From unknown Fri Aug 15 15:36:36 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#48575 <48575@debbugs.gnu.org> To: bug#48575 <48575@debbugs.gnu.org> Subject: Status: [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor). Reply-To: bug#48575 <48575@debbugs.gnu.org> Date: Fri, 15 Aug 2025 22:36:36 +0000 retitle 48575 [PATCH 00/50] Move some Bioconductor packages to (gnu package= s bioconductor). reassign 48575 guix-patches submitter 48575 zimoun severity 48575 normal tag 48575 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:22:02 2021 Received: (at submit) by debbugs.gnu.org; 21 May 2021 20:22:02 +0000 Received: from localhost ([127.0.0.1]:37637 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBek-0008T6-3C for submit@debbugs.gnu.org; Fri, 21 May 2021 16:22:02 -0400 Received: from lists.gnu.org ([209.51.188.17]:36502) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBee-0008Se-Pk for submit@debbugs.gnu.org; Fri, 21 May 2021 16:22:00 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:51080) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBee-0002n8-K5 for guix-patches@gnu.org; Fri, 21 May 2021 16:21:56 -0400 Received: from mail-wm1-x332.google.com ([2a00:1450:4864:20::332]:53114) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBeZ-00021S-9Z for guix-patches@gnu.org; Fri, 21 May 2021 16:21:56 -0400 Received: by mail-wm1-x332.google.com with SMTP id z130so11749474wmg.2 for ; Fri, 21 May 2021 13:21:50 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=ynWUtDLp3YTo3cs0Bau+BpzrlQkquNF+iWM9/0+w5N4=; b=ctN2zlcyUxRKw9/4oLC/aGFPAuNn+PfU61MqN7czG5qc7Et2bCbnehJuGRVTSosHjt JBJWpPeDV8NyAxyp/BAN+Xfhj+/AYp8rMY5oZDsHnwY0077S+IJqBNGnauQ+GCO3XTAI 0Zw6I759C6FQDPudn8XZaVwdTeYWL0apGLVX/LDKkVJrUSHySzaniZSdkyiVxhvVLDLD MwVnDphwJsdv04bbG2OMPOzgDfOjluBk+02ktH3XGHN9yOcYgJLVdq532kFZMHiq2HUD n6ZRtR1Hv4ZJBQC60n1/l2MVtRDgm5D6YHfOCBkgBjxERv1NOMPoJwlPuXf1BbNitshr 654A== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=ynWUtDLp3YTo3cs0Bau+BpzrlQkquNF+iWM9/0+w5N4=; b=Qy+OcNC1V/C24NGMvW6b+98RV3FTmWMUC6Il2n+z2qdglZXsaY96JnWzo2Lh+YgDsl doS4p503wDuTq51SnPgiBiuM0TRef1/eoimEM3f4gypG/P2mBb0jz3rjW6VZ2TLe1DCb OhB/+ceUM5jKSElAI7XNFqL2bmbF2H5NGeDKXH41w8P7AEa/E2YDUrrUvxxU/7fluiIh 1SjXygNwRsdGApvVOMremro0dTApaCUdKjRuVMS1xJjWDuzbb8LTnQmVPyPOPVSGq+WZ v6bCKQAe4F0vdrFRj5988XCuShqFp7fK+b+pTP2pt4Ci92gXYQbcaY+8JsQEu8AuYSOu nVDg== X-Gm-Message-State: AOAM530a++9v571GTPX0zD/94ht30RnVc4/hP80XmUgkbqiaYfLqhsL7 SIqWe5lwNRCG6e0Qw1iRNLqcq+ChbAA= X-Google-Smtp-Source: ABdhPJykwCsHXSQATky+WUoDIHnFsCT1pf6yXs1R2WnGSxRoyRvOqGi8xRyJ21XfEns2NWboMJYDLA== X-Received: by 2002:a1c:5544:: with SMTP id j65mr10436699wmb.174.1621628509681; Fri, 21 May 2021 13:21:49 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id g10sm3227493wrq.12.2021.05.21.13.21.49 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:21:49 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:21:36 +0200 Message-Id: <20210521202136.26524-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 X-Debbug-CC: Ricardo Wurmus X-Debbugs-CC: Ricardo Wurmus Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::332; envelope-from=zimon.toutoune@gmail.com; helo=mail-wm1-x332.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, Janitor [1] patch set. It moves Bioconductor packages from (gnu packages bioinformatics) to (gnu packages bioconductor). 1: To transfer the Copyright, I use: git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r- I did my best to preserve the copyright. But I do not guarantee it is error-free. Well, in doubt, I have been conservative. Then, I do: guix build r- --no-grafts ./pre-inst-env guix build r- --no-grafts --check To avoid a break, I check with: for ci in $(git log --format="%H" -51 --reverse); do ./pre-inst-env guix pull --commit=$ci \ -p /tmp/test-${ci} \ --url=$(pwd) --branch=janitor --disable-authentication done and everyting seems fine. At least, "guix pull" should be checked at the end of the series. Last, I have checked the imported modules in gnu/packages/bioinformatics.scm. All should be fine. Now, I get: --8<---------------cut here---------------start------------->8--- $ ag 'bioconductor' gnu/packages/bioinformatics.scm 69: #:use-module (gnu packages bioconductor) 11550: (synopsis "Extra base functions for Bioconductor") 11553:provided by Bioconductor packages.") --8<---------------cut here---------------end--------------->8--- which ends the move, I guess. Except the package r-rcurl in gnu/packages/statistics.scm, let as an exercise for the reader. ;-) On a side note about the Copyright lines, I did: git blame --date=format:"%Y)" gnu/packages/bioinformatics.scm \ | cut -d')' -f1 | cut -d'(' -f2 | sed 's/ //g' \ | sort | uniq -c and it is possible that there is some "mistake", FWIW. All the best, simon zimoun (50): gnu: r-genomicalignments: Move to (gnu packages bioconductor). gnu: r-rtracklayer: Move to (gnu packages bioconductor). gnu: r-genomicfeatures: Move to (gnu packages bioconductor). gnu: r-topgo: Move to (gnu packages bioconductor). gnu: r-bsgenome: Move to (gnu packages bioconductor). gnu: r-msnid: Move to (gnu packages bioconductor). gnu: r-msnbase: Move to (gnu packages bioconductor). gnu: r-samr: Move to (gnu packages bioconductor). gnu: r-impute: Move to (gnu packages bioconductor). gnu: r-seqpattern: Move to (gnu packages bioconductor). gnu: r-go-db: Move to (gnu packages bioconductor). gnu: r-genomation: Move to (gnu packages bioconductor). gnu: r-genomationdata: Move to (gnu packages bioconductor). gnu: r-pcamethods: Move to (gnu packages bioconductor). gnu: r-mzid: Move to (gnu packages bioconductor). gnu: r-aroma-light: Move to (gnu packages bioconductor). gnu: r-deseq: Move to (gnu packages bioconductor). gnu: r-edaseq: Move to (gnu packages bioconductor). gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor). gnu: r-annotationhub: Move to (gnu packages bioconductor). gnu: r-fastseg: Move to (gnu packages bioconductor). gnu: r-affy: Move to (gnu packages bioconductor). gnu: r-keggrest: Move to (gnu packages bioconductor). gnu: r-gage: Move to (gnu packages bioconductor). gnu: r-complexheatmap: Move to (gnu packages bioconductor). gnu: r-genomicfiles: Move to (gnu packages bioconductor). gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor). gnu: r-organismdbi: Move to (gnu packages bioconductor). gnu: r-affyio: Move to (gnu packages bioconductor). gnu: r-vsn: Move to (gnu packages bioconductor). gnu: r-biovizbase: Move to (gnu packages bioconductor). gnu: r-ensembldb: Move to (gnu packages bioconductor). gnu: r-mzr: Move to (gnu packages bioconductor). gnu: r-protgenerics: Move to (gnu packages bioconductor). gnu: r-sva: Move to (gnu packages bioconductor). gnu: r-motifrg: Move to (gnu packages bioconductor). gnu: r-seqlogo: Move to (gnu packages bioconductor). gnu: r-zlibbioc: Move to (gnu packages bioconductor). gnu: r-rhtslib: Move to (gnu packages bioconductor). gnu: r-bamsignals: Move to (gnu packages bioconductor). gnu: r-rcas: Move to (gnu packages bioconductor). gnu: r-mutationalpatterns: Move to (gnu packages bioconductor). gnu: r-tximport: Move to (gnu packages bioconductor). gnu: r-rhdf5filters: Move to (gnu packages bioconductor). gnu: r-annotationfilter: Move to (gnu packages bioconductor). gnu: r-rhdf5: Move to (gnu packages bioconductor). gnu: r-chipseq: Move to (gnu packages bioconductor). gnu: r-copyhelper: Move to (gnu packages bioconductor). gnu: r-copywriter: Move to (gnu packages bioconductor). gnu: r-methylkit: Move to (gnu packages bioconductor). gnu/packages/bioconductor.scm | 1826 +++++++++++++++++++++++++++++-- gnu/packages/bioinformatics.scm | 1645 ---------------------------- gnu/packages/cran.scm | 30 - 3 files changed, 1749 insertions(+), 1752 deletions(-) base-commit: bd382fae71d899e243e81688bf5baed26171f2ea -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:26:45 2021 Received: (at 48575) by debbugs.gnu.org; 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Fri, 21 May 2021 13:26:36 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 02/50] gnu: r-rtracklayer: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:34 +0200 Message-Id: <20210521202622.26591-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here... * gnu/packages/bioconductor.scm (r-rtracklayer): ...to here. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 48 --------------------------------- 2 files changed, 48 insertions(+), 48 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4f4ff82ad0..42a3d1fffc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2385,6 +2385,54 @@ Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.") (license license:expat))) +(define-public r-rtracklayer + (package + (name "r-rtracklayer") + (version "1.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "rtracklayer" version)) + (sha256 + (base32 + "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + ((" zlibbioc,") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-xml" ,r-xml) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/rtracklayer") + (synopsis "R interface to genome browsers and their annotation tracks") + (description + "rtracklayer is an extensible framework for interacting with multiple +genome browsers (currently UCSC built-in) and manipulating annotation tracks +in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit +built-in). The user may export/import tracks to/from the supported browsers, +as well as query and modify the browser state, such as the current viewport.") + (license license:artistic2.0))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0d0fe1df30..9fb46c0d5d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7849,54 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-rtracklayer - (package - (name "r-rtracklayer") - (version "1.50.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "rtracklayer" version)) - (sha256 - (base32 - "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-zlib - (lambda _ - (substitute* "DESCRIPTION" - ((" zlibbioc,") "")) - (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) - (native-inputs - `(("pkg-config" ,pkg-config))) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) - (home-page "https://bioconductor.org/packages/rtracklayer") - (synopsis "R interface to genome browsers and their annotation tracks") - (description - "rtracklayer is an extensible framework for interacting with multiple -genome browsers (currently UCSC built-in) and manipulating annotation tracks -in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit -built-in). The user may export/import tracks to/from the supported browsers, -as well as query and modify the browser state, such as the current viewport.") - (license license:artistic2.0))) - (define-public r-genomicfeatures (package (name "r-genomicfeatures") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:26:46 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:26:46 +0000 Received: from localhost ([127.0.0.1]:37653 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjJ-00009I-27 for submit@debbugs.gnu.org; Fri, 21 May 2021 16:26:46 -0400 Received: from mail-wm1-f53.google.com ([209.85.128.53]:39496) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjF-00008P-V3 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:43 -0400 Received: by mail-wm1-f53.google.com with SMTP id l18-20020a1ced120000b029014c1adff1edso8057867wmh.4 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:41 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=96ryHvppI/z/svia7102m8CmVmrjcXgYuzJiXt9wTTc=; b=Nl+MzmJ2HXHezlDYlzkiXu2QwEFEFpMwrGPaKgJU+grDPwNpb+ugXFrODFUWo8gfHY ikScLu+2hjFBICvP6rp9EJ+fnjV9aBWcqQPRmmdiM0Y4Z9ezOQV6pYmAS9M2NHfR3gyH mtq9NMZTVjsFw+GP1OTLQ0FbCho6XUgBYMK/ZBIaiwA4ga8uwmkbSgEfzcwex+EVwXFy E9Badx0Zh2LgX2VOkz/r00e0nVqmQWc9pB3wRy+kL3/fCnBhyo74bt+6DD03T1pbdVbv AC8HMAA6ZP/QBafum0ZpecJux/X5oVqQmPWs+2zsWedVsjxj77+NWczCE4YPUZi2WSWG riXw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=96ryHvppI/z/svia7102m8CmVmrjcXgYuzJiXt9wTTc=; b=FljrsCVRf9PDFa1bKhReCQQyq6DkT45fU87JeNkEuapay3CQVyp/TldrJf7mZXSYFK lLTJDwZj1aBscbwttrypeSfl6VFzPi4RKRMYqkEa7g0/r76c8lNsMN9TKJo2GgOaORTC sDJWDTg5ohxtK22bwdeX4h0VVJBiCFHjjmEeAUrrfWGYAe6bePj9vyKjuQVGKuFLilAL dFkpH/74JXKubZT1Gz2UpVGInGABg9sQORSTfoLJIpklwSmM4ZwC6w07wSS67a42x+ds +4DrSLpQhO1d631UvkAS7EHQFyy9kSDXyw8pFfsZa/NI2LDS2WTZ7z/Py+0pimHEWs5D yMFQ== X-Gm-Message-State: AOAM530ufECfkkkdxgB+fRPcmry87JcFaRvEhZvKOiuR3DRgImDYi7A6 K1qjagCJNnL5+KQc40fsC3rvmgQJR7I= X-Google-Smtp-Source: ABdhPJxq1bow5xEdfUhZrd3iLR8WXZobKyfJllzY3DgHYEc6eYrC19buphz6h504w518uIuXuXuk8w== X-Received: by 2002:a7b:c7ca:: with SMTP id z10mr10583698wmk.185.1621628795867; Fri, 21 May 2021 13:26:35 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.35 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:35 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 01/50] gnu: r-genomicalignments: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:33 +0200 Message-Id: <20210521202622.26591-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here... * gnu/packages/bioconductor.scm (r-genomicalignments): ...to here. --- gnu/packages/bioconductor.scm | 35 ++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 33 ------------------------------- 2 files changed, 34 insertions(+), 34 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 45e31a5760..4f4ff82ad0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft @@ -2075,6 +2075,39 @@ translation between different chromosome sequence naming conventions (e.g., names in their natural, rather than lexicographic, order.") (license license:artistic2.0))) +(define-public r-genomicalignments + (package + (name "r-genomicalignments") + (version "1.