From unknown Sun Jun 22 00:54:54 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#59329] [PATCH 000/444] Update Bioconductor to 3.16 Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Thu, 17 Nov 2022 03:57:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 59329 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 59329@debbugs.gnu.org Cc: zimoun , rekado@elephly.net X-Debbugs-Original-To: guix-patches@gnu.org X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by submit@debbugs.gnu.org id=B.166865737331492 (code B ref -1); Thu, 17 Nov 2022 03:57:02 +0000 Received: (at submit) by debbugs.gnu.org; 17 Nov 2022 03:56:13 +0000 Received: from localhost ([127.0.0.1]:58693 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ovW0a-0008Br-Mx for submit@debbugs.gnu.org; Wed, 16 Nov 2022 22:56:13 -0500 Received: from lists.gnu.org ([209.51.188.17]:37982) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ovW0W-0008Bh-9l for submit@debbugs.gnu.org; Wed, 16 Nov 2022 22:56:11 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ovW0W-0003Xb-1q for guix-patches@gnu.org; Wed, 16 Nov 2022 22:56:08 -0500 Received: from mail-wr1-x434.google.com ([2a00:1450:4864:20::434]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ovW0T-0003Xy-1w for guix-patches@gnu.org; Wed, 16 Nov 2022 22:56:07 -0500 Received: by mail-wr1-x434.google.com with SMTP id j15so940534wrq.3 for ; Wed, 16 Nov 2022 19:56:04 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:from:to:cc:subject:date:message-id:reply-to; bh=+cnxELpm5gFZMk8HKCiZVPV6JO92XtfwJdUckl1WNvM=; b=nD9bcA0P5miTHxXnJDWVMOCBCBeAnnIvg7Uq6+yMt4OfPE5b3ABb8rGa7pOihF5AZ8 0IbR4qKfjzspQnJ7Ir2EM06f8U854eNCsMhckmq4CuA4pbg2DvjJEqRsNPxl4jqbIx5O galiT3NkPj/YxZsp5GXINPzVobk5NuzvuOwDJfI6JqJ0AN2NErtp+X8hs5JQM4xboSYY b+0WGiJXERJsXis7F265rDqoy4/3pGBgD2uLyh33MmuqIaTFqu2zlwEPACaAlg6K0AWo A4neYI//ooIxO8ZF1e0cvcym5ujkx+oE8PK4a2WqK1JVDISsK5LezfvNK2sKnI9xTLys rZbA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:x-gm-message-state:from:to:cc:subject:date:message-id :reply-to; bh=+cnxELpm5gFZMk8HKCiZVPV6JO92XtfwJdUckl1WNvM=; b=66FJvAtcFfagSmTkR1vNLgyQm/lsvZtn0iKnFCoeK0xKEVvchTSn7I+vIm1ROggkhd 0n/Rgi0+yJlFxpVIVe8NhRzpmUxB846AAPN6ITh1PutGZEDAW56gH/A6wwnpR2jCZwNZ OQ/1OBOn1qFg0KjnEa3NfssYQ5jeBcW3LcnGU+RYSW47DHq5cKXNOcZ0Fcs2UX1uj8xP 53vKC30k+i9G0vdaCca2eIa3Rboe4CXnMtG/lFM2x7btITYCfD8Pr+uryhbfRyYeaBS9 s/JydqhCjFXjOZyaalJXtahQo5q8713qQupyCqxfuD5T6lszyaMzT2C+sB7asiFb9nRm +U4w== X-Gm-Message-State: ANoB5pk6JvR+P5Nrz3FJtcc3i54/6LSFzDaQi0RyAphgnEZHUCEYmB+q WRw4F+FG/jv1NxF81Z3CS0GQ+WELsyQ= X-Google-Smtp-Source: AA0mqf7DOneRqTjIoA0Hv76jh3SCt/PtSha6Hx3Jx/iytR4yMm8vNraaHY5RyUvg67BQHabjm/7Y4w== X-Received: by 2002:a05:6000:1d92:b0:241:6e0a:bfe6 with SMTP id bk18-20020a0560001d9200b002416e0abfe6mr284496wrb.34.1668657362726; Wed, 16 Nov 2022 19:56:02 -0800 (PST) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g11-20020a5d540b000000b0022cdeba3f83sm16462369wrv.84.2022.11.16.19.56.02 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 16 Nov 2022 19:56:02 -0800 (PST) From: zimoun Date: Thu, 17 Nov 2022 04:55:54 +0100 Message-Id: <20221117035554.1307869-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.38.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::434; envelope-from=zimon.toutoune@gmail.com; helo=mail-wr1-x434.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) Hi Ricardo, Sorry for the delay. Here some work, not fully polished but the final state builds. However, it requires the update of r-ggplot2 -- and this update breaks the leaf package r-ggtern. Note that the update of r-ggplot2 is only required by the Bioconductor package r-fgsea, if I remember correctly. I marked some patches as DRAFT, because it remains something -- for instance, refresh recommended the addition of a package but it builds and the tests seem fine without, so I do not know if it is a false-positive of refresh. Well, I am rebuilding to see if these updates introduce non-reproducible packages. But that's not blocking, IMHO. Last, I will not spam guix-patches with 444 emails. Please checkout the branch wip-bioconductor on: https://gitlab.com/zimoun/guix/-/tree/wip-bioconductor Cheers, simon zimoun (444): DRAFT update 3.16. gnu: Add r-hdo-db. DRAFT gnu: r-ggplot2: Update to 3.4.0. gnu: r-ggprism: Update to 1.0.4. gnu: Add r-biocbaseutils. gnu: Add r-rorcid. gnu: Add r-gson. gnu: r-abarray: Update to 1.66.0. gnu: r-absseq: Update to 1.52.0. gnu: r-adam: Update to 1.14.0. gnu: r-adamgui: Update to 1.14.0. gnu: r-adimpute: Update to 1.8.0. gnu: r-adsplit: Update to 1.68.0. gnu: r-affixcan: Update to 1.16.0. gnu: r-affyrnadegradation: Update to 1.44.0. gnu: r-agdex: Update to 1.46.0. gnu: r-aggregatebiovar: Update to 1.8.0. gnu: r-agilp: Update to 3.30.0. gnu: r-adductomicsr: Update to 1.14.0. gnu: r-agimicrorna: Update to 2.48.0. gnu: r-airpart: Update to 1.6.0. gnu: r-amountain: Update to 1.24.0. gnu: r-amaretto: Update to 1.13.0. gnu: r-anaquin: Update to 2.22.0. gnu: r-aldex2: Update to 1.30.0. gnu: r-aneufinder: Update to 1.26.0. gnu: r-anf: Update to 1.20.0. gnu: r-annmap: Update to 1.40.0. gnu: r-antiprofiles: Update to 1.38.0. gnu: r-aseb: Update to 1.42.0. gnu: r-asgsca: Update to 1.32.0. gnu: r-aspli: Update to 2.8.0. gnu: r-assessorf: Update to 1.16.0. gnu: r-asset: Update to 2.16.0. gnu: r-atena: Update to 1.4.0. gnu: r-atsnp: Update to 1.14.0. gnu: r-attract: Update to 1.50.0. gnu: r-awfisher: Update to 1.12.0. gnu: r-awst: Update to 1.6.0. gnu: r-baalchip: Update to 1.24.0. gnu: r-basespacer: Update to 1.42.0. gnu: r-bac: Update to 1.58.0. gnu: r-bader: Update to 1.36.0. gnu: r-badregionfinder: Update