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7212 Commits

Author SHA1 Message Date
Nicolas Goaziou 4df6eda30f gnu: Rename texlive-updmap.cfg' into texlive-local-tree'. 
* doc/build.scm (pdf-manual):
* doc/contributing.texi (Submitting Patches):
* gnu/packages/algebra.scm (pari-gp):
(giac):
* gnu/packages/assembly.scm (asl):
* gnu/packages/audio.scm (chow-tape-model):
* gnu/packages/bioconductor.scm (r-biocstyle):
* gnu/packages/bioinformatics.scm (discrover):
(phyml):
(velvet):
* gnu/packages/chemistry.scm (yaehmop):
* gnu/packages/chez.scm (chez-scheme-for-racket):
(stex-bootstrap):
(chez-web):
(chez-sockets):
* gnu/packages/cran.scm (r-papaja):
(r-prereg):
* gnu/packages/docbook.scm (dblatex):
* gnu/packages/emacs-xyz.scm (emacs-auctex):
* gnu/packages/engineering.scm (fastcap):
* gnu/packages/finance.scm (optionmatrix):
* gnu/packages/fsf.scm (book-faif):
* gnu/packages/gettext.scm (po4a):
(po4a-minimal):
* gnu/packages/graphics.scm (mmg):
* gnu/packages/graphviz.scm (dot2tex):
* gnu/packages/guile-xyz.scm (emacsy):
(guile-cv):
* gnu/packages/lisp.scm (sbcl):
* gnu/packages/maths.scm (cddlib):
(gnuplot):
(itpp):
(octave):
(suitesparse-amd):
(suitesparse-camd):
(suitesparse-cholmod):
(suitesparse-klu):
(suitesparse-ldl):
(suitesparse-mongoose):
(suitesparse-spex):
(suitesparse-spqr):
(suitesparse-umfpack):
(hypre):
* gnu/packages/music.scm (lilypond):
* gnu/packages/ocaml.scm (unison):
(ocaml-bibtex2html):
* gnu/packages/pdf.scm (extractpdfmark):
* gnu/packages/photo.scm (enblend-enfuse):
* gnu/packages/plotutils.scm (asymptote):
* gnu/packages/python-xyz.scm (python-numpy-documentation):
(python-ipython-documentation):
(python-pypandoc):
* gnu/packages/radio.scm (gnuradio):
(libosmo-dsp):
* gnu/packages/scheme.scm (mit-scheme):
* gnu/packages/security-token.scm (yubico-piv-tool):
* gnu/packages/sphinx.scm (python-sphinx):
(python-sphinx-5):
* gnu/packages/statistics.scm (r-with-tests):
(r-spams):
* gnu/packages/tex.scm (texlive-local-tree): Renamed from…
(texlive-updmap.cfg): … this. Deprecate the latter.
(texlive-biblatex-philosophy):
(texlive-bropd):
(texlive-fontsize):
(texlive-poetrytex):
(texlive-reverxii):
(texlive-stix):
(texlive-suftesi):
(texlive-thucoursework):
(texlive-ulqda):
(texlive-yathesis):
(texlive-makecell):
(texlive-robotarm):
(texlive-bbold):
(texlive-babel-romansh):
(texlive-polyglossia):
(texlive-innerscript):
(teximpatient):
(texlive-xkeyval):
(texlive-arabxetex):
(texlive-blox):
(texlive-ecgdraw):
(texlive-gradientframe):
(texlive-everyhook):
(texlive-actuarialangle):
(texlive-actuarialsymbol):
(texlive-autopdf):
(texlive-etaremune):
(texlive-extract):
(texlive-forarray):
(texlive-graphicx-psmin):
(texlive-ha-prosper):
(texlive-namespc):
(texlive-newspaper):
(texlive-powerdot):
(texlive-recipecard):
(texlive-show2e):
(texlive-tablists):
(texlive-ted):
(texlive-xargs):
(texlive-xpeek):
* gnu/packages/xdisorg.scm (xforms):
* gnu/packages/algebra.scm (gap):
* gnu/packages/cpp.scm (jthread):
* guix/lint.scm (check-inputs-should-be-native): Rename `texlive-updmap.cfg' into `texlive-local-tree'.