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicAlignments" version)) + (sha256 + (base32 + "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr")))) + (properties + `((upstream-name . "GenomicAlignments"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/GenomicAlignments") + (synopsis "Representation and manipulation of short genomic alignments") + (description + "This package provides efficient containers for storing and manipulating +short genomic alignments (typically obtained by aligning short reads to a +reference genome). This includes read counting, computing the coverage, +junction detection, and working with the nucleotide content of the +alignments.") + (license license:artistic2.0))) + (define-public r-genomicranges (package (name "r-genomicranges") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9c77d66a35..0d0fe1df30 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7849,39 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomicalignments - (package - (name "r-genomicalignments") - (version "1.26.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicAlignments" version)) - (sha256 - (base32 - "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr")))) - (properties - `((upstream-name . "GenomicAlignments"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (home-page "https://bioconductor.org/packages/GenomicAlignments") - (synopsis "Representation and manipulation of short genomic alignments") - (description - "This package provides efficient containers for storing and manipulating -short genomic alignments (typically obtained by aligning short reads to a -reference genome). This includes read counting, computing the coverage, -junction detection, and working with the nucleotide content of the -alignments.") - (license license:artistic2.0))) - (define-public r-rtracklayer (package (name "r-rtracklayer") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:26:47 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:26:47 +0000 Received: from localhost ([127.0.0.1]:37658 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjK-00009o-Dp for submit@debbugs.gnu.org; Fri, 21 May 2021 16:26:47 -0400 Received: from mail-wm1-f46.google.com ([209.85.128.46]:35337) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjG-00008R-C0 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:43 -0400 Received: by mail-wm1-f46.google.com with SMTP id z19-20020a7bc7d30000b029017521c1fb75so8082826wmk.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:42 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=AO60ai6Yv31OKaIMJXpVdiQ7qPCI8knfx4IYHUtJGMk=; b=UPc3CAIg+9sOLID33P08jeiKPU3Vsi0B8wpPGBVxc55sH7lG3bP7kuR8vYrQA5kI2b UrmVfw6qdsC8iay2xJGU5nLDlQyF9HmVlakucIxTV/HxGU8HyraBwL153V4bIe9zuLCp QRztotUAe5OJZw5m/OOJFM9LWUIm1F0938jCXc5Ch0mPKNNituV5luer5QLSGLtTFVu3 fzuhkrArTigNwCDAlUhxsgnWaFrexR2Zb2YN8qvQB2eOCSj5LM7qFo1bmaVYbU3HVkN+ DimIvn/ZFPaHYJRi2r92O4+fYT4+NHjLcEW3LcHOiinEGnE+XXC8P53Mx1/1nVJfjBDU noZw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=AO60ai6Yv31OKaIMJXpVdiQ7qPCI8knfx4IYHUtJGMk=; b=R0cGoZqz/TCOokqW77+uk7AYewsMX08lshkPB2gh0s5tBklGk5iEZgVx1jorLnFgq5 jg/4kSaongQ+BUvkWgd0IvDQHn83Zn2TaNjnfiEc00u0z663EFilMZIGkNzfGefCQFgF MlXH4aGu0kQUd+fGLQwLNWd2hSye/XcCXrhjagOx7dUMievtn7BnooQS3YX/yjBL0PJ9 5IYZw4qYWzh5k+Ld91XsE6tTmbDwSsMhjhPQPRJ7wGVLLIUcIZfvEu+Vh8FKP4Jzh3Z3 u9DZqWUgpsrrMAXxh5pa8KKC0pc7KEmOh1Qk+wKRX7el9+1qqSu88DB+eAu5S79vz5Aw l2cw== X-Gm-Message-State: AOAM533oasAl5u6YkSRwqjwxhx/9liBgZ/4hNwQuEhTANacKWyYpHSQo GVeuMOx+lhmLoYmEvoEnKURoejfwvY8= X-Google-Smtp-Source: ABdhPJzmDtKKP/dUQYawI8fsWuGKFP3oI5dUST7czQg0uarTYMe0daQwMh5Nv7hyCYdV4gTaGuzQcQ== X-Received: by 2002:a05:600c:4f95:: with SMTP id n21mr10812211wmq.74.1621628796800; Fri, 21 May 2021 13:26:36 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.36 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:36 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 03/50] gnu: r-genomicfeatures: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:35 +0200 Message-Id: <20210521202622.26591-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here... * gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 --------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 42a3d1fffc..2263c17cc4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2108,6 +2108,49 @@ junction detection, and working with the nucleotide content of the alignments.") (license license:artistic2.0))) +(define-public r-genomicfeatures + (package + (name "r-genomicfeatures") + (version "1.42.3") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicFeatures" version)) + (sha256 + (base32 + "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz")))) + (properties + `((upstream-name . "GenomicFeatures"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GenomicFeatures") + (synopsis "Tools for working with transcript centric annotations") + (description + "This package provides a set of tools and methods for making and +manipulating transcript centric annotations. With these tools the user can +easily download the genomic locations of the transcripts, exons and cds of a +given organism, from either the UCSC Genome Browser or a BioMart +database (more sources will be supported in the future). This information is +then stored in a local database that keeps track of the relationship between +transcripts, exons, cds and genes. Flexible methods are provided for +extracting the desired features in a convenient format.") + (license license:artistic2.0))) + (define-public r-genomicranges (package (name "r-genomicranges") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9fb46c0d5d..bf8cb2f3a5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7849,49 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomicfeatures - (package - (name "r-genomicfeatures") - (version "1.42.3") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicFeatures" version)) - (sha256 - (base32 - "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz")))) - (properties - `((upstream-name . "GenomicFeatures"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/GenomicFeatures") - (synopsis "Tools for working with transcript centric annotations") - (description - "This package provides a set of tools and methods for making and -manipulating transcript centric annotations. With these tools the user can -easily download the genomic locations of the transcripts, exons and cds of a -given organism, from either the UCSC Genome Browser or a BioMart -database (more sources will be supported in the future). This information is -then stored in a local database that keeps track of the relationship between -transcripts, exons, cds and genes. Flexible methods are provided for -extracting the desired features in a convenient format.") - (license license:artistic2.0))) - (define-public r-go-db (package (name "r-go-db") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:09 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:09 +0000 Received: from localhost ([127.0.0.1]:37683 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjU-0000CX-FH for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:09 -0400 Received: from mail-wm1-f50.google.com ([209.85.128.50]:35342) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjH-00008W-Pa for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:44 -0400 Received: by mail-wm1-f50.google.com with SMTP id z19-20020a7bc7d30000b029017521c1fb75so8082861wmk.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:43 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=tc7IxdTSryxu41PLiIjT5EDICeRvUfP0FHfUM2vWOXo=; b=gjxnfeuWkD/DbxfgGS5wvEBrwjwj/3f4FlnirQ/kia7NOQYpP3Dn9lxKPbVlMyRQ5n LLIyNTnrFzGltRWJZpbfQXX6BE/mSTOcwwKDBhmvldjZ3MeX4coZmJpUJvGOksygxVI9 B3sU2ScE4w49KNy9e/YOwm1+Ix7zqgHM9lFl4/tlmv+ngwFakVyUoj6z8NcXGTUlahnW Q/6UxJK7wiAbBph72Bx0QKDYgHulohoMACFnaRX3oMBrg+aqWs5UVQ0F6n2xtOgZVFKS IL+UW0bvICCavUnn7XStmE+y0hILuiQi+T/ypSSE1Cc609qmk31LgQbkDoaQPuZvXZSf a3VQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=tc7IxdTSryxu41PLiIjT5EDICeRvUfP0FHfUM2vWOXo=; b=N9OwlXAZM0Q/Q5Dpr71B2J4PDF1cTPO2xCzBV9sejZNHJWV58pggEsUT4hzikt05qS ylB2aTcFYtGb8sK5V/+iY2n7UT2LI7VQC2YI5HSsLuF5Wyw8IO4xpdepRvBSTkGOcKGl 8Q5kMF99bNwcvJptt5WmNISdPs8DcVIhR1JqaNh3LpPv4cwgm/wRVSTsXBOHY4w1Je0E 7FKUvFGhMyM5DdVJMWjGoHTTaXc1HICIH/5NAuss3zTjF4htDpaecV2Qsn01RGZfwXaZ Lm2f70tElcAvSzlwfzHNPlucsyd05ilfImwV9bPEZPX3ERMEq76FkB3T/h1a7Bhrsh/K MUVQ== X-Gm-Message-State: AOAM531GttB002QR+7QM5ERQK8t63ICSEZ3iWf3EuSilm4VhajwLEe9T aO9vhG5xNhZ8e2QHuJLTsTNycMngeVg= X-Google-Smtp-Source: ABdhPJwksGfDHxjEb59+pWIH5RZcobe3OElguI+Y8zYqV8bI6fm/a7gIXGLl91FAxLFwG8j2ypul+A== X-Received: by 2002:a05:600c:4f8f:: with SMTP id n15mr2925612wmq.107.1621628798155; Fri, 21 May 2021 13:26:38 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.37 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:37 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 06/50] gnu: r-msnid: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:38 +0200 Message-Id: <20210521202622.26591-6-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-msnid): Move from here... * gnu/packages/bioconductor.scm (r-msnid): ...to here. --- gnu/packages/bioconductor.scm | 52 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 52 --------------------------------- 2 files changed, 52 insertions(+), 52 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 923413135b..b5787cb207 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2312,6 +2312,58 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-msnid + (package + (name "r-msnid") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MSnID" version)) + (sha256 + (base32 + "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d")))) + (properties `((upstream-name . "MSnID"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationhub" ,r-annotationhub) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocstyle" ,r-biocstyle) + ("r-biostrings" ,r-biostrings) + ("r-data-table" ,r-data-table) + ("r-doparallel" ,r-doparallel) + ("r-dplyr" ,r-dplyr) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-iterators" ,r-iterators) + ("r-msnbase" ,r-msnbase) + ("r-msmstests" ,r-msmstests) + ("r-mzid" ,r-mzid) + ("r-mzr" ,r-mzr) + ("r-protgenerics" ,r-protgenerics) + ("r-purrr" ,r-purrr) + ("r-r-cache" ,r-r-cache) + ("r-rcpp" ,r-rcpp) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-runit" ,r-runit) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-xtable" ,r-xtable))) + (home-page "https://bioconductor.org/packages/MSnID") + (synopsis "Utilities for LC-MSn proteomics identifications") + (description + "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data +from mzIdentML (leveraging the mzID package) or text files. After collating +the search results from multiple datasets it assesses their identification +quality and optimize filtering criteria to achieve the maximum number of +identifications while not exceeding a specified false discovery rate. It also +contains a number of utilities to explore the MS/MS results and assess missed +and irregular enzymatic cleavages, mass measurement accuracy, etc.") + (license license:artistic2.0))) + (define-public r-rbgl (package (name "r-rbgl") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9c9288c6b0..5c2abe6e94 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9275,58 +9275,6 @@ structure (pcaRes) to provide a common interface to the PCA results.") of mass spectrometry based proteomics data.") (license license:artistic2.0))) -(define-public r-msnid - (package - (name "r-msnid") - (version "1.24.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "MSnID" version)) - (sha256 - (base32 - "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d")))) - (properties `((upstream-name . "MSnID"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocstyle" ,r-biocstyle) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-msnbase" ,r-msnbase) - ("r-msmstests" ,r-msmstests) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-protgenerics" ,r-protgenerics) - ("r-purrr" ,r-purrr) - ("r-r-cache" ,r-r-cache) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-runit" ,r-runit) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-xtable" ,r-xtable))) - (home-page "https://bioconductor.org/packages/MSnID") - (synopsis "Utilities for LC-MSn proteomics identifications") - (description - "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data -from mzIdentML (leveraging the mzID package) or text files. After collating -the search results from multiple datasets it assesses their identification -quality and optimize filtering criteria to achieve the maximum number of -identifications while not exceeding a specified false discovery rate. It also -contains a number of utilities to explore the MS/MS results and assess missed -and irregular enzymatic cleavages, mass measurement accuracy, etc.") - (license license:artistic2.0))) - (define-public r-aroma-light (package (name "r-aroma-light") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:10 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:11 +0000 Received: from localhost ([127.0.0.1]:37704 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjh-0000EV-LL for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:10 -0400 Received: from mail-wm1-f48.google.com ([209.85.128.48]:36534) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjH-00008U-7q for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:45 -0400 Received: by mail-wm1-f48.google.com with SMTP id n17-20020a7bc5d10000b0290169edfadac9so8084325wmk.