* gnu/packages/statistics.scm (r-with-tests, r-minimal): Update to 4.5.3.

Change-Id: I34bf7bf5706192d7c90f9f29cb1f9cfcde35b7fb
 2026-04-02 07:37:05 +02:00
Ricardo Wurmus
09013f9d0e gnu: r-rcppparallel: Use onetbb library. 
* gnu/packages/cran.scm (r-rcppparallel)[arguments]: Remove phases
'relax-gcc-14-strictness and 'gcc-compatibility.
[inputs]: Replace tbb-2020 with onetbb.

Change-Id: Ib49e21a7b44df67a46fdda899d95aa05d8b1ace9
 2026-04-02 07:37:05 +02:00
Ricardo Wurmus
06475ac99e gnu: r-nanotime: Update to 0.3.13. 
* gnu/packages/cran.scm (r-nanotime): Update to 0.3.13.
[native-inputs]: Add r-rcpp.

Change-Id: I489a84d38f24b60a097abf2c994664c14303417b
 2026-04-02 07:37:05 +02:00
Ricardo Wurmus
dec4c2c1e6 gnu: r-openmx: Update to 2.22.11. 
* gnu/packages/cran.scm (r-openmx): Update to 2.22.11.

Change-Id: Ibb358357f1e7e7ee0a42275d4f3709a1dc21055a
 2026-04-02 07:37:05 +02:00
Ricardo Wurmus
76426609b2 gnu: r-terra: Update to 1.9-1. 
* gnu/packages/cran.scm (r-terra): Update to 1.9-1.

Change-Id: I53951fe20076d8cfac359ea00f749756ada0225f
 2026-04-02 07:37:04 +02:00
Ricardo Wurmus
d2b651f16f gnu: r-rcppalgos: Update to 2.10.0. 
* gnu/packages/cran.scm (r-rcppalgos): Update to 2.10.0.

Change-Id: I76ec35173325dea89b62a5191cc7d4ba26b563d1
 2026-04-02 07:37:04 +02:00
Ricardo Wurmus
f08319c284 gnu: r-ncdfcf: Update to 0.8.2. 
* gnu/packages/cran.scm (r-ncdfcf): Update to 0.8.2.

Change-Id: I5c5affb6ec88c9c14a3d12cbb833929bcc10ddb6
 2026-04-02 07:37:04 +02:00
Ricardo Wurmus
ade2b04a62 gnu: r-nanonext: Update to 1.8.1. 
* gnu/packages/cran.scm (r-nanonext): Update to 1.8.1.

Change-Id: I1da9b899d4e7378ce32a9dbc73487987391a3f7b
 2026-04-02 07:37:04 +02:00
Ricardo Wurmus
1287f4ef5d gnu: r-ctrdata: Update to 1.26.1. 
* gnu/packages/cran.scm (r-ctrdata): Update to 1.26.1.

Change-Id: I6750a3d33588da297d8b062264dec1f23254ca3f
 2026-04-02 07:37:04 +02:00
Ricardo Wurmus
b363bd6701 gnu: r-pagoda2: Update to 1.0.14. 
* gnu/packages/cran.scm (r-pagoda2): Update to 1.0.14.

Change-Id: I1b36fe526b9c933ce393a163a4850741bb8fca51
 2026-04-02 07:37:04 +02:00
Ricardo Wurmus
9aee49d65d gnu: r-phyloseq: Update to 1.54.2. 
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.54.2.

Change-Id: Ide709c5d2e6186c9d816c65acbe3786917b549b4
 2026-04-02 07:37:04 +02:00
Ricardo Wurmus
e360849ac5 gnu: r-sparsearray: Update to 1.10.9. 
* gnu/packages/bioconductor.scm (r-sparsearray): Update to 1.10.9.

Change-Id: I9ca97aae122e788997d3f74872c1df1229be4bca
 2026-04-02 07:37:04 +02:00
Ricardo Wurmus
2184edcc66 gnu: r-enrichplot: Update to 1.30.5. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.30.5.

Change-Id: I5e3ee050327a5ea536e46a8136f2349e4440aefe
 2026-04-02 07:37:04 +02:00
Ricardo Wurmus
f767cfc824 gnu: r-systempiper: Update to 2.16.4. 
* gnu/packages/bioconductor.scm (r-systempiper): Update to 2.16.4.

Change-Id: Iac7cf251a58614b71e3d2c82e52a7180f44a55a8
 2026-04-02 07:37:04 +02:00