Change-Id: I129280807c418e57acbcbda399545ab27a9e0a33
 2025-05-06 11:25:06 +02:00
Ricardo Wurmus 446e86110e gnu: r-rhdf5: Disable tests. 
* gnu/packages/bioconductor.scm (r-rhdf5)[arguments]: Disable tests.

Change-Id: Idf7000f2471b9bac6c28f86122b78c230a61aa29
 2025-04-16 17:08:42 +02:00
Ricardo Wurmus 982efb8afd gnu: r-graph: Disable tests. 
* gnu/packages/bioconductor.scm (r-graph)[arguments]: Disable tests.

Change-Id: I9f5d2356d877f01f67bc0ab0e876f6e6c77132f8
 2025-04-16 15:49:35 +02:00
Ricardo Wurmus 3948d03772 gnu: r-coregx: Disable three tests. 
* gnu/packages/bioconductor.scm (r-coregx)[arguments]: Add phase
'disable-bad-tests.

Change-Id: Ic8d9425151250946d81770c328c9ad621a1d4a45
 2025-04-16 11:01:12 +02:00
Ricardo Wurmus 68268f5b93 gnu: Remove r-memes. 
This package cannot be used with a copy of the MEME Suite, which is
distributed under a non-free license.

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

Change-Id: Ia1ffa19b1f70b84b411e37a98a1452b696536f90
 2025-04-16 11:00:57 +02:00
Ricardo Wurmus 9302113694 gnu: bioconductor: Move packages to the correct section. 
* gnu/packages/bioconductor.scm (r-chihaya, r-cpp11bigwig, r-memes,
r-msexperiment): Move these packages to the section for generic packages.

Change-Id: Iba7ae7664c89ee2440b9e51b50926dbcc0898639
 2025-04-16 11:00:57 +02:00
Ricardo Wurmus b3c14cd7f7 gnu: r-pcaexplorer: Add test input. 
* gnu/packages/bioconductor.scm (r-pcaexplorer)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-markdown.

Change-Id: I558709266a972801e68373469aa5d4141b547971
 2025-04-16 11:00:57 +02:00
Ricardo Wurmus b274b66dbf gnu: r-tradeseq: Add test input. 
* gnu/packages/bioconductor.scm (r-tradeseq)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-clusterexperiment.

Change-Id: I21ba6dfd4fae27f6c6877ed64535d024259cd592
 2025-04-16 11:00:57 +02:00
Ricardo Wurmus 3ba03c8484 gnu: r-massspecwavelet: Add test input. 
* gnu/packages/bioconductor.scm (r-massspecwavelet)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-runit.

Change-Id: Ifc439e9baea1a83f6ee4a4d32dd76cb63e63ba08
 2025-04-16 11:00:57 +02:00
Ricardo Wurmus 8a5fd7e5a4 gnu: r-variancepartition: Add test input. 
* gnu/packages/bioconductor.scm (r-variancepartition)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-rfast.

Change-Id: Ie760f6ca655f749399bdaea88f7e622c1f07cfc7
 2025-04-16 11:00:56 +02:00
Ricardo Wurmus fddab1e499 gnu: r-tfbstools: Add test input. 
* gnu/packages/bioconductor.scm (r-tfbstools)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-jaspar2016.

Change-Id: I20a036d04ad4e23efd758408997594227258def5
 2025-04-16 11:00:56 +02:00
Ricardo Wurmus 2cd5b86b8c gnu: r-chippeakanno: Fix tests. 
* gnu/packages/bioconductor.scm (r-chippeakanno)[properties]: Record
updater-extra-native-inputs.
[arguments]: Add phase 'disable-bad-tests.
[native-inputs]: Add r-seqinr.

Change-Id: I82a17cc5cacf693ce109697e5d2c3cbe1937a420
 2025-04-16 11:00:56 +02:00
Ricardo Wurmus 92c9fd7cb1 gnu: r-seqarray: Add test input. 
* gnu/packages/bioconductor.scm (r-seqarray)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-digest.

Change-Id: If09c5a6fef540a928b32f0319f06eae8e9a76aeb
 2025-04-16 11:00:56 +02:00
Ricardo Wurmus 4137861fff gnu: r-mosdef: Disable one test. 
* gnu/packages/bioconductor.scm (r-mosdef)[arguments]: Add phase 'disable-bad-tests.