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:43 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=4gsQxzbRuhpoQd5rSV88rS+SfboPlsJKOXw3pQsN0rg=; b=EA/3rapxM0eaeGr0xK1X1Lm+kuaUsaRetC0sU1KGP8wP9HCANdrwcbUO9scBSAXwlG n+Aw280FYrpg5snqtjD2gMlFlS3qrzSbvlUCmo88LDsviBTWSGYC/VY2KxnZIL7MUpGA SIi7c/qKcS3FkrKf0oNZRV3SOZieDg2xkzr8/lzKYYS800qtXfSPZWlM5g9yG7wbFeyS 2jAwZjjKcjN4S2rKWY2bj8YOdF4jtOZS2ajcFb2TrDxRfp5Gj7u7kt3NjWuSC90QFguR c6+f0Ghn8n5mGa2C7iLYjVhwO2CZOZ93dSr2TPQPgllHlm1/hLd3w3tVKYh4fpR4jrSv ettw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=4gsQxzbRuhpoQd5rSV88rS+SfboPlsJKOXw3pQsN0rg=; b=Wii9J3XwzQky8ieIuqSyCvyZhXnyBGJru+apGt7EDB8IPXhoF8Q491cs/65D4t709z +ydWpK+oltgL+yB0VIDFMr9YN1dhI9P6ehiAD7hr1kshUOECi7t7IC6pEjFEopM6ACaL hb1lm38hutxS+It9Q+QneTxIDy/2Y5eoIRDV1tszS48XE6qaHLIZu4UNElv2fUn03ufm jSLAxV5gxWjdI+v6J2uoW+LZAsY11rEMxHJ/F3CcJqfSRDV+ZbKXcVpzt07Uwb9Dp7Ey orDZ5g/HgEwRYM22TRNaLbJPwPhLAIO/dcycE8xva1n2UIBYYloByhrSpd6aH0pt3Hps uF2w== X-Gm-Message-State: AOAM531kpeL1DNlPfM2ZU++3qkEBvAGqsKsnkcWgre/dqHLghjdI6CV4 K1dVdYItty8KoxBX6NSPTiAQD1fKvUA= X-Google-Smtp-Source: ABdhPJyEWP8ZutIDQIZ3A+Nf38Dai+D6Z0pOqZxODonLwt4aU6kVeY7haMlBgtvXSLMRi+UHrCfkZA== X-Received: by 2002:a7b:c3d4:: with SMTP id t20mr9931688wmj.13.1621628797701; Fri, 21 May 2021 13:26:37 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.37 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:37 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 05/50] gnu: r-bsgenome: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:37 +0200 Message-Id: <20210521202622.26591-5-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-bsgenome): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome): ...to here. --- gnu/packages/bioconductor.scm | 33 ++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2afb5214ee..923413135b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017 Efraim Flashner -;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu @@ -1875,6 +1875,37 @@ matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.") (license license:artistic2.0))) +(define-public r-bsgenome + (package + (name "r-bsgenome") + (version "1.58.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome" version)) + (sha256 + (base32 + "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq")))) + (properties + `((upstream-name . "BSgenome"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/BSgenome") + (synopsis "Infrastructure for Biostrings-based genome data packages") + (description + "This package provides infrastructure shared by all Biostrings-based +genome data packages and support for efficient SNP representation.") + (license license:artistic2.0))) + (define-public r-category (package (name "r-category") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 32d2b6a683..9c9288c6b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7873,37 +7873,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-bsgenome - (package - (name "r-bsgenome") - (version "1.58.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BSgenome" version)) - (sha256 - (base32 - "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq")))) - (properties - `((upstream-name . "BSgenome"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/BSgenome") - (synopsis "Infrastructure for Biostrings-based genome data packages") - (description - "This package provides infrastructure shared by all Biostrings-based -genome data packages and support for efficient SNP representation.") - (license license:artistic2.0))) - (define-public r-impute (package (name "r-impute") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:11 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:11 +0000 Received: from localhost ([127.0.0.1]:37706 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBji-0000Ex-UZ for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:11 -0400 Received: from mail-wm1-f48.google.com ([209.85.128.48]:45720) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjI-00008X-3G for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:45 -0400 Received: by mail-wm1-f48.google.com with SMTP id s5-20020a7bc0c50000b0290147d0c21c51so7796208wmh.4 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:44 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=sEI0QpP50D3ePFXyCNJNLyhBWd55pfePWc1v0CRAHCo=; b=r/KAWHTXPALECbbo/K4IW6oKfbiqbp/AYPe/DiG4u2VE/CgelvzNTB0z2mhmLfTuoz /76zSrAOCo0o7Dmchzz7fJMTOUQ6cAspT05yW5ziyzQ272jAX3d95pWOiy4e5WbVxLm2 QC4M/vexpLLsGRzHVpBZ+JmCVpItZAudt8sxglgQxo8Ra1LFbOVtu3dW+qaG4WBJ0rKK ge/a4lAHMz+RxTFa22nzHGSSpdHiLP45+eS2mioSqdRBzafZyg4heNsf/fe9JP79lZbF JenU+jLPzvq3CIhskbmNKXGiQsoE8rSSIDH9LCWjHi+5E4arQPDP6BX5x0/WjIB7k/4D iZeg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=sEI0QpP50D3ePFXyCNJNLyhBWd55pfePWc1v0CRAHCo=; b=hQWBgvslkvARgfGQR+2x3flD17Q+VYK7MEGSxGbUau7qcoQhQwX4pDWg9KG/DMr4lt CmmUwlDXgJ+55D0R3cBFCDcarpLwgIwClrnrDgb91Io5dMaU2Acopw2opoESGXQTre5U LFMMSQO45xlH6Lkg8Ejjy7YJVvNamoa51/gs7ye71M+bSLAOSUXYCWk1dH4xOqvUqh+M KmX83EjmhqPC9z2z6GQbTY6ueHUYQb9a4wTO8PePXGnrj8X+AOqOXFQfoK3fi9p2fZGD Q9pRQ95gnCQnZUSvO5CA0IB89z+Yrkk4EoXaIKrkK0B0b+x+bYrLCxeG4H6cw/DyVVY/ 6g0Q== X-Gm-Message-State: AOAM5301jfpTm2jJ6sfjgijyD5lVEcQyEcotnDQAybkb5MfwYzC97mgg Iylq2ev9JIJCQQEUFzRkjkAjXuWWDRM= X-Google-Smtp-Source: ABdhPJzuV55gxxU+38dCx7hGx2eq8hj8QreiEB/+sqR5Jilz7z8Qew6FaDVVJrw91reNnMRFNgAABA== X-Received: by 2002:a05:600c:4f0b:: with SMTP id l11mr10528436wmq.126.1621628798628; Fri, 21 May 2021 13:26:38 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.38 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:38 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 07/50] gnu: r-msnbase: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:39 +0200 Message-Id: <20210521202622.26591-7-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-msnbase): Move from here... * gnu/packages/bioconductor.scm (r-msnbase): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 --------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b5787cb207..58c8336ce5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2312,6 +2312,51 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-msnbase + (package + (name "r-msnbase") + (version "2.16.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MSnbase" version)) + (sha256 + (base32 + "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h")))) + (properties `((upstream-name . "MSnbase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-digest" ,r-digest) + ("r-ggplot2" ,r-ggplot2) + ("r-impute" ,r-impute) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-maldiquant" ,r-maldiquant) + ("r-mass" ,r-mass) + ("r-mzid" ,r-mzid) + ("r-mzr" ,r-mzr) + ("r-pcamethods" ,r-pcamethods) + ("r-plyr" ,r-plyr) + ("r-preprocesscore" ,r-preprocesscore) + ("r-protgenerics" ,r-protgenerics) + ("r-rcpp" ,r-rcpp) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-vsn" ,r-vsn) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/lgatto/MSnbase") + (synopsis "Base functions and classes for MS-based proteomics") + (description + "This package provides basic plotting, data manipulation and processing +of mass spectrometry based proteomics data.") + (license license:artistic2.0))) + (define-public r-msnid (package (name "r-msnid") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5c2abe6e94..28893c40e7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9230,51 +9230,6 @@ the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) -(define-public r-msnbase - (package - (name "r-msnbase") - (version "2.16.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "MSnbase" version)) - (sha256 - (base32 - "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h")))) - (properties `((upstream-name . "MSnbase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-digest" ,r-digest) - ("r-ggplot2" ,r-ggplot2) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-maldiquant" ,r-maldiquant) - ("r-mass" ,r-mass) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-pcamethods" ,r-pcamethods) - ("r-plyr" ,r-plyr) - ("r-preprocesscore" ,r-preprocesscore) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-vsn" ,r-vsn) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/lgatto/MSnbase") - (synopsis "Base functions and classes for MS-based proteomics") - (description - "This package provides basic plotting, data manipulation and processing -of mass spectrometry based proteomics data.") - (license license:artistic2.0))) - (define-public r-aroma-light (package (name "r-aroma-light") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:11 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:11 +0000 Received: from localhost ([127.0.0.1]:37708 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjj-0000F4-Aw for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:11 -0400 Received: from mail-wm1-f54.google.com ([209.85.128.54]:45726) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjI-00008Y-Jd for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:45 -0400 Received: by mail-wm1-f54.google.com with SMTP id s5-20020a7bc0c50000b0290147d0c21c51so7796219wmh.4 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:44 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=FpMwdoUajN9MlX1EuMrEntzImgJjKlsOi0ZsYhyH0JM=; b=YGwFhuJKZjIWPmx3uMxKPLW7LkagKPP9ifXCjmlayAkJODC4QzwwRmoE5kPzSGMdOD iUi0egdSgC+WVaygyQYrya9thH3jIUdqOxBnuDoAW+OENNtpzX5XSFmh5XJwpRZkX1F7 ljeereC5x98XVzJV7SoVJByjbKHBTBAtH9mX6Xib5D4nGKpNIiUqZiJmjTxpp/aPZEiL MRLkuT2NnJGDVKTrkC5cs+BRnqO8JOTyLhxT5mnZWioQactMtEN6JX0MnRfc0Sws9NI0 m2P/FgZSzo2W/KXYXXu+0LNIIC1m5obfJuhQsh7SPXEUCqFpcrLHYpsf4ML78C7HC67/ sf0Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=FpMwdoUajN9MlX1EuMrEntzImgJjKlsOi0ZsYhyH0JM=; b=hbwGGsEG/BgMox0uAugrxLSnyiR9eZC/co3EUIhQ3JSrUPRu59yJ990qOgdJAvtQLn pB//dDwDfphor+3z8V8J8olVtyuNcAOupsOq1/2C4ePycNBLwQNF2zJDcuUU2il+CJIR U3zxld6DCYEVy/0+UWJjafjn1nyz78mxTOepaItVmyMBiu81akha0u/iARJGXhUJnqM9 Jo8jFxdH3yjje46gyl9zbl50/hK29eQpFGMTyQS+JSL+vBy53susklRVPfBS9iGreRpq RAT36yFBZcz5hfGhKuWfWhtDafHfK8UdsWn+nApRU3xauiwS5hiDqGVXXLZvwThEClGK q7EA== X-Gm-Message-State: AOAM533BwF1/mMQsKcdlxQ0eXkIs/gBi+afRN+WlDAkqVWNiC1sdJIU4 7Wp+wPLkJLtAS6ec9TzusFPXXEk2H1Y= X-Google-Smtp-Source: ABdhPJyXBvBW1pfFNJk2S8n2rdKz2IiIHMY8qgg0v1zhqHbsd9ObYegx337yUleKXB5My42p9aELuA== X-Received: by 2002:a7b:c5cd:: with SMTP id n13mr10317337wmk.97.1621628799042; Fri, 21 May 2021 13:26:39 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.38 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:38 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 08/50] gnu: r-samr: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:40 +0200 Message-Id: <20210521202622.26591-8-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/cran.scm (r-samr): Move from here... * gnu/packages/bioconductor.scm (r-samr): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/cran.scm | 30 ------------------------------ 2 files changed, 31 insertions(+), 30 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 58c8336ce5..f9aa34d254 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2021 Hong Li +;;; Copyright © 2021 Tim Howes ;;; ;;; This file is part of GNU Guix. ;;; @@ -2604,6 +2605,36 @@ built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on a Bioconductor package. +(define-public r-samr + (package + (name "r-samr") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "samr" version)) + (sha256 + (base32 + "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) + (properties `((upstream-name . "samr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gsa" ,r-gsa) + ("r-impute" ,r-impute) + ("r-matrixstats" ,r-matrixstats) + ("r-openxlsx" ,r-openxlsx) + ("r-shiny" ,r-shiny) + ("r-shinyfiles" ,r-shinyfiles))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://statweb.stanford.edu/~tibs/SAM/") + (synopsis "Significance analysis of Microarrays") + (description + "This is a package for significance analysis of Microarrays for +differential expression analysis, RNAseq data and related problems.") + ;; Any version of the LGPL + (license license:lgpl3+))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8709cd21fa..e5d1db7cb6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33,7 +33,6 @@ ;;; Copyright © 2020 Magali Lemes ;;; Copyright © 2020 Simon Tournier ;;; Copyright © 2020 Aniket Patil -;;; Copyright © 2021 Tim Howes ;;; ;;; This file is part of GNU Guix. ;;; @@ -28629,35 +28628,6 @@ indicator, a quantitative variable or a survival time.") ;; Any version of the LGPL (license license:lgpl3+))) -(define-public r-samr - (package - (name "r-samr") - (version "3.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "samr" version)) - (sha256 - (base32 - "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) - (properties `((upstream-name . "samr"))) - (build-system r-build-system) - (propagated-inputs - `(("r-gsa" ,r-gsa) - ("r-impute" ,r-impute) - ("r-matrixstats" ,r-matrixstats) - ("r-openxlsx" ,r-openxlsx) - ("r-shiny" ,r-shiny) - ("r-shinyfiles" ,r-shinyfiles))) - (native-inputs `(("gfortran" ,gfortran))) - (home-page "https://statweb.stanford.edu/~tibs/SAM/") - (synopsis "Significance analysis of Microarrays") - (description - "This is a package for significance analysis of Microarrays for -differential expression analysis, RNAseq data and related problems.") - ;; Any version of the LGPL - (license license:lgpl3+))) - (define-public r-randomforestsrc (package (name "r-randomforestsrc") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:12 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:12 +0000 Received: from localhost ([127.0.0.1]:37710 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjj-0000FB-Pa for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:12 -0400 Received: from mail-wm1-f43.google.com ([209.85.128.43]:35337) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjJ-00008a-1t for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:46 -0400 Received: by mail-wm1-f43.google.com with SMTP id z19-20020a7bc7d30000b029017521c1fb75so8082897wmk.