to 1.26.0. gnu: r-bambu: Update to 3.0.1. gnu: r-bandits: Update to 1.14.0. gnu: r-banocc: Update to 1.22.0. gnu: r-barcodetrackr: Update to 1.6.0. gnu: r-biocversion: Update to 3.16.0. gnu: r-biocgenerics: Update to 0.44.0. gnu: r-coverageview: Update to 1.36.0. gnu: r-cummerbund: Update to 2.40.0. gnu: r-dama: Update to 1.70.0. gnu: r-damefinder: Update to 1.10.0. gnu: r-dearseq: Update to 1.10.0. gnu: r-debcam: Update to 1.16.0. gnu: r-decipher: Update to 2.26.0. gnu: r-deco: Update to 1.13.0. gnu: r-decomplexdisease: Update to 1.18.0. gnu: r-decomptumor2sig: Update to 2.14.0. gnu: r-deconrnaseq: Update to 1.40.0. gnu: r-decontam: Update to 1.18.0. gnu: r-deconvr: Update to 1.4.0. gnu: r-decoupler: Update to 2.4.0. gnu: r-deepsnv: Update to 1.44.0. gnu: r-delayedarray: Update to 0.24.0. gnu: r-derfinderhelper: Update to 1.32.0. gnu: r-drimseq: Update to 1.26.0. gnu: r-bluster: Update to 1.8.0. gnu: r-ideoviz: Update to 1.34.0. gnu: r-infercnv: Update to 1.14.0. gnu: r-iranges: Update to 2.32.0. gnu: r-isoformswitchanalyzer: Update to 1.20.0. gnu: r-affy: Update to 1.76.0. gnu: r-affycomp: Update to 1.74.0. gnu: r-affycompatible: Update to 1.58.0. gnu: r-affycontam: Update to 1.56.0. gnu: r-affycoretools: Update to 1.70.0. gnu: r-affyio: Update to 1.68.0. gnu: r-affxparser: Update to 1.70.0. gnu: r-annotate: Update to 1.76.0. gnu: r-annotationdbi: Update to 1.60.0. gnu: r-annotationfilter: Update to 1.22.0. gnu: r-annotationforge: Update to 1.40.0. gnu: r-annotationhub: Update to 3.6.0. gnu: r-aroma-light: Update to 3.28.0. gnu: r-bamsignals: Update to 1.30.0. gnu: r-biobase: Update to 2.58.0. gnu: r-biomart: Update to 2.54.0. gnu: r-biocparallel: Update to 1.32.1. gnu: r-biostrings: Update to 2.66.0. gnu: r-biovizbase: Update to 1.46.0. gnu: r-bsgenome: Update to 1.66.1. gnu: r-category: Update to 2.64.0. gnu: r-chipseeker: Update to 1.34.0. gnu: r-chipseq: Update to 1.48.0. gnu: r-complexheatmap: Update to 2.14.0. gnu: r-copywriter: Update to 2.29.0. gnu: r-deseq2: Update to 1.38.1. gnu: r-dexseq: Update to 1.44.0. gnu: r-diffcyt: Update to 1.18.0. gnu: r-dirichletmultinomial: Update to 1.40.0. gnu: r-dittoseq: Update to 1.10.0. gnu: r-edaseq: Update to 2.32.0. gnu: r-edger: Update to 3.40.0. gnu: r-ensembldb: Update to 2.22.0. gnu: r-fastseg: Update to 1.44.0. gnu: r-gage: Update to 2.48.0. gnu: r-genefilter: Update to 1.80.0. gnu: r-geneoverlap: Update to 1.34.0. gnu: r-genomation: Update to 1.30.0. gnu: r-genomeinfodb: Update to 1.34.3. gnu: r-genomicalignments: Update to 1.34.0. gnu: r-genomicfeatures: Update to 1.50.2. gnu: r-genomicfiles: Update to 1.34.0. gnu: r-genomicranges: Update to 1.50.1. gnu: r-gostats: Update to 2.64.0. gnu: r-gseabase: Update to 1.60.0. gnu: r-hpar: Update to 1.40.0. gnu: r-rhtslib: Update to 2.0.0. gnu: r-impute: Update to 1.72.1. gnu: r-interactivedisplaybase: Update to 1.36.0. gnu: r-keggrest: Update to 1.38.0. gnu: r-lfa: Update to 1.28.0. gnu: r-limma: Update to 3.54.0. gnu: r-made4: Update to 1.72.0. gnu: r-methylkit: Update to 1.24.0. gnu: r-muscat: Update to 1.12.0. gnu: r-mutationalpatterns: Update to 3.8.0. gnu: r-msnbase: Update to 2.24.0. gnu: r-msnid: Update to 1.32.0. gnu: r-mzid: Update to 1.36.0. gnu: r-mzr: Update to 2.32.0. gnu: r-organism-dplyr: Update to 1.26.0. gnu: r-organismdbi: Update to 1.40.0. gnu: r-pcaexplorer: Update to 2.24.0. gnu: r-pcamethods: Update to 1.90.0. gnu: r-protgenerics: Update to 1.30.0. gnu: r-rbgl: Update to 1.74.0. gnu: r-rcas: Update to 1.24.0. gnu: r-regioner: Update to 1.30.0. gnu: r-reportingtools: Update to 2.38.0. gnu: r-rhdf5: Update to 2.42.0. gnu: r-rhdf5filters: Update to 1.10.0. gnu: r-rsamtools: Update to 2.14.0. gnu: r-rtracklayer: Update to 1.58.0. gnu: r-scannotatr: Update to 1.4.0. gnu: r-scdblfinder: Update to 1.12.0. gnu: r-scmap: Update to 1.20.0. gnu: r-scry: Update to 1.10.0. gnu: r-seqlogo: Update to 1.64.0. gnu: r-seqpattern: Update to 1.30.0. gnu: r-shortread: Update to 1.56.0. gnu: r-simplifyenrichment: Update to 1.8.0. gnu: r-transcriptr: Update to 1.26.0. gnu: r-trajectoryutils: Update to 1.6.0. gnu: r-slingshot: Update to 2.6.0. gnu: r-stager: Update to 1.20.0. gnu: r-stringdb: Update to 2.10.0. gnu: r-structuralvariantannotation: Update to 1.13.0. gnu: r-summarizedexperiment: Update to 1.28.0. gnu: r-sva: Update to 3.46.0. gnu: r-systempiper: Update to 2.4.0. gnu: r-topgo: Update to 2.50.0. gnu: r-tximport: Update to 1.26.0. gnu: r-variantannotation: Update to 1.44.0. gnu: r-vsn: Update to 3.66.0. gnu: r-xina: Update to 1.16.0. gnu: r-xmapbridge: Update to 1.56.0. gnu: r-xvector: Update to 0.38.0. gnu: r-zlibbioc: Update to 1.44.0. gnu: r-zellkonverter: Update to 1.8.0. gnu: r-geneplotter: Update to 1.76.0. gnu: r-oligoclasses: Update to 1.60.0. gnu: r-oligo: Update to 1.62.0. gnu: r-qvalue: Update to 2.30.0. gnu: r-apeglm: Update to 1.20.0. gnu: r-greylistchip: Update to 1.30.0. gnu: r-diffbind: Update to 3.8.1. gnu: r-mbkmeans: Update to 1.14.0. gnu: r-multtest: Update to 2.54.0. gnu: r-graph: Update to 1.76.0. gnu: r-chippeakanno: Update to 3.32.0. gnu: r-matrixgenerics: Update to 1.10.0. gnu: r-marray: Update to 1.76.0. gnu: r-cghbase: Update to 1.58.0. gnu: r-cghcall: Update to 2.60.0. gnu: r-qdnaseq: Update to 1.34.0. gnu: r-bayseq: Update to 2.31.0. gnu: r-chipcomp: Update to 1.28.0. gnu: r-riboprofiling: Update to 1.28.0. gnu: r-riboseqr: Update to 1.32.0. gnu: r-interactionset: Update to 1.26.0. gnu: r-genomicinteractions: Update to 1.32.0. gnu: r-ctc: Update to 1.72.0. gnu: r-goseq: Update to 1.50.0. gnu: r-glimma: Update to 2.8.0. gnu: r-rots: Update to 1.26.0. gnu: r-plgem: Update to 1.70.0. gnu: r-inspect: Update to 1.28.0. gnu: r-dnabarcodes: Update to 1.28.0. gnu: r-ruvseq: Update to 1.32.0. gnu: r-biocneighbors: Update to 1.16.0. gnu: r-scaledmatrix: Update to 1.6.0. gnu: r-treeio: Update to 1.22.0. gnu: r-ggtree: Update to 3.6.2. gnu: r-metapod: Update to 1.6.0. gnu: r-biocsingular: Update to 1.14.0. gnu: r-destiny: Update to 3.12.0. gnu: r-savr: Update to 1.36.0. gnu: r-chipexoqual: Update to 1.22.0. gnu: r-copynumber: Update to 1.38.0. gnu: r-dnacopy: Update to 1.72.0. gnu: r-ebseq: Update to 1.38.0. gnu: r-karyoploter: Update to 1.24.0. gnu: r-lpsymphony: Update to 1.26.0. gnu: r-ihw: Update to 1.26.0. gnu: r-icobra: Update to 1.26.0. gnu: r-residualmatrix: Update to 1.8.0. gnu: r-batchelor: Update to 1.14.0. gnu: r-mast: Update to 1.24.0. gnu: r-monocle: Update to 2.26.0. gnu: r-noiseq: Update to 2.42.0. gnu: r-scdd: Update to 1.22.0. gnu: r-scone: Update to 1.22.0. gnu: r-geoquery: Update to 2.66.0. gnu: r-illuminaio: Update to 0.40.0. gnu: r-siggenes: Update to 1.72.0. gnu: r-bumphunter: Update to 1.40.0. gnu: r-microbiome: Update to 1.20.0. gnu: r-milor: Update to 1.6.0. gnu: r-minfi: Update to 1.44.0. gnu: r-methylumi: Update to 2.44.0. gnu: r-lumi: Update to 2.50.0. gnu: r-linnorm: Update to 2.22.0. gnu: r-ioniser: Update to 2.22.0. gnu: r-tradeseq: Update to 1.12.0. gnu: r-varianttools: Update to 1.40.0. gnu: r-heatplus: Update to 3.6.0. gnu: r-gosemsim: Update to 2.24.0. gnu: r-anota: Update to 1.46.0. gnu: r-sigpathway: Update to 1.66.0. gnu: r-fcscan: Update to 1.12.0. gnu: r-fgsea: Update to 1.24.0. gnu: r-dose: Update to 3.24.1. DRAFT gnu: r-enrichplot: Update to 1.18.0. gnu: r-clusterprofiler: Update to 4.6.0. gnu: r-clusterexperiment: Update to 2.18.0. gnu: r-mlinterfaces: Update to 1.78.0. gnu: r-annaffy: Update to 1.70.0. gnu: r-a4core: Update to 1.46.0. gnu: r-a4classif: Update to 1.46.0. gnu: r-a4preproc: Update to 1.46.0. gnu: r-a4reporting: Update to 1.46.0. gnu: r-a4base: Update to 1.46.0. gnu: r-a4: Update to 1.46.0. gnu: r-abseqr: Update to 1.16.0. gnu: r-bacon: Update to 1.26.0. gnu: r-rgadem: Update to 2.46.0. gnu: r-motifdb: Update to 1.40.0. gnu: r-motifbreakr: Update to 2.12.0. gnu: r-motifstack: Update to 1.42.0. gnu: r-genomicscores: Update to 2.10.0. gnu: r-atacseqqc: Update to 1.22.0. gnu: r-gofuncr: Update to 1.18.0. gnu: r-annotationtools: Update to 1.72.0. gnu: r-allelicimbalance: Update to 1.36.0. gnu: r-aucell: Update to 1.20.1. gnu: r-ebimage: Update to 4.40.0. gnu: r-yamss: Update to 1.24.0. gnu: r-gtrellis: Update to 1.30.0. gnu: r-somaticsignatures: Update to 2.34.0. gnu: r-yapsa: Update to 1.24.0. gnu: r-gcrma: Update to 2.70.0. gnu: r-quantro: Update to 1.32.0. gnu: r-yarn: Update to 1.24.0. gnu: r-roar: Update to 1.34.0. gnu: r-massspecwavelet: Update to 1.64.0. gnu: r-xcms: Update to 3.20.0. gnu: r-wppi: Update to 1.6.0. gnu: r-wrench: Update to 1.16.0. gnu: r-wiggleplotr: Update to 1.22.0. gnu: r-widgettools: Update to 1.76.0. gnu: r-webbioc: Update to 1.70.0. gnu: r-zinbwave: Update to 1.20.0. gnu: r-zfpkm: Update to 1.20.0. gnu: r-rbowtie2: Update to 2.4.0. gnu: r-progeny: Update to 1.20.0. gnu: r-arrmnormalization: Update to 1.38.0. gnu: r-biocfilecache: Update to 2.6.0. gnu: r-iclusterplus: Update to 1.34.0. gnu: r-rbowtie: Update to 1.38.0. gnu: r-sgseq: Update to 1.32.0. gnu: r-rhisat2: Update to 1.14.0. gnu: r-quasr: Update to 1.38.0. gnu: r-rqc: Update to 1.32.0. gnu: r-birewire: Update to 3.30.0. gnu: r-multidataset: Update to 1.26.0. DRAFT gnu: r-ropls: Update to 1.30.0. gnu: r-biosigner: Update to 1.26.0. gnu: r-annotatr: Update to 1.24.0. gnu: r-rsubread: Update to 2.12.0. gnu: r-consensusclusterplus: Update to 1.62.0. gnu: r-cytolib: Update to 2.10.0. gnu: r-flowcore: Update to 2.10.0. gnu: r-flowmeans: Update to 1.58.0. gnu: r-ncdfflow: Update to 2.44.0. gnu: r-ggcyto: Update to 1.26.0. gnu: r-flowviz: Update to 1.62.0. gnu: r-flowclust: Update to 3.36.0. gnu: r-rprotobuflib: Update to 2.10.0. gnu: r-flowworkspace: Update to 4.10.0. gnu: r-flowstats: Update to 4.10.0. gnu: r-opencyto: Update to 2.10.0. gnu: r-cytoml: Update to 2.10.0. gnu: r-flowsom: Update to 2.6.0. gnu: r-mixomics: Update to 6.22.0. gnu: r-depecher: Update to 1.14.0. gnu: r-rcistarget: Update to 1.17.0. gnu: r-chicago: Update to 1.26.0. gnu: r-cicero: Update to 1.16.0. gnu: r-circrnaprofiler: Update to 1.12.0. gnu: r-genie3: Update to 1.20.0. gnu: r-roc: Update to 1.74.0. gnu: r-watermelon: Update to 2.4.0. gnu: r-gdsfmt: Update to 1.34.0. gnu: r-bigmelon: Update to 1.24.0. gnu: r-seqbias: Update to 1.46.0. gnu: r-reqon: Update to 1.44.0. gnu: r-wavcluster: Update to 2.32.0. gnu: r-variantfiltering: Update to 1.34.0. gnu: r-variancepartition: Update to 1.28.0. gnu: r-htqpcr: Update to 1.52.0. gnu: r-unifiedwmwqpcr: Update to 1.34.0. gnu: r-universalmotif: Update to 1.16.0. gnu: r-ace: Update to 1.16.0. gnu: r-acgh: Update to 1.76.0. gnu: r-acme: Update to 2.54.0. gnu: r-acde: Update to 1.28.0. gnu: r-bgmix: Update to 1.58.0. gnu: r-bgx: Update to 1.64.0. gnu: r-bhc: Update to 1.50.0. gnu: r-bicare: Update to 1.56.0. gnu: r-bifet: Update to 1.18.0. gnu: r-rsbml: Update to 2.56.0. gnu: r-hypergraph: Update to 1.70.0. gnu: r-hyperdraw: Update to 1.50.0. gnu: r-biggr: Update to 1.34.0. gnu: r-bigpint: Update to 1.14.0. gnu: r-chemminer: Update to 3.50.0. gnu: r-fmcsr: Update to 1.40.0. gnu: r-bioassayr: Update to 1.36.0. gnu: r-biobroom: Update to 1.30.0. gnu: r-graphite: Update to 1.44.0. gnu: r-reactomepa: Update to 1.42.0. gnu: r-ebarrays: Update to 2.62.0. gnu: r-bioccheck: Update to 1.34.0. gnu: r-biocgraph: Update to 1.60.0. gnu: r-biocstyle: Update to 2.26.0. gnu: r-biocviews: Update to 1.66.0. gnu: r-experimenthub: Update to 2.6.0. gnu: r-grohmm: Update to 1.32.0. gnu: r-multiassayexperiment: Update to 1.24.0. gnu: r-bioconcotk: Update to 1.18.0. gnu: r-biocor: Update to 1.22.0. gnu: r-biocpkgtools: Update to 1.16.0. gnu: r-biocset: Update to 1.12.0. gnu: r-biocworkflowtools: Update to 1.24.0. gnu: r-biodist: Update to 1.70.0. gnu: r-pcatools: Update to 2.10.0. DRAFT gnu: r-rgreat: Update to 2.0.1. gnu: r-m3c: Update to 1.20.0. gnu: r-icens: Update to 1.70.0. gnu: r-preprocesscore: Update to 1.60.0. gnu: r-s4vectors: Update to 0.36.0. gnu: r-rgraphviz: Update to 2.42.0. gnu: r-fishpond: Update to 2.4.0. gnu: r-fithic: Update to 1.24.0. gnu: r-hitc: Update to 1.42.0. gnu: r-hdf5array: Update to 1.26.0. gnu: r-rhdf5lib: Update to 1.20.0. gnu: r-beachmat: Update to 2.14.0. gnu: r-cner: Update to 1.34.0. gnu: r-tfbstools: Update to 1.36.0. gnu: r-maftools: Update to 2.14.0. gnu: r-motifmatchr: Update to 1.20.0. gnu: r-chromvar: Update to 1.20.0. gnu: r-singlecellexperiment: Update to 1.20.0. gnu: r-singler: Update to 2.0.0. gnu: r-scuttle: Update to 1.8.0. gnu: r-scater: Update to 1.26.1. gnu: r-scran: Update to 1.26.0. gnu: r-sparsematrixstats: Update to 1.10.0. gnu: r-delayedmatrixstats: Update to 1.20.0. gnu: r-mscoreutils: Update to 1.10.0. gnu: r-msfeatures: Update to 1.6.0. gnu: r-biocio: Update to 1.8.0. gnu: r-msmseda: Update to 1.36.0. gnu: r-msmstests: Update to 1.36.0. gnu: r-catalyst: Update to 1.22.0. gnu: r-erma: Update to 1.14.0. gnu: r-ggbio: Update to 1.46.0. gnu: r-gviz: Update to 1.42.0. gnu: r-gwascat: Update to 2.30.0. gnu: r-kegggraph: Update to 1.58.0. gnu: r-ldblock: Update to 1.28.0. gnu: r-pathview: Update to 1.38.0. gnu: r-snpstats: Update to 1.48.0. gnu: r-chromstar: Update to 1.24.0. gnu: r-guitar: Update to 2.14.0. gnu: r-ballgown: Update to 2.30.0. gnu: r-megadepth: Update to 1.8.0. gnu: r-beclear: Update to 2.14.0. gnu: r-bgeecall: Update to 1.14.0. gnu: r-bgeedb: Update to 2.24.0. gnu: r-biobtreer: Update to 1.10.0. gnu: r-minet: Update to 3.56.0. gnu: r-genetclassifier: Update to 1.38.0. gnu: r-dir-expiry: Update to 1.6.0. gnu: r-basilisk-utils: Update to 1.10.0. gnu: r-basilisk: Update to 1.10.2. gnu: r-biocthis: Update to 1.8.1. gnu: r-biocdockermanager: Update to 1.10.0. gnu: r-biodb: Update to 1.6.0. gnu: r-biomformat: Update to 1.26.0. gnu: r-mvcclass: Update to 1.72.0. gnu: r-biomvcclass: Update to 1.66.0. gnu: r-biomvrcns: Update to 1.38.0. gnu: r-bionero: Update to 1.6.0. gnu: r-bionet: Update to 1.58.0. gnu: r-bionetstat: Update to 1.18.0. gnu: r-bioqc: Update to 1.26.0. gnu: r-biotip: Update to 1.12.0. gnu: r-biotmle: Update to 1.22.0. gnu: r-bsseq: Update to 1.34.0. gnu: r-dada2: Update to 1.26.0. gnu: r-dmrseq: Update to 1.18.0. gnu: r-omicade4: Update to 1.38.0. gnu: r-omnipathr: Update to 3.5.25. gnu: r-biscuiteer: Update to 1.12.0. gnu: r-tcgabiolinks: Update to 2.25.3. gnu: r-tricycle: Update to 1.6.0. gnu: r-tximeta: Update to 1.16.0. gnu: r-phyloseq: Update to 1.42.0. gnu/packages/bioconductor.scm | 1860 +++++++++++++++++---------------- gnu/packages/cran.scm | 52 +- gnu/packages/statistics.scm | 9 +- guix/build-system/r.scm | 2 +- guix/import/cran.scm | 4 +- 5 files changed, 1031 insertions(+), 896 deletions(-) -- 2.38.1 From unknown Sun Jun 22 00:54:54 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#59329] [PATCH 000/444] Update Bioconductor to 3.16 Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 17 Nov 2022 10:04:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 59329 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 59329@debbugs.gnu.org Cc: rekado@elephly.net Received: via spool by 59329-submit@debbugs.gnu.org id=B59329.166867943312060 (code B ref 59329); 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Thu, 17 Nov 2022 02:03:41 -0800 (PST) From: zimoun In-Reply-To: <20221117035554.1307869-1-zimon.toutoune@gmail.com> References: <20221117035554.1307869-1-zimon.toutoune@gmail.com> Date: Thu, 17 Nov 2022 11:03:36 +0100 Message-ID: <86edu1lwxz.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi, On Thu, 17 Nov 2022 at 04:55, zimoun wrote: > Well, I am rebuilding to see if these updates introduce non-reproducible > packages. But that's not blocking, IMHO. The only non-reproducible packages is r-omnipathr but it was not before the update. Cheers, simon From unknown Sun Jun 22 00:54:54 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#59329: closed (Re: bug#59329: [PATCH 000/444] Update Bioconductor to 3.16) Message-ID: References: <861qprcs40.fsf@gmail.com> <20221117035554.1307869-1-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 59329 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 59329@debbugs.gnu.org Date: Fri, 25 Nov 2022 09:31:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1669368663-12447-1" This is a multi-part message in MIME format... ------------=_1669368663-12447-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #59329: [PATCH 000/444] Update Bioconductor to 3.16 which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 59329@debbugs.gnu.org. --=20 59329: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D59329 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1669368663-12447-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 59329-done) by debbugs.gnu.org; 25 Nov 2022 09:30:03 +0000 Received: from localhost ([127.0.0.1]:33487 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oyV23-0003Bl-0Z for submit@debbugs.gnu.org; Fri, 25 Nov 2022 04:30:03 -0500 Received: from mail-wm1-f41.google.com ([209.85.128.41]:35427) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oyV1y-0003AG-Ub for 59329-done@debbugs.gnu.org; Fri, 25 Nov 2022 04:29:59 -0500 Received: by mail-wm1-f41.google.com with SMTP id r9-20020a1c4409000000b003d02dd48c45so5401126wma.0 for <59329-done@debbugs.gnu.org>; Fri, 25 Nov 2022 01:29:58 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:user-agent:message-id:in-reply-to:date:references :subject:cc:to:from:from:to:cc:subject:date:message-id:reply-to; bh=0FPUVmDcYr/kQJMVwyVT7m1Sy5z9WiFCMrQt0O816Ko=; b=XOf3EjA2TDvyMYnmSb/s7qgl2rBMSzy7vLk725ySaPNG7VOfSdevZUwgYcrdlb/KX5 5hbSFfY51fKQd05qNMr/fzaFzZ6lKnQp+aFKM4dNqb5k7BW98TbmGcuXAmrMlO10BNFw A5tbxRurfOJeLY1phScyGZ5vXCPY2+IP/mP65cljeLPQSu9px6YT+gtyLN3j5R2h7DcC iA4k4vA67JJuorvzlyqpVRPFoeMY4dszxN91sjTRmtjGnC0AUOAQYJpMFSWam41KKWuX 3u5fZxcJ+3szfiwKpyeK7T6fBAflWPrcH+Ag35Kv0tb4fa7Z9XI/g5dQ4uYQE13KDmVJ N0wg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=mime-version:user-agent:message-id:in-reply-to:date:references :subject:cc:to:from:x-gm-message-state:from:to:cc:subject:date :message-id:reply-to; bh=0FPUVmDcYr/kQJMVwyVT7m1Sy5z9WiFCMrQt0O816Ko=; b=AGpnFDC/7t8HLw4HHUBm8z4x6R/a6ajmQTgWMYoN/sGUxNoLWLVBIbM4gF1VWpexRd V0clyAnbZHBSKjWcB7BzK4LWjLw3z6lplR3rZG+l+1o32s04gvFASh6p4P8uekhtQfd6 N6hTp/txnfardfN5EKfHcsCE2z/E25/mW+IiUbOmyIbOGt1nBp1vD7KX/wRiBTEF2mew IkbzGsKUP1Z6vma5kTjD8AQqk73zsmmWrbAg9wF/163bU9OSv/GzE5A9C+J6olRkSQx8 eEjyTkC9LZV/oXwavuVd6h9M07VeCrTLyO3HCJ4Gs5Z2dRGbjq+XC5If5hZilxWkf5nM Bb0A== X-Gm-Message-State: ANoB5pkzrREfsoA3C+1UtWJ/0yXgf9emS+K53t+TythWvyrtVxB/XFsb 6N05N03Pw24DgcRRhLxfNJAoVnGubao= X-Google-Smtp-Source: AA0mqf4Kr5xGrcpF4pV8iWrIjL5wtlwVhatc9YqH7rFYQsa4H4QzQ1wg9rwbytRmaKJSEAb0EuzD4w== X-Received: by 2002:a05:600c:6012:b0:3cf:cb16:f242 with SMTP id az18-20020a05600c601200b003cfcb16f242mr18604553wmb.82.1669368592974; Fri, 25 Nov 2022 01:29:52 -0800 (PST) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id i4-20020a5d55c4000000b0023647841c5bsm3291146wrw.60.2022.11.25.01.29.52 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 25 Nov 2022 01:29:52 -0800 (PST) From: zimoun To: 59329-done@debbugs.gnu.org Subject: Re: bug#59329: [PATCH 000/444] Update Bioconductor to 3.16 References: <20221117035554.1307869-1-zimon.toutoune@gmail.com> Date: Fri, 25 Nov 2022 10:15:27 +0100 In-Reply-To: <20221117035554.1307869-1-zimon.toutoune@gmail.com> (zimoun's message of "Thu, 17 Nov 2022 04:55:54 +0100") Message-ID: <861qprcs40.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 59329-done Cc: rekado@elephly.net X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi, Thanks Ricardo! Merged starting at f4a7ccc976a8974803ed4b0bfe72af0bd44a9773, closing. Cheers, simon ------------=_1669368663-12447-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 17 Nov 2022 03:56:13 +0000 Received: from localhost ([127.0.0.1]:58693 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ovW0a-0008Br-Mx for submit@debbugs.gnu.org; Wed, 16 Nov 2022 22:56:13 -0500 Received: from lists.gnu.org ([209.51.188.17]:37982) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ovW0W-0008Bh-9l for submit@debbugs.gnu.org; Wed, 16 Nov 2022 22:56:11 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ovW0W-0003Xb-1q for guix-patches@gnu.org; Wed, 16 Nov 2022 22:56:08 -0500 Received: from mail-wr1-x434.google.com ([2a00:1450:4864:20::434]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ovW0T-0003Xy-1w for guix-patches@gnu.org; Wed, 16 Nov 2022 22:56:07 -0500 Received: by mail-wr1-x434.google.com with SMTP id j15so940534wrq.3 for ; Wed, 16 Nov 2022 19:56:04 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:from:to:cc:subject:date:message-id:reply-to; bh=+cnxELpm5gFZMk8HKCiZVPV6JO92XtfwJdUckl1WNvM=; b=nD9bcA0P5miTHxXnJDWVMOCBCBeAnnIvg7Uq6+yMt4OfPE5b3ABb8rGa7pOihF5AZ8 0IbR4qKfjzspQnJ7Ir2EM06f8U854eNCsMhckmq4CuA4pbg2DvjJEqRsNPxl4jqbIx5O galiT3NkPj/YxZsp5GXINPzVobk5NuzvuOwDJfI6JqJ0AN2NErtp+X8hs5JQM4xboSYY b+0WGiJXERJsXis7F265rDqoy4/3pGBgD2uLyh33MmuqIaTFqu2zlwEPACaAlg6K0AWo A4neYI//ooIxO8ZF1e0cvcym5ujkx+oE8PK4a2WqK1JVDISsK5LezfvNK2sKnI9xTLys rZbA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:x-gm-message-state:from:to:cc:subject:date:message-id :reply-to; bh=+cnxELpm5gFZMk8HKCiZVPV6JO92XtfwJdUckl1WNvM=; b=66FJvAtcFfagSmTkR1vNLgyQm/lsvZtn0iKnFCoeK0xKEVvchTSn7I+vIm1ROggkhd 0n/Rgi0+yJlFxpVIVe8NhRzpmUxB846AAPN6ITh1PutGZEDAW56gH/A6wwnpR2jCZwNZ OQ/1OBOn1qFg0KjnEa3NfssYQ5jeBcW3LcnGU+RYSW47DHq5cKXNOcZ0Fcs2UX1uj8xP 53vKC30k+i9G0vdaCca2eIa3Rboe4CXnMtG/lFM2x7btITYCfD8Pr+uryhbfRyYeaBS9 s/JydqhCjFXjOZyaalJXtahQo5q8713qQupyCqxfuD5T6lszyaMzT2C+sB7asiFb9nRm +U4w== X-Gm-Message-State: ANoB5pk6JvR+P5Nrz3FJtcc3i54/6LSFzDaQi0RyAphgnEZHUCEYmB+q WRw4F+FG/jv1NxF81Z3CS0GQ+WELsyQ= X-Google-Smtp-Source: AA0mqf7DOneRqTjIoA0Hv76jh3SCt/PtSha6Hx3Jx/iytR4yMm8vNraaHY5RyUvg67BQHabjm/7Y4w== X-Received: by 2002:a05:6000:1d92:b0:241:6e0a:bfe6 with SMTP id bk18-20020a0560001d9200b002416e0abfe6mr284496wrb.34.1668657362726; Wed, 16 Nov 2022 19:56:02 -0800 (PST) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g11-20020a5d540b000000b0022cdeba3f83sm16462369wrv.84.2022.11.16.19.56.02 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 16 Nov 2022 19:56:02 -0800 (PST) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 000/444] Update Bioconductor to 3.16 Date: Thu, 17 Nov 2022 04:55:54 +0100 Message-Id: <20221117035554.1307869-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.38.1 MIME-Version: 1.0 X-Debbugs-CC: rekado@elephly.net Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::434; envelope-from=zimon.toutoune@gmail.com; helo=mail-wr1-x434.