Change-Id: Ie5f715cfedd88154811fded0fb72ed619ae42fe8
 2025-04-16 11:00:56 +02:00
Ricardo Wurmus a8a8996524 gnu: r-ancombc: Add test input. 
* gnu/packages/bioconductor.scm (r-ancombc)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-microbiome.

Change-Id: I11bf5ffdfc4f9c9c92098d41abf4f31354fd0025
 2025-04-16 11:00:56 +02:00
Ricardo Wurmus 9e9e3d659b gnu: r-tcgautils: Disable some tests. 
* gnu/packages/bioconductor.scm (r-tcgautils)[arguments]: Add phase
'disable-bad-tests.

Change-Id: I1a4712e74ed1b02197440fbc70d1219c0d0d2401
 2025-04-16 11:00:56 +02:00
Ricardo Wurmus 208ff58bbb gnu: r-slingshot: Add test input. 
* gnu/packages/bioconductor.scm (r-slingshot)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-delayedmatrixstats.

Change-Id: Iffd910d576eca7279ea48b13d4ec9f287bb66a37
 2025-04-16 11:00:56 +02:00
Ricardo Wurmus 6a92622bdf gnu: Remove duplicate of r-leidenbase. 
* gnu/packages/bioconductor.scm (r-leidenbase): Remove variable.

Change-Id: Idedbc1b3924996beb92d7c566d811d34911d4416
 2025-04-16 11:00:55 +02:00
Ricardo Wurmus 740dd14b33 gnu: r-bgeedb: Disable tests. 
* gnu/packages/bioconductor.scm (r-bgeedb)[arguments]: Disable tests.

Change-Id: I76c3ecfead5ba4547ea137a8c2fc052c1612b796
 2025-04-16 11:00:55 +02:00
Ricardo Wurmus ec84c1c145 gnu: r-fishpond: Add test input. 
* gnu/packages/bioconductor.scm (r-fishpond)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-tximportdata.

Change-Id: Iacd3350a79a3b5234af9f7d4df91b8f10d7fa496
 2025-04-16 11:00:55 +02:00
Ricardo Wurmus 612d035a42 gnu: r-diffbind: Add test inputs. 
* gnu/packages/bioconductor.scm (r-diffbind)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-csaw and r-edger.

Change-Id: I4bd705dcf39eafdad0d169ea8d8d15f872ff682c
 2025-04-16 11:00:55 +02:00
Ricardo Wurmus 7ad183fb85 gnu: r-cummerbund: Correct indentation. 
* gnu/packages/bioconductor.scm (r-cummerbund): Correctly indent the expression.

Change-Id: I7cb31f8172c8977b9d2afd31cc9d68db3e5a91f7
 2025-04-16 11:00:55 +02:00
Ricardo Wurmus ee67d29e01 gnu: r-bionero: Add test input. 
* gnu/packages/bioconductor.scm (r-bionero)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-networkd3.

Change-Id: I45e5adacd16c70b194f878a7831550860ec4a16b
 2025-04-16 11:00:55 +02:00
Ricardo Wurmus cb2f52c7ea gnu: r-animalcules: Fix tests. 
* gnu/packages/bioconductor.scm (r-animalcules)[properties]: Record
updater-extra-native-inputs.
[arguments]: Add phase 'skip-bad-tests.
[native-inputs]: Add r-glmnet.

Change-Id: I24c6da9b6927cbf2756fb3411a5a29be19594276
 2025-04-16 11:00:55 +02:00
Ricardo Wurmus 6b33095a54 gnu: r-transcriptr: Add tests input. 
* gnu/packages/bioconductor.scm (r-transcriptr)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-txdb-hsapiens-ucsc-hg19-knowngene.

Change-Id: I12ec86acd5fb1fb7be24ffc947f035dc23945d59
 2025-04-16 11:00:54 +02:00
Ricardo Wurmus 8814cd92f8 gnu: r-trajectoryutils: Add test input. 
* gnu/packages/bioconductor.scm (r-trajectoryutils)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-biocparallel.