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:45 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=UlvPVd/RNzKO8kaBX7Chi2pGsq/foEj0l7hjxhhY4IU=; b=E/7ckTKmo5ndqOWKd3jjznAKHniFvTrgTGh2u8ULpFdAz7WtDwgeK6ODKpeRdvXaUY 5Ra6PNi1am9Ambe6Ty+PzmqYo4VT8HOERZHo2NY6lkJjNC6XAK/QIJ1nxSAxxDxmD1Vy 4FXTym2g1wjEnNtJt0RzdOZW7q9TPMpn0s/CQmMl90JdE56AxG66Atbv7LrDIlfmjF6v MT7skQK4pT8XKRbBDBMx5JZwQpLXzNQ4bea0tju95OQlnzERu6w2H5390jeaOnpygswx Bpe6GUAYf3vE6g0bNAh5Yh9cgiDkmXO/gZyneSyq9OdxDhqSL1WXNcDIYr11NqKo8hfW JQkA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=UlvPVd/RNzKO8kaBX7Chi2pGsq/foEj0l7hjxhhY4IU=; b=VADy+jqa6t5y11m6GWg+H9yYctd+kjXx2bowyFPDC9bfn8wB8P1/KxQaKPIETeb7lA Dfn7MxuJrXkc/5YO/rq01m/S6k6syaTfCLXfc5rX2EZE2Sx6MQb6lsSh/ZwpZv2ODKYM bzviPCbq7UrzaWDddwLtNpzLOycYT8xZLDYqyGXkRZ/YBmfAWoxiKU2vmsPLvqTzlRpN D5TiRmAXkYxOzPIM9pvlzzRw++XAAcqwvuXACcdi9hKn2fbT0FQZbNtFWdrWaOUmp1N+ IW47LsqzWfkASY5ZlvUmKV2i96VKbJG3vNqeQW5U4A3lauOGlNjhpzcDkBmq4/SnYFRN v96Q== X-Gm-Message-State: AOAM530glmHs4J3bWzh5AavqewgIxn4VOtdGqr3eyKgS1kgraHWjTf3e AQZkq36JUZOWA+H9Ie0UcafQwDduIGI= X-Google-Smtp-Source: ABdhPJzEeTlCx3iTTwvMmM7LUEr9wzvjd+gcBJH9eVm/ZdrZkFAFSRtujAQlZX+hYPfZSfIVNm2U9w== X-Received: by 2002:a05:600c:49a2:: with SMTP id h34mr10862381wmp.64.1621628799534; Fri, 21 May 2021 13:26:39 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.39 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:39 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 09/50] gnu: r-impute: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:41 +0200 Message-Id: <20210521202622.26591-9-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-impute): Move from here... * gnu/packages/bioconductor.scm (r-impute): ...to here. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ gnu/packages/bioinformatics.scm | 20 -------------------- 2 files changed, 20 insertions(+), 20 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f9aa34d254..0b40d70397 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2294,6 +2294,26 @@ Enrichment Analysis} (GSEA).") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-impute + (package + (name "r-impute") + (version "1.64.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "impute" version)) + (sha256 + (base32 + "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa")))) + (native-inputs + `(("gfortran" ,gfortran))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/impute") + (synopsis "Imputation for microarray data") + (description + "This package provides a function to impute missing gene expression +microarray data, using nearest neighbor averaging.") + (license license:gpl2+))) + (define-public r-limma (package (name "r-limma") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 28893c40e7..ef5c1a3323 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7873,26 +7873,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-impute - (package - (name "r-impute") - (version "1.64.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "impute" version)) - (sha256 - (base32 - "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa")))) - (native-inputs - `(("gfortran" ,gfortran))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/impute") - (synopsis "Imputation for microarray data") - (description - "This package provides a function to impute missing gene expression -microarray data, using nearest neighbor averaging.") - (license license:gpl2+))) - (define-public r-seqpattern (package (name "r-seqpattern") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:12 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:12 +0000 Received: from localhost ([127.0.0.1]:37712 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjk-0000FJ-5P for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:12 -0400 Received: from mail-wm1-f47.google.com ([209.85.128.47]:43629) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjJ-00008b-F1 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:46 -0400 Received: by mail-wm1-f47.google.com with SMTP id z85-20020a1c7e580000b029017a76f3afbaso5254727wmc.2 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:45 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=oJpu37ZGZSHienBIpUNS1smzwtnN+P+v9Fbp2Aa9ihw=; b=u63C2jazNgnlGPEyrLGVj6nVi3ArY8nRKv3YAz1k3h2XXXHefde4mljiaTJM3Yxeu1 /uhFmTF3Y5o86U7qm3G+VFuWE0Kjg2YYQObpDAtu+w+SJpDg8nxDx0DmIS8QquUqoLs9 Mg4fwjh/GNFkFgzYoH7zeSQcA3SURU91McNdCSIux3vifRJgGzLDswsiEwF5gd4/geBE 4zye9g6L//RpqJdGQjDXMTjacr8aqrfzf5Tw5tXdIlmkDT2T+HXdI4D+OhyITtjHvh3A s1xc9M440ESXQHfSyy9Q2F0ry7xAkM6+lTCDMO7CnJyJVEC9twx+rWv18tnTYnXDyqhA LPzA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=oJpu37ZGZSHienBIpUNS1smzwtnN+P+v9Fbp2Aa9ihw=; b=CU5K+eiwhz7Le5SlQrbhANAcfzRbVnVpHU3oZAt9AIbIoLVTlJB/lcrTeYt4zh6dzx yvKsIwPUhwizXBjAExKUpajC/ZZrdZK0/tUTv16n8U6inrT8LeVT6kJ2tGcKqYKhaanr dhmJJrF//ASnMUAX7D8NnGyJ6YEO8DMIBKuzrGGL3GKOWDLybPBGgdHm3pAqb8nIvxo+ 9KFYlk1b3PHrHlWY/sXQ8IrJniqXt35Aa5n9WJrb2D/WxnjTB4JOW/XDymrSjU71GaqO RIawBQkvnQh13PHjw2h5P+NniwjmNSKUzmi6HjLmqKEUtfeLu5QhJYwBLWD9g1KSo3f5 Btaw== X-Gm-Message-State: AOAM5329SThS4zQfSBR4YdcFtf+VKtJRtygY1V45pUMUrShbwdYcBvby BbOs7lyLXheci5JsGPvllu8Yjv3FyLg= X-Google-Smtp-Source: ABdhPJz+Srv90X+ctq/pQBNlTUlADCRkgOVXH5ygTkYp/PtL+rOUk2WTQYN2mSDBETHQOMQW2Kg9qA== X-Received: by 2002:a05:600c:3227:: with SMTP id r39mr10335501wmp.26.1621628799950; Fri, 21 May 2021 13:26:39 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.39 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:39 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 10/50] gnu: r-seqpattern: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:42 +0200 Message-Id: <20210521202622.26591-10-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-seqpattern): Move from here... * gnu/packages/bioconductor.scm (r-seqpattern): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b40d70397..1b1b00cde0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2655,6 +2655,33 @@ differential expression analysis, RNAseq data and related problems.") ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-seqpattern + (package + (name "r-seqpattern") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "seqPattern" version)) + (sha256 + (base32 + "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq")))) + (properties + `((upstream-name . "seqPattern"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) + ("r-plotrix" ,r-plotrix))) + (home-page "https://bioconductor.org/packages/seqPattern") + (synopsis "Visualising oligonucleotide patterns and motif occurrences") + (description + "This package provides tools to visualize oligonucleotide patterns and +sequence motif occurrences across a large set of sequences centred at a common +reference point and sorted by a user defined feature.") + (license license:gpl3+))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ef5c1a3323..71e1481af2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7873,33 +7873,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-seqpattern - (package - (name "r-seqpattern") - (version "1.22.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "seqPattern" version)) - (sha256 - (base32 - "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq")))) - (properties - `((upstream-name . "seqPattern"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-plotrix" ,r-plotrix))) - (home-page "https://bioconductor.org/packages/seqPattern") - (synopsis "Visualising oligonucleotide patterns and motif occurrences") - (description - "This package provides tools to visualize oligonucleotide patterns and -sequence motif occurrences across a large set of sequences centred at a common -reference point and sorted by a user defined feature.") - (license license:gpl3+))) - (define-public r-genomation (package (name "r-genomation") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:12 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:13 +0000 Received: from localhost ([127.0.0.1]:37714 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjk-0000FR-Ha for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:12 -0400 Received: from mail-wm1-f46.google.com ([209.85.128.46]:45720) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjJ-00008d-VH for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:46 -0400 Received: by mail-wm1-f46.google.com with SMTP id s5-20020a7bc0c50000b0290147d0c21c51so7796250wmh.4 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:45 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=NupaNl4ohhkSij9CCb7VPSvDXbPWgFprF2Ufq1jtiq0=; b=EN8JTcXnTtzeOV6GcbJ0GxSKBbKb7p3Kiitap7rJYU+Wx486EJUT4SPHhll3X04Xpj CHBK5/EQjddfJObPKl9XBCb1Mmt+Ckp4njcs80ISVWGhaoQBsPPhV2nEr63uHGABWvNe XMTDdPj6EiHqjNXOFMG+9X5NCJ1GzuVCamL1cNroGqf5lAz6qqItnv2DYAXKdctTM8vY w6450xSYnA9JjS3NgOG2XNoSt87Ne5od1ZD0KV1L+8oxc08rYORRHJhZaW8cxyXNvKZL KiHdhmxzmYjlvHdTLCyn4S1atIeliV0wqt09dNWsOrFLV3YsUT3NAFX6FuDQC000eNqR AQUA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=NupaNl4ohhkSij9CCb7VPSvDXbPWgFprF2Ufq1jtiq0=; b=Z9tJaiHOMDILWYibxpcwzcImEQORf+/OiWMSF5H3+98wLBy1YxgVK0SLx/A7wj06oV wGHFQ/fTbkYMOMY/hkUeO7o/IIn6dt0Ntdjj4xe16U6h4Gu9c6uM9ZaFlQDgY8h3yVpE A37zUt5BTPlyB2Ej2UScjevxNsBGLN0vNS7Kumiwa5wp1NE/WYeMdp0S2zf9z3SHptAj dgeFz4NKol1iUNyjHxsLYWdbO5zCcpJKg156puKos9xs2Q69lZPSEPkrjRWLEm34ripp Hwf9jDCba+Ug7ZdAPOeldrAxM0OxqcYA+Hqd/ZgpPbtu1ZYNjP4CgarrjPgOgCl3KqBb Zj1Q== X-Gm-Message-State: AOAM533fGRVIo6Ak3a1Kz3ZQ/+ouGGX30fU7CDnbq/gq7crCWy4F2e6O U0PF9FrdAEJau3ZSiJNhqJLWZymVdSw= X-Google-Smtp-Source: ABdhPJxpAwhUsS0cLwKmVP1GbYGg4BbYlabslwTc98y2mrCzz8Ob0NIFd0A1AwgEj2RhQsPQEv22EA== X-Received: by 2002:a1c:7516:: with SMTP id o22mr10594002wmc.91.1621628800431; Fri, 21 May 2021 13:26:40 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.40 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:40 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 11/50] gnu: r-go-db: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:43 +0200 Message-Id: <20210521202622.26591-11-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-go-db): Move from here... * gnu/packages/bioconductor.scm (r-go-db): ...to here. [source]: Replace 'string-append' by 'bioconductor-uri' with 'annotation. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 22 insertions(+), 24 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1b1b00cde0..eb73909723 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -413,6 +413,28 @@ in Biostrings objects.") ID and species. It is used by functions in the GenomeInfoDb package.") (license license:artistic2.0))) +(define-public r-go-db + (package + (name "r-go-db") + (version "3.7.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GO.db" version 'annotation)) + (sha256 + (base32 + "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5")))) + (properties + `((upstream-name . "GO.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/GO.db") + (synopsis "Annotation maps describing the entire Gene Ontology") + (description + "The purpose of this GO.db annotation package is to provide detailed +information about the latest version of the Gene Ontologies.") + (license license:artistic2.0))) + (define-public r-homo-sapiens (package (name "r-homo-sapiens") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 71e1481af2..71f07748b6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7849,30 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-go-db - (package - (name "r-go-db") - (version "3.7.0") - (source (origin - (method url-fetch) - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/GO.db_" - version ".tar.gz")) - (sha256 - (base32 - "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5")))) - (properties - `((upstream-name . "GO.db"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) - (home-page "https://bioconductor.org/packages/GO.db") - (synopsis "Annotation maps describing the entire Gene Ontology") - (description - "The purpose of this GO.db annotation package is to provide detailed -information about the latest version of the Gene Ontologies.") - (license license:artistic2.0))) - (define-public r-genomation (package (name "r-genomation") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:25 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:25 +0000 Received: from localhost ([127.0.0.1]:37719 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjx-0000G3-0w for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:25 -0400 Received: from mail-wm1-f48.google.com ([209.85.128.48]:41776) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjK-00008e-Em for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:47 -0400 Received: by mail-wm1-f48.google.com with SMTP id l11-20020a05600c4f0bb029017a7cd488f5so5153338wmq.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:46 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=uV9J60wXEm55wLqIR3zB80d1Sl46wMxTOfb2GfAMYO0=; b=O8StaTHkWTaCnqgAADYgb9eKD2mU4Dx/rOMfisSzbwNpWInM52ADpC1Rw/bTp6p6VN mOXzu0Cjr4FyGtlqiCz/j+q0DTrpucChsG3mJrf598fseK3zgd45bomPkRq1HQX2MzRP Y3xkNR4nH9sd4zE+js8XWi4cJLJ8yEA4TUC+J9LQglsiV5EnCGSAUUv4O7evAwZvtF8u kxwBKYcs4ImGoM1yofpSRAMaF0vEShUPSQKQ5F+zWK65SLekJtLEecYbm+0+/v5XxYp7 uRXNu5/TiExV23ehYGcKh1qNADGxDZo0OQ+H8ZSXFTHw3zsjc8zVUBLKMHdqoHK2bJD4 hGww== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=uV9J60wXEm55wLqIR3zB80d1Sl46wMxTOfb2GfAMYO0=; b=EYLNqLOPszssn5/2GThejasLN4vH5bLPSZHeoUpxF8lmxCtchY8WTGSQIEMElVVDn6 XOJ3PFDAiA9Ds78FtxesxEYRVhAFkZx5tpbXTGQfyRJONGvfiOhi2n4FfhLINf5URk9Z KAfhygtmhFAMEeL6KsW9mWN6IK+9VPdEZlDatZFKBfLXdrd9qNNTx1HftTaoVKCfk9WV QxXpXgDoBFy9wlz///VvoRLSM6jUhDa5SrUNC2Ogq3AQI0jsRDGMPtf1CYR00Nsg3Ptw Q7dIwqxwyjx4/9cgQqHvKQf3B6vB/7c6S5a5c4qB7ABCJRqesNBbGtNyjsza6CrLcYNR 7Hmw== X-Gm-Message-State: AOAM532XloYI1Xyf4C+wsZ4dn+Ce6t9Arbgf3ZH7QK5ElMYeTZgzumAa 0F64awHwy3MPoorK7/6qM55ppc/cxL0= X-Google-Smtp-Source: ABdhPJw+jHmMkMLRxzbyD54P1njnaL/VP5j06dYFJwikkhBhgzN05vHhl12mG+5RQOt1FhdwcCzo5w== X-Received: by 2002:a05:600c:410a:: with SMTP id j10mr10586240wmi.5.1621628800928; Fri, 21 May 2021 13:26:40 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.40 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:40 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 12/50] gnu: r-genomation: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:44 +0200 Message-Id: <20210521202622.26591-12-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.7 (/) X-Debbugs-Envelope-To: 48575 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: -0.3 (/) * gnu/packages/bioinformatics.scm (r-genomation): Move from here... * gnu/packages/bioconductor.scm (r-genomation): ...to here. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 48 --------------------------------- 2 files changed, 48 insertions(+), 48 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eb73909723..2be7920770 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2099,6 +2099,54 @@ CAGE.