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) Hi Ricardo, Sorry for the delay. Here some work, not fully polished but the final state builds. However, it requires the update of r-ggplot2 -- and this update breaks the leaf package r-ggtern. Note that the update of r-ggplot2 is only required by the Bioconductor package r-fgsea, if I remember correctly. I marked some patches as DRAFT, because it remains something -- for instance, refresh recommended the addition of a package but it builds and the tests seem fine without, so I do not know if it is a false-positive of refresh. Well, I am rebuilding to see if these updates introduce non-reproducible packages. But that's not blocking, IMHO. Last, I will not spam guix-patches with 444 emails. Please checkout the branch wip-bioconductor on: https://gitlab.com/zimoun/guix/-/tree/wip-bioconductor Cheers, simon zimoun (444): DRAFT update 3.16. gnu: Add r-hdo-db. DRAFT gnu: r-ggplot2: Update to 3.4.0. gnu: r-ggprism: Update to 1.0.4. gnu: Add r-biocbaseutils. gnu: Add r-rorcid. gnu: Add r-gson. gnu: r-abarray: Update to 1.66.0. gnu: r-absseq: Update to 1.52.0. gnu: r-adam: Update to 1.14.0. gnu: r-adamgui: Update to 1.14.0. gnu: r-adimpute: Update to 1.8.0. gnu: r-adsplit: Update to 1.68.0. gnu: r-affixcan: Update to 1.16.0. gnu: r-affyrnadegradation: Update to 1.44.0. gnu: r-agdex: Update to 1.46.0. gnu: r-aggregatebiovar: Update to 1.8.0. gnu: r-agilp: Update to 3.30.0. gnu: r-adductomicsr: Update to 1.14.0. gnu: r-agimicrorna: Update to 2.48.0. gnu: r-airpart: Update to 1.6.0. gnu: r-amountain: Update to 1.24.0. gnu: r-amaretto: Update to 1.13.0. gnu: r-anaquin: Update to 2.22.0. gnu: r-aldex2: Update to 1.30.0. gnu: r-aneufinder: Update to 1.26.0. gnu: r-anf: Update to 1.20.0. gnu: r-annmap: Update to 1.40.0. gnu: r-antiprofiles: Update to 1.38.0. gnu: r-aseb: Update to 1.42.0. gnu: r-asgsca: Update to 1.32.0. gnu: r-aspli: Update to 2.8.0. gnu: r-assessorf: Update to 1.16.0. gnu: r-asset: Update to 2.16.0. gnu: r-atena: Update to 1.4.0. gnu: r-atsnp: Update to 1.14.0. gnu: r-attract: Update to 1.50.0. gnu: r-awfisher: Update to 1.12.0. gnu: r-awst: Update to 1.6.0. gnu: r-baalchip: Update to 1.24.0. gnu: r-basespacer: Update to 1.42.0. gnu: r-bac: Update to 1.58.0. gnu: r-bader: Update to 1.36.0. gnu: r-badregionfinder: Update to 1.26.0. gnu: r-bambu: Update to 3.0.1. gnu: r-bandits: Update to 1.14.0. gnu: r-banocc: Update to 1.22.0. gnu: r-barcodetrackr: Update to 1.6.0. gnu: r-biocversion: Update to 3.16.0. gnu: r-biocgenerics: Update to 0.44.0. gnu: r-coverageview: Update to 1.36.0. gnu: r-cummerbund: Update to 2.40.0. gnu: r-dama: Update to 1.70.0. gnu: r-damefinder: Update to 1.10.0. gnu: r-dearseq: Update to 1.10.0. gnu: r-debcam: Update to 1.16.0. gnu: r-decipher: Update to 2.26.0. gnu: r-deco: Update to 1.13.0. gnu: r-decomplexdisease: Update to 1.18.0. gnu: r-decomptumor2sig: Update to 2.14.0. gnu: r-deconrnaseq: Update to 1.40.0. gnu: r-decontam: Update to 1.18.0. gnu: r-deconvr: Update to 1.4.0. gnu: r-decoupler: Update to 2.4.0. gnu: r-deepsnv: Update to 1.44.0. gnu: r-delayedarray: Update to 0.24.0. gnu: r-derfinderhelper: Update to 1.32.0. gnu: r-drimseq: Update to 1.26.0. gnu: r-bluster: Update to 1.8.0. gnu: r-ideoviz: Update to 1.34.0. gnu: r-infercnv: Update to 1.14.0. gnu: r-iranges: Update to 2.32.0. gnu: r-isoformswitchanalyzer: Update to 1.20.0. gnu: r-affy: Update to 1.76.0. gnu: r-affycomp: Update to 1.74.0. gnu: r-affycompatible: Update to 1.58.0. gnu: r-affycontam: Update to 1.56.0. gnu: r-affycoretools: Update to 1.70.0. gnu: r-affyio: Update to 1.68.0. gnu: r-affxparser: Update to 1.70.0. gnu: r-annotate: Update to 1.76.0. gnu: r-annotationdbi: Update to 1.60.0. gnu: r-annotationfilter: Update to 1.22.0. gnu: r-annotationforge: Update to 1.40.0. gnu: r-annotationhub: Update to 3.6.0. gnu: r-aroma-light: Update to 3.28.0. gnu: r-bamsignals: Update to 1.30.0. gnu: r-biobase: Update to 2.58.0. gnu: r-biomart: Update to 2.54.0. gnu: r-biocparallel: Update to 1.32.1. gnu: r-biostrings: Update to 2.66.0. gnu: r-biovizbase: Update to 1.46.0. gnu: r-bsgenome: Update to 1.66.1. gnu: r-category: Update to 2.64.0. gnu: r-chipseeker: Update to 1.34.0. gnu: r-chipseq: Update to 1.48.0. gnu: r-complexheatmap: Update to 2.14.0. gnu: r-copywriter: Update to 2.29.0. gnu: r-deseq2: Update to 1.38.1. gnu: r-dexseq: Update to 1.44.0. gnu: r-diffcyt: Update to 1.18.0. gnu: r-dirichletmultinomial: Update to 1.40.0. gnu: r-dittoseq: Update to 1.10.0. gnu: r-edaseq: Update to 2.32.0. gnu: r-edger: Update to 3.40.0. gnu: r-ensembldb: Update to 2.22.0. gnu: r-fastseg: Update to 1.44.0. gnu: r-gage: Update to 2.48.0. gnu: r-genefilter: Update to 1.80.0. gnu: r-geneoverlap: Update to 1.34.0. gnu: r-genomation: Update to 1.30.0. gnu: r-genomeinfodb: Update to 1.34.3. gnu: r-genomicalignments: Update to 1.34.0. gnu: r-genomicfeatures: Update to 1.50.2. gnu: r-genomicfiles: Update to 1.34.0. gnu: r-genomicranges: Update to 1.50.1. gnu: r-gostats: Update to 2.64.0. gnu: r-gseabase: Update to 1.60.0. gnu: r-hpar: Update to 1.40.0. gnu: r-rhtslib: Update to 2.0.0. gnu: r-impute: Update to 1.72.1. gnu: r-interactivedisplaybase: Update to 1.36.0. gnu: r-keggrest: Update to 1.38.0. gnu: r-lfa: Update to 1.28.0. gnu: r-limma: Update to 3.54.0. gnu: r-made4: Update to 1.72.0. gnu: r-methylkit: Update to 1.24.0. gnu: r-muscat: Update to 1.12.0. gnu: r-mutationalpatterns: Update to 3.8.0. gnu: r-msnbase: Update to 2.24.0. gnu: r-msnid: Update to 1.32.0. gnu: r-mzid: Update to 1.36.0. gnu: r-mzr: Update to 2.32.0. gnu: r-organism-dplyr: Update to 1.26.0. gnu: r-organismdbi: Update to 1.40.0. gnu: r-pcaexplorer: Update to 2.24.0. gnu: r-pcamethods: Update to 1.90.0. gnu: r-protgenerics: Update to 1.30.0. gnu: r-rbgl: Update to 1.74.0. gnu: r-rcas: Update to 1.24.0. gnu: r-regioner: Update to 1.30.0. gnu: r-reportingtools: Update to 2.38.0. gnu: r-rhdf5: Update to 2.42.0. gnu: r-rhdf5filters: Update to 1.10.0. gnu: r-rsamtools: Update to 2.14.0. gnu: r-rtracklayer: Update to 1.58.0. gnu: r-scannotatr: Update to 1.4.0. gnu: r-scdblfinder: Update to 1.12.0. gnu: r-scmap: Update to 1.20.0. gnu: r-scry: Update to 1.10.0. gnu: r-seqlogo: Update to 1.64.0. gnu: r-seqpattern: Update to 1.30.0. gnu: r-shortread: Update to 1.56.0. gnu: r-simplifyenrichment: Update to 1.8.0. gnu: r-transcriptr: Update to 1.26.0. gnu: r-trajectoryutils: Update to 1.6.0. gnu: r-slingshot: Update to 2.6.0. gnu: r-stager: Update to 1.20.0. gnu: r-stringdb: Update to 2.10.0. gnu: r-structuralvariantannotation: Update to 1.13.0. gnu: r-summarizedexperiment: Update to 1.28.0. gnu: r-sva: Update to 3.46.0. gnu: r-systempiper: Update to 2.4.0. gnu: r-topgo: Update to 2.50.0. gnu: r-tximport: Update to 1.26.0. gnu: r-variantannotation: Update to 1.44.0. gnu: r-vsn: Update to 3.66.0. gnu: r-xina: Update to 1.16.0. gnu: r-xmapbridge: Update to 1.56.0. gnu: r-xvector: Update to 0.38.0. gnu: r-zlibbioc: Update to 1.44.0. gnu: r-zellkonverter: Update to 1.8.0. gnu: r-geneplotter: Update to 1.76.0. gnu: r-oligoclasses: Update to 1.60.0. gnu: r-oligo: Update to 1.62.0. gnu: r-qvalue: Update to 2.30.0. gnu: r-apeglm: Update to 1.20.0. gnu: r-greylistchip: Update to 1.30.0. gnu: r-diffbind: Update to 3.8.1. gnu: r-mbkmeans: Update to 1.14.0. gnu: r-multtest: Update to 2.54.0. gnu: r-graph: Update to 1.76.0. gnu: r-chippeakanno: Update to 3.32.0. gnu: r-matrixgenerics: Update to 1.10.0. gnu: r-marray: Update to 1.76.0. gnu: r-cghbase: Update to 1.58.0. gnu: r-cghcall: Update to 2.60.0. gnu: r-qdnaseq: Update to 1.34.0. gnu: r-bayseq: Update to 2.31.0. gnu: r-chipcomp: Update to 1.28.0. gnu: r-riboprofiling: Update to 1.28.0. gnu: r-riboseqr: Update to 1.32.0. gnu: r-interactionset: Update to 1.26.0. gnu: r-genomicinteractions: Update to 1.32.0. gnu: r-ctc: Update to 1.72.0. gnu: r-goseq: Update to 1.50.0. gnu: r-glimma: Update to 2.8.0. gnu: r-rots: Update to 1.26.0. gnu: r-plgem: Update to 1.70.0. gnu: r-inspect: Update to 1.28.0. gnu: r-dnabarcodes: Update to 1.28.0. gnu: r-ruvseq: Update to 1.32.0. gnu: r-biocneighbors: Update to 1.16.0. gnu: r-scaledmatrix: Update to 1.6.0. gnu: r-treeio: Update to 1.22.0. gnu: r-ggtree: Update to 3.6.2. gnu: r-metapod: Update to 1.6.0. gnu: r-biocsingular: Update to 1.14.0. gnu: r-destiny: Update to 3.12.0. gnu: r-savr: Update to 1.36.0. gnu: r-chipexoqual: Update to 1.22.0. gnu: r-copynumber: Update to 1.38.0. gnu: r-dnacopy: Update to 1.72.0. gnu: r-ebseq: Update to 1.38.0. gnu: r-karyoploter: Update to 1.24.0. gnu: r-lpsymphony: Update to 1.26.0. gnu: r-ihw: Update to 1.26.0. gnu: r-icobra: Update to 1.26.0. gnu: r-residualmatrix: Update to 1.8.0. gnu: r-batchelor: Update to 1.14.0. gnu: r-mast: Update to 1.24.0. gnu: r-monocle: Update to 2.26.0. gnu: r-noiseq: Update to 2.42.0. gnu: r-scdd: Update to 1.22.0. gnu: r-scone: Update to 1.22.0. gnu: r-geoquery: Update to 2.66.0. gnu: r-illuminaio: Update to 0.40.0. gnu: r-siggenes: Update to 1.72.0. gnu: r-bumphunter: Update to 1.40.0. gnu: r-microbiome: Update to 1.20.0. gnu: r-milor: Update to 1.6.0. gnu: r-minfi: Update to 1.44.0. gnu: r-methylumi: Update to 2.44.0. gnu: r-lumi: Update to 2.50.0. gnu: r-linnorm: Update to 2.22.0. gnu: r-ioniser: Update to 2.22.0. gnu: r-tradeseq: Update to 1.12.0. gnu: r-varianttools: Update to 1.40.0. gnu: r-heatplus: Update to 3.6.0. gnu: r-gosemsim: Update to 2.24.0. gnu: r-anota: Update to 1.46.0. gnu: r-sigpathway: Update to 1.66.0. gnu: r-fcscan: Update to 1.12.0. gnu: r-fgsea: Update to 1.24.0. gnu: r-dose: Update to 3.24.1. DRAFT gnu: r-enrichplot: Update to 1.18.0. gnu: r-clusterprofiler: Update to 4.6.0. gnu: r-clusterexperiment: Update to 2.18.0. gnu: r-mlinterfaces: Update to 1.78.0. gnu: r-annaffy: Update to 1.70.0. gnu: r-a4core: Update to 1.46.0. gnu: r-a4classif: Update to 1.46.0. gnu: r-a4preproc: Update to 1.46.0. gnu: r-a4reporting: Update to 1.46.0. gnu: r-a4base: Update to 1.46.0. gnu: r-a4: Update to 1.46.0. gnu: r-abseqr: Update to 1.16.0. gnu: r-bacon: Update to 1.26.0. gnu: r-rgadem: Update to 2.46.0. gnu: r-motifdb: Update to 1.40.0. gnu: r-motifbreakr: Update to 2.12.0. gnu: r-motifstack: Update to 1.42.0. gnu: r-genomicscores: Update to 2.10.0. gnu: r-atacseqqc: Update to 1.22.0. gnu: r-gofuncr: Update to 1.18.0. gnu: r-annotationtools: Update to 1.72.0. gnu: r-allelicimbalance: Update to 1.36.0. gnu: r-aucell: Update to 1.20.1. gnu: r-ebimage: Update to 4.40.0. gnu: r-yamss: Update to 1.24.0. gnu: r-gtrellis: Update to 1.30.0. gnu: r-somaticsignatures: Update to 2.34.0. gnu: r-yapsa: Update to 1.24.0. gnu: r-gcrma: Update to 2.70.0. gnu: r-quantro: Update to 1.32.0. gnu: r-yarn: Update to 1.24.0. gnu: r-roar: Update to 1.34.0. gnu: r-massspecwavelet: Update to 1.64.0. gnu: r-xcms: Update to 3.20.0. gnu: r-wppi: Update to 1.6.0. gnu: r-wrench: Update to 1.16.0. gnu: r-wiggleplotr: Update to 1.22.0. gnu: r-widgettools: Update to 1.76.0. gnu: r-webbioc: Update to 1.70.0. gnu: r-zinbwave: Update to 1.20.0. gnu: r-zfpkm: Update to 1.20.0. gnu: r-rbowtie2: Update to 2.4.0. gnu: r-progeny: Update to 1.20.0. gnu: r-arrmnormalization: Update to 1.38.0. gnu: r-biocfilecache: Update to 2.6.0. gnu: r-iclusterplus: Update to 1.34.0. gnu: r-rbowtie: Update to 1.38.0. gnu: r-sgseq: Update to 1.32.0. gnu: r-rhisat2: Update to 1.14.0. gnu: r-quasr: Update to 1.38.0. gnu: r-rqc: Update to 1.32.0. gnu: r-birewire: Update to 3.30.0. gnu: r-multidataset: Update to 1.26.0. DRAFT gnu: r-ropls: Update to 1.30.0. gnu: r-biosigner: Update to 1.26.0. gnu: r-annotatr: Update to 1.24.0. gnu: r-rsubread: Update to 2.12.0. gnu: r-consensusclusterplus: Update to 1.62.0. gnu: r-cytolib: Update to 2.10.0. gnu: r-flowcore: Update to 2.10.0. gnu: r-flowmeans: Update to 1.58.0. gnu: r-ncdfflow: Update to 2.44.0. gnu: r-ggcyto: Update to 1.26.0. gnu: r-flowviz: Update to 1.62.0. gnu: r-flowclust: Update to 3.36.0. gnu: r-rprotobuflib: Update to 2.10.0. gnu: r-flowworkspace: Update to 4.10.0. gnu: r-flowstats: Update to 4.10.0. gnu: r-opencyto: Update to 2.10.0. gnu: r-cytoml: Update to 2.10.0. gnu: r-flowsom: Update to 2.6.0. gnu: r-mixomics: Update to 6.22.0. gnu: r-depecher: Update to 1.14.0. gnu: r-rcistarget: Update to 1.17.0. gnu: r-chicago: Update to 1.26.0. gnu: r-cicero: Update to 1.16.0. gnu: r-circrnaprofiler: Update to 1.12.0. gnu: r-genie3: Update to 1.20.0. gnu: r-roc: Update to 1.74.0. gnu: r-watermelon: Update to 2.4.0. gnu: r-gdsfmt: Update to 1.34.0. gnu: r-bigmelon: Update to 1.24.0. gnu: r-seqbias: Update to 1.46.0. gnu: r-reqon: Update to 1.44.0. gnu: r-wavcluster: Update to 2.32.0. gnu: r-variantfiltering: Update to 1.34.0. gnu: r-variancepartition: Update to 1.28.0. gnu: r-htqpcr: Update to 1.52.0. gnu: r-unifiedwmwqpcr: Update to 1.34.0. gnu: r-universalmotif: Update to 1.16.0. gnu: r-ace: Update to 1.16.0. gnu: r-acgh: Update to 1.76.0. gnu: r-acme: Update to 2.54.0. gnu: r-acde: Update to 1.28.0. gnu: r-bgmix: Update to 1.58.0. gnu: r-bgx: Update to 1.64.0. gnu: r-bhc: Update to 1.50.0. gnu: r-bicare: Update to 1.56.0. gnu: r-bifet: Update to 1.18.0. gnu: r-rsbml: Update to 2.56.0. gnu: r-hypergraph: Update to 1.70.0. gnu: r-hyperdraw: Update to 1.50.0. gnu: r-biggr: Update to 1.34.0. gnu: r-bigpint: Update to 1.14.0. gnu: r-chemminer: Update to 3.50.0. gnu: r-fmcsr: Update to 1.40.0. gnu: r-bioassayr: Update to 1.36.0. gnu: r-biobroom: Update to 1.30.0. gnu: r-graphite: Update to 1.44.0. gnu: r-reactomepa: Update to 1.42.0. gnu: r-ebarrays: Update to 2.62.0. gnu: r-bioccheck: Update to 1.34.0. gnu: r-biocgraph: Update to 1.60.0. gnu: r-biocstyle: Update to 2.26.0. gnu: r-biocviews: Update to 1.66.0. gnu: r-experimenthub: Update to 2.6.0. gnu: r-grohmm: Update to 1.32.0. gnu: r-multiassayexperiment: Update to 1.24.0. gnu: r-bioconcotk: Update to 1.18.0. gnu: r-biocor: Update to 1.22.0. gnu: r-biocpkgtools: Update to 1.16.0. gnu: r-biocset: Update to 1.12.0. gnu: r-biocworkflowtools: Update to 1.24.0. gnu: r-biodist: Update to 1.70.0. gnu: r-pcatools: Update to 2.10.0. DRAFT gnu: r-rgreat: Update to 2.0.1. gnu: r-m3c: Update to 1.20.0. gnu: r-icens: Update to 1.70.0. gnu: r-preprocesscore: Update to 1.60.0. gnu: r-s4vectors: Update to 0.36.0. gnu: r-rgraphviz: Update to 2.42.0. gnu: r-fishpond: Update to 2.4.0. gnu: r-fithic: Update to 1.24.0. gnu: r-hitc: Update to 1.42.0. gnu: r-hdf5array: Update to 1.26.0. gnu: r-rhdf5lib: Update to 1.20.0. gnu: r-beachmat: Update to 2.14.0. gnu: r-cner: Update to 1.34.0. gnu: r-tfbstools: Update to 1.36.0. gnu: r-maftools: Update to 2.14.0. gnu: r-motifmatchr: Update to 1.20.0. gnu: r-chromvar: Update to 1.20.0. gnu: r-singlecellexperiment: Update to 1.20.0. gnu: r-singler: Update to 2.0.0. gnu: r-scuttle: Update to 1.8.0. gnu: r-scater: Update to 1.26.1. gnu: r-scran: Update to 1.26.0. gnu: r-sparsematrixstats: Update to 1.10.0. gnu: r-delayedmatrixstats: Update to 1.20.0. gnu: r-mscoreutils: Update to 1.10.0. gnu: r-msfeatures: Update to 1.6.0. gnu: r-biocio: Update to 1.8.0. gnu: r-msmseda: Update to 1.36.0. gnu: r-msmstests: Update to 1.36.0. gnu: r-catalyst: Update to 1.22.0. gnu: r-erma: Update to 1.14.0. gnu: r-ggbio: Update to 1.46.0. gnu: r-gviz: Update to 1.42.0. gnu: r-gwascat: Update to 2.30.0. gnu: r-kegggraph: Update to 1.58.0. gnu: r-ldblock: Update to 1.28.0. gnu: r-pathview: Update to 1.38.0. gnu: r-snpstats: Update to 1.48.0. gnu: r-chromstar: Update to 1.24.0. gnu: r-guitar: Update to 2.14.0. gnu: r-ballgown: Update to 2.30.0. gnu: r-megadepth: Update to 1.8.0. gnu: r-beclear: Update to 2.14.0. gnu: r-bgeecall: Update to 1.14.0. gnu: r-bgeedb: Update to 2.24.0. gnu: r-biobtreer: Update to 1.10.0. gnu: r-minet: Update to 3.56.0. gnu: r-genetclassifier: Update to 1.38.0. gnu: r-dir-expiry: Update to 1.6.0. gnu: r-basilisk-utils: Update to 1.10.0. gnu: r-basilisk: Update to 1.10.2. gnu: r-biocthis: Update to 1.8.1. gnu: r-biocdockermanager: Update to 1.10.0. gnu: r-biodb: Update to 1.6.0. gnu: r-biomformat: Update to 1.26.0. gnu: r-mvcclass: Update to 1.72.0. gnu: r-biomvcclass: Update to 1.66.0. gnu: r-biomvrcns: Update to 1.38.0. gnu: r-bionero: Update to 1.6.0. gnu: r-bionet: Update to 1.58.0. gnu: r-bionetstat: Update to 1.18.0. gnu: r-bioqc: Update to 1.26.0. gnu: r-biotip: Update to 1.12.0. gnu: r-biotmle: Update to 1.22.0. gnu: r-bsseq: Update to 1.34.0. gnu: r-dada2: Update to 1.26.0. gnu: r-dmrseq: Update to 1.18.0. gnu: r-omicade4: Update to 1.38.0. gnu: r-omnipathr: Update to 3.5.25. gnu: r-biscuiteer: Update to 1.12.0. gnu: r-tcgabiolinks: Update to 2.25.3. gnu: r-tricycle: Update to 1.6.0. gnu: r-tximeta: Update to 1.16.0. gnu: r-phyloseq: Update to 1.42.0. gnu/packages/bioconductor.scm | 1860 +++++++++++++++++---------------- gnu/packages/cran.scm | 52 +- gnu/packages/statistics.scm | 9 +- guix/build-system/r.scm | 2 +- guix/import/cran.scm | 4 +- 5 files changed, 1031 insertions(+), 896 deletions(-) -- 2.38.1 ------------=_1669368663-12447-1--