Change-Id: I01242353b10c92c2b548da5bf611438adb86a932
 2025-04-16 11:00:54 +02:00
Ricardo Wurmus 31cfb6f6e0 gnu: r-scry: Add test input. 
* gnu/packages/bioconductor.scm (r-scry)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-hdf5array.

Change-Id: I534051156a642e6f844be66a91a852b675d5fe9a
 2025-04-16 11:00:54 +02:00
Ricardo Wurmus 6c755665db gnu: r-screpertoire: Add test inputs. 
* gnu/packages/bioconductor.scm (r-screpertoire)[properties]: Record
updater-extra-native-inputs.
[arguments]: Add phase 'disable-bad-tests.
[native-inputs]: Add r-seurat and r-vdiffr.

Change-Id: I93c4a64abc7f4a02927e10203583c22dca70a176
 2025-04-16 11:00:54 +02:00
Ricardo Wurmus bca25b1e88 gnu: r-karyoploter: Add test input. 
* gnu/packages/bioconductor.scm (r-karyoploter)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg19.

Change-Id: I140222f23a34218da02ef792853663d836a527f5
 2025-04-16 11:00:54 +02:00
Ricardo Wurmus d89f7a9fb5 gnu: r-scannotatr: Disable tests. 
* gnu/packages/bioconductor.scm (r-scannotatr)[arguments]: Disable tests.

Change-Id: I6e0b0a9e62bb91bc00e16ce0de5f0f6baebb5e3f
 2025-04-16 11:00:54 +02:00
Ricardo Wurmus 460b62b507 gnu: r-bioccheck: Disable tests. 
* gnu/packages/bioconductor.scm (r-bioccheck)[arguments]: Disable tests.

Change-Id: I02e281be27ed93a7e0aff172fa5490492ccf6efc
 2025-04-16 11:00:53 +02:00
Ricardo Wurmus 3b72b4b999 gnu: r-txdbmaker: Add test input. 
* gnu/packages/bioconductor.scm (r-txdbmaker)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-runit.

Change-Id: I43a34f8a96060cd7742425c22959b8063c3e9643
 2025-04-16 11:00:53 +02:00
Ricardo Wurmus 311e86ed9f gnu: r-rcistarget: Add test inputs. 
* gnu/packages/bioconductor.scm (r-rcistarget)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-doparallel and
r-rcistarget-hg19-motifdbs-cisbponly-500bp.

Change-Id: Icf6bb96a8bce319b4497bb23caebe00f527543f4
 2025-04-16 11:00:53 +02:00
Ricardo Wurmus 4ee3e42ce2 gnu: r-alpine: Disable tests. 
* gnu/packages/bioconductor.scm (r-alpine)[arguments]: Disable tests.

Change-Id: If7bc7cfacaf3796ddb0b1457cfeb797a049bd5fe
 2025-04-16 11:00:53 +02:00
Ricardo Wurmus e95a7343e0 gnu: r-plyranges: Fix tests. 
* gnu/packages/bioconductor.scm (r-plyranges)[properties]: Record
updater-extra-native-inputs.
[arguments]: Disable three tests in new phase 'disable-bad-tests.
[native-inputs]: Add r-helloranges.

Change-Id: I4c091ee0b091a4152a62f4abf3a69573b486cedd
 2025-04-16 11:00:53 +02:00
Ricardo Wurmus 914ec5ff61 gnu: r-nebulosa: Add test input. 
* gnu/packages/bioconductor.scm (r-nebulosa)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-seurat.

Change-Id: I8a042f6658b027bc1e30b554792799e8b25cfa53
 2025-04-16 11:00:53 +02:00
Ricardo Wurmus 58f1ecca6f gnu: r-mousegastrulationdata: Disable tests. 
* gnu/packages/bioconductor.scm (r-mousegastrulationdata)[arguments]: Disable
tests.

Change-Id: I2728d77ce339469862396cb19bd3649684ec840d
 2025-04-16 11:00:53 +02:00
Ricardo Wurmus 1ed4151792 gnu: r-mlinterfaces: Add test input. 
* gnu/packages/bioconductor.scm (r-mlinterfaces)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-e1071.

Change-Id: Icb884f7b6deeba4146ab08536e0ce5c82c5aa6f9
 2025-04-16 11:00:52 +02:00
Ricardo Wurmus a9a54099a7 gnu: r-bandits: Add test input. 
* gnu/packages/bioconductor.scm (r-bandits)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-tximport.