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-genomation + (package + (name "r-genomation") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "genomation" version)) + (sha256 + (base32 + "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-data-table" ,r-data-table) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-gridbase" ,r-gridbase) + ("r-impute" ,r-impute) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-plotrix" ,r-plotrix) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) + ("r-readr" ,r-readr) + ("r-reshape2" ,r-reshape2) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-runit" ,r-runit) + ("r-s4vectors" ,r-s4vectors) + ("r-seqpattern" ,r-seqpattern))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioinformatics.mdc-berlin.de/genomation/") + (synopsis "Summary, annotation and visualization of genomic data") + (description + "This package provides a package for summary and annotation of genomic +intervals. Users can visualize and quantify genomic intervals over +pre-defined functional regions, such as promoters, exons, introns, etc. The +genomic intervals represent regions with a defined chromosome position, which +may be associated with a score, such as aligned reads from HT-seq experiments, +TF binding sites, methylation scores, etc. The package can use any tabular +genomic feature data as long as it has minimal information on the locations of +genomic intervals. In addition, it can use BAM or BigWig files as input.") + (license license:artistic2.0))) + (define-public r-genomeinfodb (package (name "r-genomeinfodb") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 71f07748b6..f8e7b2cab9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7849,54 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomation - (package - (name "r-genomation") - (version "1.22.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "genomation" version)) - (sha256 - (base32 - "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-data-table" ,r-data-table) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridbase" ,r-gridbase) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-plotrix" ,r-plotrix) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-runit" ,r-runit) - ("r-s4vectors" ,r-s4vectors) - ("r-seqpattern" ,r-seqpattern))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioinformatics.mdc-berlin.de/genomation/") - (synopsis "Summary, annotation and visualization of genomic data") - (description - "This package provides a package for summary and annotation of genomic -intervals. Users can visualize and quantify genomic intervals over -pre-defined functional regions, such as promoters, exons, introns, etc. The -genomic intervals represent regions with a defined chromosome position, which -may be associated with a score, such as aligned reads from HT-seq experiments, -TF binding sites, methylation scores, etc. The package can use any tabular -genomic feature data as long as it has minimal information on the locations of -genomic intervals. In addition, it can use BAM or BigWig files as input.") - (license license:artistic2.0))) - (define-public r-genomationdata (package (name "r-genomationdata") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:25 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:25 +0000 Received: from localhost ([127.0.0.1]:37716 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjk-0000FY-T5 for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:24 -0400 Received: from mail-wm1-f42.google.com ([209.85.128.42]:36528) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjG-00008T-RK for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:47 -0400 Received: by mail-wm1-f42.google.com with SMTP id n17-20020a7bc5d10000b0290169edfadac9so8084315wmk.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:42 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=UV9O53g0n60AWk1dh5JP6SRfk4+pzTyD9hpiRQggXSM=; b=mGuAJa46Ivkwv+o2dpE1gtvQb7A6PtODgm8xdoqkJCU4W4qvKRk1y9Tv1Mt+A0qLSc LANg4ZJKPwWNHD6XTbA5JMpUnUblIxVlQCBhAAL+vWdsHdgN2vTCHcp9aTOtnC4Ci42m Elju0B5vD58+F49qVt+FWmi7Guj0f8Is0amvMpAcxdzuZZcI0Yb31QrtDgeCmnakUwAk 9y1YEzBaCTeOaIqmcx/Pyi29Y1oWK/vJcaWgoN0u22B7MpIbs2KNGTrcPypvZoKjbFRx YBLsmtz8TmFxA/u9V1GGLldcDcHpsSV1QU1N6EriccNvBCDVSaUiuW9OSc5bnM0lHcP+ X3Pw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=UV9O53g0n60AWk1dh5JP6SRfk4+pzTyD9hpiRQggXSM=; b=dWr8tMHPq4DAL1yPA+Aw0szKqbspY7ooUbpnNdvL8Cun/Rsj3ElewPCGdvDRdRWIKB POBOsrLxyUEDCGPLIHnEiVyfY5/PB1w2/hNMwEEl3yTwebEnKiVXCFZB4SysO24iL2cU zQE2pHHvdBmWjESSdUAuHlFokUyik9Z+9y1euQonfmd7DhQD7gKBqRslijzoBihDzvS1 ds5BL/zYhEOoR7K1ivpeZ988Q6H0lLbGvyypPGCP3fNsBfN3OJAvRYcT/hRoLPcdPA3R pXaDk11fJqGy8nZeTR3wft7VEsA9hrI+scYXiZ4ao4lIKE6Nv2Lz1dm7QO9tvKlM7wD0 wWPg== X-Gm-Message-State: AOAM532T2NXw+qDcBGlwt+8exd4a38LWuaxcfmVI+ZteXfxY9L66W7z0 HEZTPoE37FgHa+IfCejNmsWFCL7A0UU= X-Google-Smtp-Source: ABdhPJxx/DtnaRZX1KVlSEwZ2dTO6EIamPPfC4hi0ajH+Kft1OnE/pTiHZhzZ6XdFY6RAV9Q7xR9Aw== X-Received: by 2002:a1c:b702:: with SMTP id h2mr10277355wmf.99.1621628797284; Fri, 21 May 2021 13:26:37 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.36 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:37 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 04/50] gnu: r-topgo: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:36 +0200 Message-Id: <20210521202622.26591-4-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-topgo): Move from here... * gnu/packages/bioconductor.scm (r-topgo): ...to here. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 33 --------------------------------- 2 files changed, 33 insertions(+), 33 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2263c17cc4..2afb5214ee 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2607,6 +2607,39 @@ experimental designs is facilitated by a consistently implemented sample annotation infrastructure.") (license license:artistic2.0))) +(define-public r-topgo + (package + (name "r-topgo") + (version "2.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "topGO" version)) + (sha256 + (base32 + "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl")))) + (properties + `((upstream-name . "topGO"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-dbi" ,r-dbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-go-db" ,r-go-db) + ("r-graph" ,r-graph) + ("r-lattice" ,r-lattice) + ("r-matrixstats" ,r-matrixstats) + ("r-sparsem" ,r-sparsem))) + (home-page "https://bioconductor.org/packages/topGO") + (synopsis "Enrichment analysis for gene ontology") + (description + "The topGO package provides tools for testing @dfn{gene ontology} (GO) +terms while accounting for the topology of the GO graph. Different test +statistics and different methods for eliminating local similarities and +dependencies between GO terms can be implemented and applied.") + ;; Any version of the LGPL applies. + (license license:lgpl2.1+))) + (define-public r-variantannotation (package (name "r-variantannotation") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bf8cb2f3a5..32d2b6a683 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7873,39 +7873,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-topgo - (package - (name "r-topgo") - (version "2.42.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "topGO" version)) - (sha256 - (base32 - "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl")))) - (properties - `((upstream-name . "topGO"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dbi" ,r-dbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-lattice" ,r-lattice) - ("r-matrixstats" ,r-matrixstats) - ("r-sparsem" ,r-sparsem))) - (home-page "https://bioconductor.org/packages/topGO") - (synopsis "Enrichment analysis for gene ontology") - (description - "The topGO package provides tools for testing @dfn{gene ontology} (GO) -terms while accounting for the topology of the GO graph. Different test -statistics and different methods for eliminating local similarities and -dependencies between GO terms can be implemented and applied.") - ;; Any version of the LGPL applies. - (license license:lgpl2.1+))) - (define-public r-bsgenome (package (name "r-bsgenome") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:25 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:26 +0000 Received: from localhost ([127.0.0.1]:37721 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjx-0000GB-Fq for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:25 -0400 Received: from mail-wm1-f48.google.com ([209.85.128.48]:36538) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjK-00008f-Se for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:47 -0400 Received: by mail-wm1-f48.google.com with SMTP id n17-20020a7bc5d10000b0290169edfadac9so8084403wmk.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:46 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=80w92BXZjgOm14vxOMEb4DGdk2zZO34cRdVYW4UtgCQ=; b=rkF6hMQOfjtBQ1XV4Jx/KOcFUk5kcH/nv/ntJnczcKUURhCiSmr7xhtkhL7f1wyQHZ ARjGYemV/EnIkbvCD5IEyw9yLXdy3G8/Hu98NBj26+FK9wnf465KoZ2F6J+D2kKkxOgy TBoXzxoOJRVhITZdXDYKzARFf5kWryutraDtdpS626SXdfz4alMrp5Vj2H/JPuhohCN9 hRP7is6wZHSGy6YfT2z5cFZXqQFqfCIrUGJBbFFTb4sm2oUExjhSXp8LoKrVFVIXIo/k an+hnecvU7FhKMg1iA4w+R8Tkbuca4VTQk72IrTZWRBzisLAXAnjoaO8mjiWG/Kv0Jod Xl3g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=80w92BXZjgOm14vxOMEb4DGdk2zZO34cRdVYW4UtgCQ=; b=LUtwLsl4a6yfSBsAia0mWBmdfPG5GaiqhV7I0fJP3jIrLxAFV2rRNK1KM0/0O28BLX 9AsbgkOfBfeTkuar2Y+fQKVdSKjNuZJBvjt3k8/T0LtcvCM/A68mGTQ1AZxUbPyj+xdX IvM7bdtktILpdtzXIMXcODDoEVdYi+Bm9+NuXC34FzuXSHbG9kCitVxlOUx3qOuvBUcJ s9us11dfTfW+0K401SBJ9KbzDceXd5I2VI9QqPJ25oFU9aLEI26trZFt5N6acgtV7DhM 2bDm9D4MhFpmNyw6Nuo0N8lHsIjKU9p75dHQ1IYhM5hawIoZUmXQAcsMAX1NZExrrk0F jh7w== X-Gm-Message-State: AOAM531b8m2nr4gdjPtFFKX33cIkrW+QurQMc+uOq8gva7/n3x9hF3+J GdUergppFTjArwkP9hG2Cm/ivBTrjm4= X-Google-Smtp-Source: ABdhPJzVFRvCBDMczBTj88pCEYxtcXYLO04C0/p9NvMoYfu/KvPntl/mPGdLsO/d78WgcXg63TyLdQ== X-Received: by 2002:a1c:b087:: with SMTP id z129mr10377128wme.67.1621628801405; Fri, 21 May 2021 13:26:41 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.41 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:41 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 13/50] gnu: r-genomationdata: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:45 +0200 Message-Id: <20210521202622.26591-13-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.7 (/) X-Debbugs-Envelope-To: 48575 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: -0.3 (/) * gnu/packages/bioinformatics.scm (r-genomationdata): Move from here... * gnu/packages/bioconductor.scm (r-genomationdata): ...to here. [source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 26 insertions(+), 28 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2be7920770..22b5a6068e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1021,6 +1021,32 @@ chromstaR package.") genomes and gene ID formats, largely based on the UCSC table browser.") (license license:lgpl2.0+))) +(define-public r-genomationdata + (package + (name "r-genomationdata") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "genomationData" version 'experiment)) + (sha256 + (base32 + "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g")))) + (properties + `((upstream-name . "genomationData"))) + (build-system r-build-system) + ;; As this package provides little more than large data files, it doesn't + ;; make sense to build substitutes. + (arguments `(#:substitutable? #f)) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioinformatics.mdc-berlin.de/genomation/") + (synopsis "Experimental data for use with the genomation package") + (description + "This package contains experimental genetic data for use with the +genomation package. Included are Chip Seq, Methylation and Cage data, +downloaded from Encode.") + (license license:gpl3+))) + (define-public r-pasilla (package (name "r-pasilla") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f8e7b2cab9..87254a9058 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7849,34 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomationdata - (package - (name "r-genomationdata") - (version "1.22.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://bioconductor.org/packages/" - "release/data/experiment/src/contrib/" - "genomationData_" version ".tar.gz")) - (sha256 - (base32 - "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g")))) - (build-system r-build-system) - ;; As this package provides little more than large data files, it doesn't - ;; make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioinformatics.mdc-berlin.de/genomation/") - (synopsis "Experimental data for use with the genomation package") - (description - "This package contains experimental genetic data for use with the -genomation package. Included are Chip Seq, Methylation and Cage data, -downloaded from Encode.") - (license license:gpl3+))) - (define-public r-seqlogo (package (name "r-seqlogo") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:26 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:26 +0000 Received: from localhost ([127.0.0.1]:37723 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjx-0000GI-Tz for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:26 -0400 Received: from mail-wm1-f47.google.com ([209.85.128.47]:35343) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjL-00008i-AO for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:48 -0400 Received: by mail-wm1-f47.google.com with SMTP id z19-20020a7bc7d30000b029017521c1fb75so8082942wmk.