Change-Id: I13b9f0b9e0ffb6f0de8396c70420b1cbedd7562e
 2025-04-16 11:00:52 +02:00
Ricardo Wurmus 432c3a4adf gnu: r-flowsorted-blood-epic: Disable tests. 
* gnu/packages/bioconductor.scm (r-flowsorted-blood-epic)[arguments]: Disable
tests.

Change-Id: Ie568042f1d6ab6577fbb8719a449e3d7dd4e81fe
 2025-04-16 11:00:52 +02:00
Ricardo Wurmus 56e314260d gnu: r-alevinqc: Add test input. 
* gnu/packages/bioconductor.scm (r-alevinqc)[native-inputs]: Add r-biocstyle.
[properties]: Record updater-extra-native-inputs.

Change-Id: I271c16a8823022dc27bf1a851def881d21d493d4
 2025-04-16 11:00:52 +02:00
Ricardo Wurmus fb0e8ec133 gnu: r-cner: Add test inputs. 
* gnu/packages/bioconductor.scm (r-cner)[arguments]: Add phase
'disable-bad-tests.
[native-inputs]: Add r-bsgenome-drerio-ucsc-danrer10 and
r-bsgenome-hsapiens-ucsc-hg38.

Change-Id: I61f28337a3b7f36e8163fe7ce66cd7d31fbfc77b
 2025-04-16 11:00:52 +02:00
Ricardo Wurmus 6b091044f3 gnu: r-basics: Fix tests. 
* gnu/packages/bioconductor.scm (r-basics)[arguments]: Disable ERCC tests.
[properties]; Record updater-extra-native-inputs.
[native-inputs]: Add r-scrnaseq.

Change-Id: Ic60eb7ca4ca17c1328d779352c1692a394814b9e
 2025-04-16 11:00:52 +02:00
Ricardo Wurmus f4115911c1 gnu: r-scrnaseq: Disable tests. 
* gnu/packages/bioconductor.scm (r-scrnaseq)[arguments]: Disable tests.

Change-Id: Ibf0483760443a12735d9e9eb8012084b4104f1d4
 2025-04-16 11:00:52 +02:00
Ricardo Wurmus 9cefde2bfa gnu: r-batchelor: Disable one more test. 
* gnu/packages/bioconductor.scm (r-batchelor)[arguments]: Disable additional test.

Change-Id: I6519df53252d5ffd1b9bedf18941742c66fa0c73
 2025-04-16 11:00:51 +02:00
Ricardo Wurmus c62a30615c gnu: r-bambu: Disable tests. 
* gnu/packages/bioconductor.scm (r-bambu)[arguments]: Disable tests.

Change-Id: I49c9c43dfb87edc5659ca1e07b53762763118a37
 2025-04-16 11:00:51 +02:00
Ricardo Wurmus da17b14a6d gnu: r-alabaster-matrix: Add test input. 
* gnu/packages/bioconductor.scm (r-alabaster-matrix)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-chihaya.

Change-Id: Ic5696d44b545deec2799aa9821279eb6edb02b3c
 2025-04-16 11:00:51 +02:00
Ricardo Wurmus 7bccb2feec gnu: r-tcgabiolinks: Add test inputs. 
* gnu/packages/bioconductor.scm (r-tcgabiolinks)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-edaseq, r-edger, and r-survminer.

Change-Id: I69d7936dbe829103c8fb3d9362d941e607b3166d
 2025-04-16 11:00:51 +02:00
Ricardo Wurmus a542ac06fa gnu: r-universalmotif: Add test inputs. 
* gnu/packages/bioconductor.scm (r-universalmotif)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Addd r-ape and r-ggtree.

Change-Id: Ie2feef6efeaaa33c9c2d18fbc2bc3949fb04042e
 2025-04-16 11:00:51 +02:00
Ricardo Wurmus b5fcc5706e gnu: r-sesame: Disable tests. 
* gnu/packages/bioconductor.scm (r-sesame)[arguments]: Disable tests.

Change-Id: I45d6e701bbfd091a0ef4703e71bf172f3c7ba6f6
 2025-04-16 11:00:51 +02:00