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:47 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=vXPEXl3f2GvJD5MJv8Gt6hn4aM1kFQlLGP3n9BTq2YQ=; b=Bag2t7SQKW/ntUUgXmXBuw0U3O3PiMg3Zc/gCwNRc2xYqq25JMYxLjEt7hjdIZ/onM mvh6Um+Esjyd/QVFA0L+ybXHQyqciTXFGJxq+8Xp9tpL6RREv0QCCfI+B0zB8SfyfqxX uCseFY/Nk9u4KYE/JsnKspQUXlwe5Gcqj7KOYuk8y7nGKE/ElNhbTyJUjtQ+wh262Z4Q GRa5pZKsHCmQAGTdLrmfBJXEWKcqcIHWQEfmzPHqCnk5Y3p/XCUJlI9BtmGdIoIbhRMp Lm8r4440F/XY922BsfDpCCZxLUvUcG1hh7ZfOjgBKOOJrGSTFRxUZr6LLTT2tMza6knO ntbw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=vXPEXl3f2GvJD5MJv8Gt6hn4aM1kFQlLGP3n9BTq2YQ=; b=DQwhuszpU8CH5QrDAWQMDBnX9t3NZ8nKscz5fCWIGaGKEIPP/JY6Q1yb+fbC7DDBaD GrrSNMJomEYNR3bExnsChQy+Z9w9ZDXDjFx6G6E7n/4shMOfnIPycjJioi0C5x6W3SSH xlFCGgY1bA0PbrVgvk+zEXS2mDwjcP3LJ/ZzhsOj+tJS0Eu9mgZIqGKzMMBP2qVB6npA PvWddI5Mn143H1vNO0gqxFfrkz9W3tWA608Ls5hFslxl3DtmD6xqnWqg+e9PqanhO0Uf XQLOpx2bH6jcAHndUp5y43bahy5MymyE86xW4/hcm77BSEwQWEmKNL/9aQZkT/KIdTx0 Yxtw== X-Gm-Message-State: AOAM530uP9a1gHSjTQb78E/WzEAccK0jPGec6bD8k2LLSeshrwDE7446 oFKwpZQZFJB070dvsf67GwvEW4FaPf0= X-Google-Smtp-Source: ABdhPJzjbxwzSSMVALYDHXvN+jHBZpqgEJaMF/IQDGWZcTmoNG5wEut50BvtWlbgFG7AVjTOJph7Ag== X-Received: by 2002:a1c:c90f:: with SMTP id f15mr10710828wmb.142.1621628801843; Fri, 21 May 2021 13:26:41 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.41 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:41 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 14/50] gnu: r-pcamethods: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:46 +0200 Message-Id: <20210521202622.26591-14-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-pcamethods): Move from here... * gnu/packages/bioconductor.scm (r-pcamethods): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 22b5a6068e..1533e5b8f9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2526,6 +2526,36 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) +(define-public r-pcamethods + (package + (name "r-pcamethods") + (version "1.82.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pcaMethods" version)) + (sha256 + (base32 + "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0")))) + (properties `((upstream-name . "pcaMethods"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/hredestig/pcamethods") + (synopsis "Collection of PCA methods") + (description + "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, +Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method +for missing value estimation is included for comparison. BPCA, PPCA and +NipalsPCA may be used to perform PCA on incomplete data as well as for +accurate missing value estimation. A set of methods for printing and plotting +the results is also provided. All PCA methods make use of the same data +structure (pcaRes) to provide a common interface to the PCA results.") + (license license:gpl3+))) + (define-public r-rbgl (package (name "r-rbgl") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 87254a9058..a98f3d5d8a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9053,36 +9053,6 @@ mzIdentML files with the drawback of having less pretty output than a vendor specific parser.") (license license:gpl2+))) -(define-public r-pcamethods - (package - (name "r-pcamethods") - (version "1.82.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "pcaMethods" version)) - (sha256 - (base32 - "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0")))) - (properties `((upstream-name . "pcaMethods"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp))) - (home-page "https://github.com/hredestig/pcamethods") - (synopsis "Collection of PCA methods") - (description - "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, -Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method -for missing value estimation is included for comparison. BPCA, PPCA and -NipalsPCA may be used to perform PCA on incomplete data as well as for -accurate missing value estimation. A set of methods for printing and plotting -the results is also provided. All PCA methods make use of the same data -structure (pcaRes) to provide a common interface to the PCA results.") - (license license:gpl3+))) - (define-public r-aroma-light (package (name "r-aroma-light") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:26 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:26 +0000 Received: from localhost ([127.0.0.1]:37725 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjy-0000GP-AI for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:26 -0400 Received: from mail-wm1-f45.google.com ([209.85.128.45]:51727) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjL-00008k-QJ for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:48 -0400 Received: by mail-wm1-f45.google.com with SMTP id u133so11744821wmg.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:47 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=ePOu/WOmhRx9vzCfP9R7pDT0sp4w/OutgjJuExwrTy0=; b=DOcAeEW8GgDzRYazjzSs17nd1ySJK736St39aoiXWdZogOjNGv6ESWCKf9gAzDEKDe n450KyIgHO19LPwLcXNaXEneLsQHASvdsd59JTaxv8r75IZ9TWYN5VTkebH0j2PFGVgw VMPGXS/VpxHnV7zg3qmoV1bP15HjxMPe7HKxV4o6YCY2+WwiuA+QkQ78H1PNcJx/wqsO SqctMDcjBLi70GsLGpsK4wlnfO/6tsz/nTOmN1eLEKFj7CDGvSex0WhnyVjC/mHZx2TX AAX86g6bHhERFbkrXcLJSw3L8iFyqbgLow/yRbJsoFdeRJ4TpMn9K0xiPPKmkz9WKmu2 nz6Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=ePOu/WOmhRx9vzCfP9R7pDT0sp4w/OutgjJuExwrTy0=; b=nYMK05Hp3Pq0NC1jsdZZ5b9A33oD9ETh3vDpz53YjGhHH3DpIk5TKgWTqsEWlP4AT3 NiXkLFU7V3tbJLLIJadG7Jr7hhILDHeWirfA9u5jnNDP+uj2AWzB5p6BKNREBp/vFZJo BOk019Y/v1AxvqvAYaxHnv81LOBLJij5vW1H1/F85NhDfiPpKlqzZgu8l2XI2SFMV63z ctyNjv13JjyQcttC6Svh+JSMRdYw55NVJJJNLg/FoLDVj41eDf46S2+vJ+taOa+hWE5b Zgoi5EjosWTLEYCW+SAxFESVANssqp5sOaL85rPLdp7Ozd8SVdpE6DoNDSDyYb983cZb raDw== X-Gm-Message-State: AOAM533aFwpj4G95hhG45yOFrql/GCBFuAlnxZPP/T2Bwwg93tpWbhLH +J0n1ufJ2kBottamS3eFlNQEhNIPc10= X-Google-Smtp-Source: ABdhPJxOoaKGHLY1upRxZzX4NwrhGC33iemyoiQXxzXM3vTnywP9AHuQv/L5TeUewj4jXu53LBPCZQ== X-Received: by 2002:a1c:c911:: with SMTP id f17mr10438184wmb.45.1621628802273; Fri, 21 May 2021 13:26:42 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.41 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:42 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 15/50] gnu: r-mzid: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:47 +0200 Message-Id: <20210521202622.26591-15-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-mzid): Move from here... * gnu/packages/bioconductor.scm (r-mzid): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1533e5b8f9..5e0b722e2f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2526,6 +2526,37 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) +(define-public r-mzid + (package + (name "r-mzid") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mzID" version)) + (sha256 + (base32 + "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2")))) + (properties `((upstream-name . "mzID"))) + (build-system r-build-system) + (propagated-inputs + `(("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-iterators" ,r-iterators) + ("r-plyr" ,r-plyr) + ("r-protgenerics" ,r-protgenerics) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/mzID") + (synopsis "Parser for mzIdentML files") + (description + "This package provides a parser for mzIdentML files implemented using the +XML package. The parser tries to be general and able to handle all types of +mzIdentML files with the drawback of having less pretty output than a vendor +specific parser.") + (license license:gpl2+))) + (define-public r-pcamethods (package (name "r-pcamethods") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a98f3d5d8a..5b6426e17d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9022,37 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-mzid - (package - (name "r-mzid") - (version "1.28.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "mzID" version)) - (sha256 - (base32 - "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2")))) - (properties `((upstream-name . "mzID"))) - (build-system r-build-system) - (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/mzID") - (synopsis "Parser for mzIdentML files") - (description - "This package provides a parser for mzIdentML files implemented using the -XML package. The parser tries to be general and able to handle all types of -mzIdentML files with the drawback of having less pretty output than a vendor -specific parser.") - (license license:gpl2+))) - (define-public r-aroma-light (package (name "r-aroma-light") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:27 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:27 +0000 Received: from localhost ([127.0.0.1]:37727 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjy-0000GX-M7 for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:27 -0400 Received: from mail-wm1-f42.google.com ([209.85.128.42]:55099) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjM-00008r-51 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:48 -0400 Received: by mail-wm1-f42.google.com with SMTP id o127so11748550wmo.4 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:48 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=/u8rovKZ0Gjsn0qr/2vksvjgQll2ckz8xJFStYmLxKc=; b=pRtXINn11bIaie7cPWB353ENvNLTYqBCeB/RzlZdjU/fKvZ3YaEto5x9ZPGBVN6JQb PIvTFQ5o5PQRGFreE+1jBH/zRD9rUSEVqhm3hVhuHU1oSSp1tkceFrpzLlAAmtjXW+fG D1Jj3kzJvUVTqn4hXkwoV/4RUDnXYvSTm2DV/6C8aNA36hjvwDxZ6GpDeszx0r/9YFc1 GVc3xynzifhmX7/XtnU/oie9qvnxHhX1QFc9/ZSdxg6ZZCLQkqMn8lu+5XyRxu5fhBY3 oryYSILjRjAK6pcW3wklK7SDzSw/monT9vYo4kF612Wpj5ULxXeYDLj/YG8FYsxSQMjy tSgg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=/u8rovKZ0Gjsn0qr/2vksvjgQll2ckz8xJFStYmLxKc=; b=d6OqZfHNF717jIzP8lqXi9McfDj78QIP2xoBRWcG6JAobpcAVpXyIsj0tXjhUK5ZYf 5HUJfaj1d0cmYrXNv0VUXf3dOHzOJbzYxK+HdWC5wJMR+foncRHGgILmtRN6+VZvmAcG mLK7XmiXBiWjNcjwWO7RQFVxe6Pfd2/PYC5HVuDBDFo5/sqNgPqz4BKuEpjcqWJYhnnE qy5z8MU4VV5vocdUoA8X+vUCFBVIGAcDLtPhJAv7sHd/zNoKc1Hf++A1D2YuRZx85uMn TEve79NtdR/9wmPbTguM/pZ6B9mUNYVPMNoegCjeytB9DrgZL5M2cDsjtB0XoRgjmTwW STUQ== X-Gm-Message-State: AOAM531LTfkBqonaU0pSrq034v94H7EbHZo09CkfRNCCs8NnaVLznnKw JGusi4QAcRR5sLmZZe7oqIy2rBPwjoc= X-Google-Smtp-Source: ABdhPJxO5l8hpp/Dv/Kst7/Lw+AM55eatpLNKgovUBSItaYyPnW8uhApElEH7LkSnGq51LzphHagLA== X-Received: by 2002:a7b:cb04:: with SMTP id u4mr10342199wmj.146.1621628802685; Fri, 21 May 2021 13:26:42 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.42 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:42 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 16/50] gnu: r-aroma-light: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:48 +0200 Message-Id: <20210521202622.26591-16-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-aroma-light): Move from here... * gnu/packages/bioconductor.scm (r-aroma-light): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5e0b722e2f..e58cd66fef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1782,6 +1782,33 @@ annotation data packages using SQLite data storage.") databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-aroma-light + (package + (name "r-aroma-light") + (version "3.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "aroma.light" version)) + (sha256 + (base32 + "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0")))) + (properties `((upstream-name . "aroma.light"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrixstats" ,r-matrixstats) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/aroma.light") + (synopsis "Methods for normalization and visualization of microarray data") + (description + "This package provides methods for microarray analysis that take basic +data types such as matrices and lists of vectors. These methods can be used +standalone, be utilized in other packages, or be wrapped up in higher-level +classes.") + (license license:gpl2+))) + (define-public r-biobase (package (name "r-biobase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5b6426e17d..c8444eea9f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9022,33 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-aroma-light - (package - (name "r-aroma-light") - (version "3.20.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "aroma.light" version)) - (sha256 - (base32 - "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0")))) - (properties `((upstream-name . "aroma.light"))) - (build-system r-build-system) - (propagated-inputs - `(("r-matrixstats" ,r-matrixstats) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) - (home-page "https://github.com/HenrikBengtsson/aroma.light") - (synopsis "Methods for normalization and visualization of microarray data") - (description - "This package provides methods for microarray analysis that take basic -data types such as matrices and lists of vectors. These methods can be used -standalone, be utilized in other packages, or be wrapped up in higher-level -classes.") - (license license:gpl2+))) - (define-public r-deseq (package (name "r-deseq") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:27 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:27 +0000 Received: from localhost ([127.0.0.1]:37729 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjz-0000Ge-1y for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:27 -0400 Received: from mail-wm1-f48.google.com ([209.85.128.48]:47092) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjN-000095-12 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:49 -0400 Received: by mail-wm1-f48.google.com with SMTP id l18-20020a1c79120000b0290181c444b2d0so1223078wme.5 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:48 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=sJGeC38b9hZlAv1K9htVm4kPdSkSuf9nTVatC5DMh5Y=; b=eCmQDNbK/6cizOeBzPRJblguHN9GpQYSPq0Jsmo/oaRbTMhgNDIeOs8ff5LOxZamaH XrV4nnFYcYhfJp2QDY5P0hGPArAanp1necVVvsPAqP6+mTFbyF9DvZ0o8VlfMpEihN+E xDTJk+cGB/5WJTFQ1giYOzRr1Wt4b6eK6Ie92YrZ1cJctu895CdUhhES5ZGmQbxHXEAZ Q1AVeGsLjW6KlOn6kYY6XXbxNlbg79cG5hGNUbHDL43TnTIh0cHeh3dDlpKS3naxy8c0 yAkdPT1IMvZlISJlDs6tP3u2dQdSuvH2f3FZp5+Lf7TrvSnqgHzHc6emhzmoxXB63YCC uQzw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=sJGeC38b9hZlAv1K9htVm4kPdSkSuf9nTVatC5DMh5Y=; b=WEu6HFOEr297niZMWs5zz2cTNzLSQIYSnQpZtcCOMsuSIkt/ykpw5hVKc7ZUYbO+B/ 8j6PSPs1VWYuv4Ad2opOBrifw0zAqNl5h72OTTQv1dk1KoYQHmMdgpMxLm2UijLK72TM /vTf9oxjUc+THuFBJvGEDnnqhiQ2GqQDc8hpgmJVokWNn4J1HB6SuKJUseOy0Zi4VeIE 6jde3t0YlWYmXUrJjYBWNyrDpGTPU8DT4ximdZmDh+1vBhV32KkSOHoWWj0mdaWl9SJH ymhQA7uEdBXyPqWRH8nnKXOI9LlG83X/qFHDonl1M5VAvIbN4KwTQUGUYGhuAxorgd+R vGyA== X-Gm-Message-State: AOAM530DbsARz37cMUvxDZY4V5C51TdcVzwtnXy+at3+QNcEAOY7DT0m XUhGE3unIfUFaf9EmTr/McovrnVBRDs= X-Google-Smtp-Source: ABdhPJz/hYHNnJ8Qj2MzclPsk/N5LkEKeee+/2CKtztewk4xI77wrEkZHnPy3pCkAXOFZtvOs/kHog== X-Received: by 2002:a05:600c:19c8:: with SMTP id u8mr10554960wmq.25.1621628803545; Fri, 21 May 2021 13:26:43 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:43 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 18/50] gnu: r-edaseq: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:50 +0200 Message-Id: <20210521202622.26591-18-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-edaseq): Move from here... * gnu/packages/bioconductor.scm (r-edaseq): ...to here. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 40 --------------------------------- 2 files changed, 40 insertions(+), 40 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 69ef513bc6..beb662984d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2127,6 +2127,46 @@ testing. The package also provides functions for the visualization and exploration of the results.") (license license:gpl3+))) +(define-public r-edaseq + (package + (name "r-edaseq") + (version "2.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EDASeq" version)) + (sha256 + (base32 + "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip")))) + (properties `((upstream-name . "EDASeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-aroma-light" ,r-aroma-light) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-shortread" ,r-shortread))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/drisso/EDASeq") + (synopsis "Exploratory data analysis and normalization for RNA-Seq") + (description + "This package provides support for numerical and graphical summaries of +RNA-Seq genomic read data. Provided within-lane normalization procedures to +adjust for GC-content effect (or other gene-level effects) on read counts: +loess robust local regression, global-scaling, and full-quantile +normalization. Between-lane normalization procedures to adjust for +distributional differences between lanes (e.g., sequencing depth): +global-scaling and full-quantile normalization.") + (license license:artistic2.0))) + (define-public r-edger (package (name "r-edger") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2edb501f9b..b0de0d9880 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9022,46 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-edaseq - (package - (name "r-edaseq") - (version "2.24.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "EDASeq" version)) - (sha256 - (base32 - "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip")))) - (properties `((upstream-name . "EDASeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-aroma-light" ,r-aroma-light) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/drisso/EDASeq") - (synopsis "Exploratory data analysis and normalization for RNA-Seq") - (description - "This package provides support for numerical and graphical summaries of -RNA-Seq genomic read data. Provided within-lane normalization procedures to -adjust for GC-content effect (or other gene-level effects) on read counts: -loess robust local regression, global-scaling, and full-quantile -normalization. Between-lane normalization procedures to adjust for -distributional differences between lanes (e.g., sequencing depth): -global-scaling and full-quantile normalization.") - (license license:artistic2.0))) - (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:27 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:28 +0000 Received: from localhost ([127.0.0.1]:37731 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjz-0000Gn-Gj for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:27 -0400 Received: from mail-wr1-f42.google.com ([209.85.221.42]:38449) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjM-000094-Td for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:49 -0400 Received: by mail-wr1-f42.google.com with SMTP id j14so20456950wrq.5 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:48 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=uS+iR7ArIs9A0QBxPdV6EFOExjvOpBKgBKACbdodBh4=; b=sOw+odoCzoPDXnzhuWNaEzq7yFsdQ+Cj8VIi+y9b1pDzuPa6dU+aR1HfAfMU273gvM YNCpg0jPX15+LYI4RJU5XDWb69pT3rHkK9waDlAGLlOutRa7TwkiVTGB398zv8FX9vQY VOzTrUoKNBIHgeokem0cC6lS9XZt5QcZhCmBA3eOe70g8P2638I/4nXxxyREeZ9WYk6y 6w2TgkQoGCTjjjWxx2XNqrkxSxCaVqVi1e+mN3OVIKRvavgn0InLk9fQlhT1pXCtK6dP 7hSKIqIvjG1htIms/8Nxk0Rv/BMJ15zfnGdb4KXtlR9Ocvcc7o/8zJeNNyBSbRa+c3JH dYug== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=uS+iR7ArIs9A0QBxPdV6EFOExjvOpBKgBKACbdodBh4=; b=aQG5gvQxbYcUrBHdOQrMfLpkUoxy3W+H2fWzkBjeviQBPivHVIXtCHa5V5k6E/REsb PpguypDg2+IZWEqBSEDljSYL2BT4yYN+ZycFW7MF2kuzbsYZnskamb1C32gsbHq9F+pp wKsTdt+Oj24N6Tt8tx2zzuqwi9XeNC6GRvLiz4i959RqZIcbKm9xkGeVWm59Cr2mcXEI jIFdModh1/lIo+PxA6+ElakDg31+yqzm2APPK3pROfKm9pOh/UzbTgRnDPh/uOPttQBV RagIavgB54mUOAko+O7x98RQ3LPy/IR1EEmDjjQRTpAXqIzIhZhoURoWC0cGFFEFLF63 RGPA== X-Gm-Message-State: AOAM5305wIxFFAy7TEFMJFxGtUlf3lV66RD3xmEjjjXVqQbVfwok5mo7 CRohLxAR6XyxZK7PQkElgkNcp9oEpnY= X-Google-Smtp-Source: ABdhPJzoR7HKMFcpA9VYY094OO6TfCNo8L0KvfIeB94VKuy94E+lf10zpuxifvKu9wzyXTPo8lm2og== X-Received: by 2002:a5d:46c7:: with SMTP id g7mr11319126wrs.394.1621628803098; Fri, 21 May 2021 13:26:43 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.42 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:42 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 17/50] gnu: r-deseq: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:49 +0200 Message-Id: <20210521202622.26591-17-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-deseq): Move from here... * gnu/packages/bioconductor.scm (r-deseq): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e58cd66fef..69ef513bc6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2013,6 +2013,37 @@ genome data packages and support for efficient SNP representation.") analysis.") (license license:artistic2.0))) +(define-public r-deseq + (package + (name "r-deseq") + (version "1.39.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DESeq" version)) + (sha256 + (base32 + "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1")))) + (properties `((upstream-name . "DESeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-lattice" ,r-lattice) + ("r-locfit" ,r-locfit) + ("r-mass" ,r-mass) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://www-huber.embl.de/users/anders/DESeq/") + (synopsis "Differential gene expression analysis") + (description + "This package provides tools for estimating variance-mean dependence in +count data from high-throughput genetic sequencing assays and for testing for +differential expression based on a model using the negative binomial +distribution.") + (license license:gpl3+))) + (define-public r-deseq2 (package (name "r-deseq2") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c8444eea9f..2edb501f9b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9022,37 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-deseq - (package - (name "r-deseq") - (version "1.39.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DESeq" version)) - (sha256 - (base32 - "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1")))) - (properties `((upstream-name . "DESeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-lattice" ,r-lattice) - ("r-locfit" ,r-locfit) - ("r-mass" ,r-mass) - ("r-rcolorbrewer" ,r-rcolorbrewer))) - (home-page "https://www-huber.embl.de/users/anders/DESeq/") - (synopsis "Differential gene expression analysis") - (description - "This package provides tools for estimating variance-mean dependence in -count data from high-throughput genetic sequencing assays and for testing for -differential expression based on a model using the negative binomial -distribution.") - (license license:gpl3+))) - (define-public r-edaseq (package (name "r-edaseq") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:28 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:28 +0000 Received: from localhost ([127.0.0.1]:37733 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjz-0000Gv-VD for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:28 -0400 Received: from mail-wm1-f45.google.com ([209.85.128.45]:35343) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjN-000099-GR for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:50 -0400 Received: by mail-wm1-f45.google.com with SMTP id z19-20020a7bc7d30000b029017521c1fb75so8082979wmk.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:49 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=TYBWK23ZB338xbEjAJUqAauS/ByH0/h8gzSwsfy0fXs=; b=DU2i2uU8Be2kwijcWvYvxQhXSOBb3gHdxqaJt5fqEvUggvUXelLWzAmOnj+X9bf9UJ 5WGRb8tpbt1OSqWJSAbqyTo6WcLEesmYwWGtxHewpiWSPk9uxlR3NZY0oS0H5hQ+LBxA OVc8XAQNYO/DYwsnIkfh4hTYJgTGiwOxPvZysBASdWxOgRg5zAX96nbBys/Wq8sqq54N S6KGMeIikRTxNufjDG/Qja2/ok2QcJe4TyQiY3abAfdW2JEmjV+i1yA0FHbFUgZewCdX 3qX/fNQPx3E5t4iAF09lQ3g0Cw2tfTHwPRTyCDz3NFmEzsyOlBeviXhZrPgtw8fYmaIU yV2A== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=TYBWK23ZB338xbEjAJUqAauS/ByH0/h8gzSwsfy0fXs=; b=aIpVzD4TpyXAy+fe86LqHH+s5uTX2SyDruWHkI4ni9evHPu8/BkgAcFNVHDVShEcqM 3VmhEv5jzYXsGkqlz4Iar4cethuq1rLP+xuwgo9vSY++gJaZLpEZrv4yb6OYxaurkAU0 tiUQ1+TxohRyhDgC78OrhEMgsca1fp1Rjm0QOBS1iv3MR5UXIEAMUna5OGn5eOl6ZAi9 f2XPzlRy6Vd1jNGfjpgyyOPnHUGKIGMc5u9hB2DImTi9Hbn+rTAJgZQv84ObmmKu3YPw TM7v1/nMiNa7/3A1x0csIJ3N6UxFp+USQMegrQBCsI4WUxKn2kF6B3NOgUHuUeEP3AjW h7JQ== X-Gm-Message-State: AOAM530Kw0XB1BmgVkM4CRTwuijuBEVmsRxgrLD7BfzLX7dB95clHqOS j6a+scf5hfA/PtmnRYGS6KKjT+A7kBc= X-Google-Smtp-Source: ABdhPJwkecAhyZN1byIrc7O17kGtC8/8sVeGVCczJalPUR3++TbsQQ1Xe4eDD2khsvZD7U0tEYxzfQ== X-Received: by 2002:a7b:c7ca:: with SMTP id z10mr10584061wmk.185.1621628804042; Fri, 21 May 2021 13:26:44 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:43 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 19/50] gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:51 +0200 Message-Id: <20210521202622.26591-19-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Move from here... * gnu/packages/bioconductor.scm (r-interactivedisplaybase): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index beb662984d..9619ce5464 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2508,6 +2508,33 @@ the Human Protein Atlas project.") microarray data, using nearest neighbor averaging.") (license license:gpl2+))) +(define-public r-interactivedisplaybase + (package + (name "r-interactivedisplaybase") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "interactiveDisplayBase" version)) + (sha256 + (base32 + "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01")))) + (properties + `((upstream-name . "interactiveDisplayBase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-dt" ,r-dt) + ("r-shiny" ,r-shiny))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/interactiveDisplayBase") + (synopsis "Base package for web displays of Bioconductor objects") + (description + "This package contains the basic methods needed to generate interactive +Shiny-based display methods for Bioconductor objects.") + (license license:artistic2.0))) + (define-public r-limma (package (name "r-limma") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b0de0d9880..b367dcae98 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9022,33 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-interactivedisplaybase - (package - (name "r-interactivedisplaybase") - (version "1.28.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "interactiveDisplayBase" version)) - (sha256 - (base32 - "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01")))) - (properties - `((upstream-name . "interactiveDisplayBase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-dt" ,r-dt) - ("r-shiny" ,r-shiny))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/interactiveDisplayBase") - (synopsis "Base package for web displays of Bioconductor objects") - (description - "This package contains the basic methods needed to generate interactive -Shiny-based display methods for Bioconductor objects.") - (license license:artistic2.0))) - (define-public r-annotationhub (package (name "r-annotationhub") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:28 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:28 +0000 Received: from localhost ([127.0.0.1]:37735 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk0-0000H2-BS for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:28 -0400 Received: from mail-wm1-f54.google.com ([209.85.128.54]:38830) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjN-00009G-Vf for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:50 -0400 Received: by mail-wm1-f54.google.com with SMTP id u4-20020a05600c00c4b02901774b80945cso8061341wmm.3 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:49 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=lWp5iRRc16IVy1RyUvSSRWm6Pa0SbaLjN1QS6FjYR9A=; b=c43HmBom37Rtqfqg44njcTzDqfpKbhFpdxdw9K4OYcCIKcQjBGUA7fj4DqvONt9Pym Ckyw1iyZdB6fOYIEs2NkGk0H9BSdMnUOmFgAqCdGadXHS0FkuDuzgNLSP+hNSxY23ATt FDpCd5NFqCEuAv+Ja4/0K/pV5LX19qN25aInqk3Odt0mggpxMmUGWpfxEwDWD+9g8Be4 vkX7KvzLjxrnaLVuXTGHFkC3fNcDKjJ8gDHS6sBnvtaTXYTptCs539qEjB+5h9B+EEuh C7J8TFOzho8AbtjZhX6deudMPNz5oS43GmaX8wiWrq0z9MgQTCyA7D6o4sL6eIwR+g9C UhFQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=lWp5iRRc16IVy1RyUvSSRWm6Pa0SbaLjN1QS6FjYR9A=; b=bY+Z7VxRg047HnaUxS4+ErmXpuO+8/A2ZCuiYALtz7L13TmEETTftkwDcnlTWsCXfG ha2fawc9ZUOBLLQcGndLJAnnKrc34UMzNSRxug4liNW9isOvcx4RQFH3yEzebWIwztZK w7LN6NuvQY4Kjeh9SkcJ8wS8fdMulaqtdCwj3z8QKe4nRioVD0VP6GR1+Xz4/ly9YNsl 7ABnRh5nE1HTd/i8uy5+/aWiri1Owh7FlurGlm/sQS5ac6lQWf7aqfZRb3XxpYwyGpHL k1i0H2WwlYzrVniP1/qjaPBJW+Fls6lyHhldYby41C9sTYdJzjGQlKJoTXr0ko/bGB6H gbvw== X-Gm-Message-State: AOAM530gUPXwibRYP8NU2e8yVAZ7Zb5nwCU4vRxBgC8oScyHblXKQsE9 x97W0ueJUMrRC/Zqd3SRXnAkv17Mw4k= X-Google-Smtp-Source: ABdhPJzCrDN7FYGPYVqCwxCsteKUx7YvaoRRJjrf0VTxc21kvXrJOomk6ckIjD+d4R4iQ8UvN06uFQ== X-Received: by 2002:a7b:c93a:: with SMTP id h26mr10664387wml.141.1621628804467; Fri, 21 May 2021 13:26:44 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.44 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:44 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 20/50] gnu: r-annotationhub: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:52 +0200 Message-Id: <20210521202622.26591-20-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-annotationhub): Move from here... * gnu/packages/bioconductor.scm (r-annotationhub): ...to here. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 41 --------------------------------- 2 files changed, 41 insertions(+), 41 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9619ce5464..4657b0fa8b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1782,6 +1782,47 @@ annotation data packages using SQLite data storage.") databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-annotationhub + (package + (name "r-annotationhub") + (version "2.22.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationHub" version)) + (sha256 + (base32 + "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5")))) + (properties `((upstream-name . "AnnotationHub"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-biocversion" ,r-biocversion) + ("r-curl" ,r-curl) + ("r-dplyr" ,r-dplyr) + ("r-httr" ,r-httr) + ("r-interactivedisplaybase" ,r-interactivedisplaybase) + ("r-rappdirs" ,r-rappdirs) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors) + ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/AnnotationHub") + (synopsis "Client to access AnnotationHub resources") + (description + "This package provides a client for the Bioconductor AnnotationHub web +resource. The AnnotationHub web resource provides a central location where +genomic files (e.g. VCF, bed, wig) and other resources from standard +locations (e.g. UCSC, Ensembl) can be discovered. The resource includes +metadata about each resource, e.g., a textual description, tags, and date of +modification. The client creates and manages a local cache of files retrieved +by the user, helping with quick and reproducible access.") + (license license:artistic2.0))) + (define-public r-aroma-light (package (name "r-aroma-light") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b367dcae98..1dc2d6f977 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9022,47 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-annotationhub - (package - (name "r-annotationhub") - (version "2.22.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "AnnotationHub" version)) - (sha256 - (base32 - "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5")))) - (properties `((upstream-name . "AnnotationHub"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biocversion" ,r-biocversion) - ("r-curl" ,r-curl) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-interactivedisplaybase" ,r-interactivedisplaybase) - ("r-rappdirs" ,r-rappdirs) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/AnnotationHub") - (synopsis "Client to access AnnotationHub resources") - (description - "This package provides a client for the Bioconductor AnnotationHub web -resource. The AnnotationHub web resource provides a central location where -genomic files (e.g. VCF, bed, wig) and other resources from standard -locations (e.g. UCSC, Ensembl) can be discovered. The resource includes -metadata about each resource, e.g., a textual description, tags, and date of -modification. The client creates and manages a local cache of files retrieved -by the user, helping with quick and reproducible access.") - (license license:artistic2.0))) - (define-public r-fastseg (package (name "r-fastseg") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:29 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:29 +0000 Received: from localhost ([127.0.0.1]:37737 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk0-0000HA-PU for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:29 -0400 Received: from mail-wm1-f42.google.com ([209.85.128.42]:51727) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjO-00009R-BZ for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:51 -0400 Received: by mail-wm1-f42.google.com with SMTP id u133so11744876wmg.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:50 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=sbY4kmXYlvZqB3uWJBCYUX61JhV9giynZDkg9CH2Aog=; b=s/p4mkArmGmZ9h1ODqv6YGHylh0EYE0dO1WVq2UHrLcXi8Omwcv9VB2XFhTNqNzq9O nlYrD3oTMjLIHUzOPC8u5TvPzVrRAEutoAjkEEPtqExGBYEjprJKCJ8J6BWUbsEAPTGw 94ID8Dvjug3Or+v8tqmDmG4mHfYk7V3gjo31DWTqFjvFIGDUPUnKDo+QnL9nol4mvuU0 eqaYMiRzefdd3lMZMZIHzZLb1AXcKjc75DvoVyC/R0xbMWn7owANwlk2aHrQV3Y9fsEB JlSRYhZQfa5x0bv5BDGGReb6Wt3RLvi/J+2b8nFWKbqGeoiUiT0WjBzHTJd17k4fbdI4 Glqw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=sbY4kmXYlvZqB3uWJBCYUX61JhV9giynZDkg9CH2Aog=; b=G7R3wYSt6jXnK0u+XcYsxIhJBc9nRsfG/xH3vSbTQUkM8fRIfn25bcrzTrh0/0f1Og T58iQD3M/MyoOsnxrSqsi17u3usA6bf8KmfqRH2DY0q4z/SHq990T/SoCUWeFtVRurrX vDuiF1CgOSBYecXLyerJxGTxf3i/GBkDUWshlCNeto82ITmhZlbYBDzECm3jLGjv2JI6 Yzogk510SYlZZn9ulS8QI2O9gbUl4ku46TnaTQQQuKiYN2BFlpic5jcfI4y8APYUg/J1 wPniFt1Ny/EU+xpMm6y6LnPcayZu6EFHy1zmy+NBPywLSjNn2gZLHPRH22C6/yugPfGg o1rQ== X-Gm-Message-State: AOAM532gFNTe3FinrhRi8GaSGOPpn1vvUbexjJhdyDsKeTcBbXNRS5k3 l5p754cTtCfzJXbAHvYWYY7lTH4J6WE= X-Google-Smtp-Source: ABdhPJzsxPlK5QpHHy8G+lL970XSJsZfwGSN6EG4kGIAdyMXQr0vBH5EV2ndanJg9ukskzp7Gj9qDQ== X-Received: by 2002:a05:600c:4f95:: with SMTP id n21mr10812579wmq.74.1621628804900; Fri, 21 May 2021 13:26:44 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.44 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:44 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 21/50] gnu: r-fastseg: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:53 +0200 Message-Id: <20210521202622.26591-21-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-fastseg): Move from here... * gnu/packages/bioconductor.scm (r-fastseg): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4657b0fa8b..313ed7e36f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2236,6 +2236,36 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.") (license license:gpl2+))) +(define-public r-fastseg + (package + (name "r-fastseg") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "fastseg" version)) + (sha256 + (base32 + "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") + (synopsis "Fast segmentation algorithm for genetic sequencing data") + (description + "Fastseg implements a very fast and efficient segmentation algorithm. +It can segment data from DNA microarrays and data from next generation +sequencing for example to detect copy number segments. Further it can segment +data from RNA microarrays like tiling arrays to identify transcripts. Most +generally, it can segment data given as a matrix or as a vector. Various data +formats can be used as input to fastseg like expression set objects for +microarrays or GRanges for sequencing data.") + (license license:lgpl2.0+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1dc2d6f977..33680c283d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9022,36 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-fastseg - (package - (name "r-fastseg") - (version "1.36.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "fastseg" version)) - (sha256 - (base32 - "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") - (synopsis "Fast segmentation algorithm for genetic sequencing data") - (description - "Fastseg implements a very fast and efficient segmentation algorithm. -It can segment data from DNA microarrays and data from next generation -sequencing for example to detect copy number segments. Further it can segment -data from RNA microarrays like tiling arrays to identify transcripts. Most -generally, it can segment data given as a matrix or as a vector. Various data -formats can be used as input to fastseg like expression set objects for -microarrays or GRanges for sequencing data.") - (license license:lgpl2.0+))) - (define-public r-keggrest (package (name "r-keggrest") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:29 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:29 +0000 Received: from localhost ([127.0.0.1]:37739 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk1-0000HH-6o for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:29 -0400 Received: from mail-wm1-f51.google.com ([209.85.128.51]:47097) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjO-00009a-RO for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:51 -0400 Received: by mail-wm1-f51.google.com with SMTP id l18-20020a1c79120000b0290181c444b2d0so1223119wme.5 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:50 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=deaCVm8SOhRhD2+sm/FYS9WzJouqhTkW4U8yaV43umg=; b=F6/MqVYj7EcWyOAzAljDWl76qtZGuHTBULaow6HKY6P4zQDDZ7uBxtBtnemrLsTw9N 2GyM4B9jn/fT/QriN+oFLFec7vKw2jreTJygfprkNQQFNr53HWDmQRF5T3RKVdIrnR6S jb/VMKItevGGYgr0U9C7XAwBpl0Y6MnVFoPtgyyB/HQjC0Gl4o1cYjDH3LT4d+ypFCfF Hl7fmb6RPKC1yKh4zN9njc3goW/IRNvIU04vGPqqYUDGvvpmR+0F3FkFAXMsWy3lEuGx 7Xac4XeRWfoLr+fL53JfkRtNKYZoQsvRfxVSVJjQFPfh6IkJEfZFT6V5ld1rN+Gac+hk 5eGg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=deaCVm8SOhRhD2+sm/FYS9WzJouqhTkW4U8yaV43umg=; b=imw1Jkh0eJ9i9MJNRW7NkVON4rLtSDiY2ssyJZa/BkOyH1EXoLVW20sYCZ82DOtLOM 54nIw/hrjHA5zhnxHEBjrbAPR06fr/bEEkMyglQnu17rJFAx33nm7VHUisOwkqAsvAG5 XkycaFrp5VOERU/kfn4/ELVtrpYHhe+ZAM6GBwKn/9T0EODbYYpPFBP5YzSecHdGGW8Z HU8NGLw9T4mRa3YE4JUQ+AyBDeAvRi89Y9pfWAQqyfPxtuOKLE5yjqyG9Bgf7ycT7gPq Dv/9PkOywHTn2XcO+gzbbIKuESvTUY615F8A5PCV6eNjj0BwxOUwIBhk6I+buS8itQXz P2nA== X-Gm-Message-State: AOAM530XflUQOw6o6Lp750Y0pdAZZKnNDxWZu0onps10aT3TfIynaM3N l/mBJtrv9O8KA4k2kKux9+QKG1v2dyI= X-Google-Smtp-Source: ABdhPJwdNa8YvqzzZVdJiymKM2iWIx6fz+SJ5VVoVDviT913TfTVnBuIbsEExrK8EWX0GRgXvfv38w== X-Received: by 2002:a05:600c:35cc:: with SMTP id r12mr10028655wmq.157.1621628805323; Fri, 21 May 2021 13:26:45 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.44 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:45 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 22/50] gnu: r-affy: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:54 +0200 Message-Id: <20210521202622.26591-22-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-affy): Move from here... * gnu/packages/bioconductor.scm (r-affy): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 28 insertions(+), 28 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 313ed7e36f..6d60b5884c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1550,6 +1550,34 @@ optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.") (license license:gpl2+))) +(define-public r-affy + (package + (name "r-affy") + (version "1.68.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affy" version)) + (sha256 + (base32 + "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affyio" ,r-affyio) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-preprocesscore" ,r-preprocesscore) + ("r-zlibbioc" ,r-zlibbioc))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://bioconductor.org/packages/affy") + (synopsis "Methods for affymetrix oligonucleotide arrays") + (description + "This package contains functions for exploratory oligonucleotide array +analysis.") + (license license:lgpl2.0+))) + (define-public r-affycomp (package (name "r-affycomp") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 33680c283d..b789ecd977 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8958,34 +8958,6 @@ upon file format information. The primary focus is on accessing the CEL and CDF file formats.") (license license:lgpl2.0+))) -(define-public r-affy - (package - (name "r-affy") - (version "1.68.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "affy" version)) - (sha256 - (base32 - "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06")))) - (build-system r-build-system) - (propagated-inputs - `(("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-preprocesscore" ,r-preprocesscore) - ("r-zlibbioc" ,r-zlibbioc))) - (inputs - `(("zlib" ,zlib))) - (home-page "https://bioconductor.org/packages/affy") - (synopsis "Methods for affymetrix oligonucleotide arrays") - (description - "This package contains functions for exploratory oligonucleotide array -analysis.") - (license license:lgpl2.0+))) - (define-public r-vsn (package (name "r-vsn") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:29 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:30 +0000 Received: from localhost ([127.0.0.1]:37741 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk1-0000HO-Hm for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:29 -0400 Received: from mail-wm1-f47.google.com ([209.85.128.47]:40838) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjP-00009g-6q for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:51 -0400 Received: by mail-wm1-f47.google.com with SMTP id f6-20020a1c1f060000b0290175ca89f698so8049113wmf.5 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:51 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=5ASJt7NLUKS2jhQ62ZHnfqDYbm/o/myoTU5KS14EMC4=; b=Tfjez3V9BgI/ty3Pl5l85xJXIZY9MklFzcmwIdpgqG7i1W7t6OKbpmD7IpCW0G4LtZ otns8RVSlkZ6VSXpsdjFdh16HW18FWQUxg3WBjhG8nUN/kST7wqA0NhlSSgduxcs/kBo DIGLHnQ4ziocAxjFZV5wjgeQJeAMslxJtU29j53yBKvEQfU97AXR19RAeTQtQgZDO+m7 nTjATZrny2P1LFn0Pe8HhN0CTog3KHXUbf7CLwLXYB+iB0Ig2xWoNsImQ+WG5awpd/L1 M+La0PvuP7LcakY7aPHgF7UR16dD915tUQuUkHow8EmSq2NwgD5ISP2dSoexVw4NESUp dmMA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=5ASJt7NLUKS2jhQ62ZHnfqDYbm/o/myoTU5KS14EMC4=; b=p8gS2ZTfdGnIxGxahr53Ekejfc68Qdugtak1EfJLe5LIkVxUi97NeT7N8NB50J8HaM 3p8QftPIdUBn87oU597ik8ABGGBtJJfSXt6HCmvwUuk3pT2xW1sreW8PP0G7T6zo9UUy MFxZ/YlIQO4v5VDB0F5Fcyubs1mnw5zQy+l2quwsulQQv7ti4jSkx35NHcJoQIwx8Wbq twecPkX1gnvrKP255iKEWkED8Xr0G5LquLGrh78kdddebGh02laUOLayzJJEkINl/6Vu ynzTAbSmV14CGu0HZLT6FLSsBHTrr9YQH/69xENzHe1piIBXQbalCH5+een+5qdoqqIz /MVQ== X-Gm-Message-State: AOAM533zRyN+cBgxmcUsM2JQbpayEibfoJxEcP3xiX3SyW5QxFhtQmml YH4XfcZ51WAQDTLZRD2cWdwTyKCwGqA= X-Google-Smtp-Source: ABdhPJxt/jST7gQ3vW46fYBKAuP2tOCNWzFewhhYGL/m5cLba6Vl/Qx/lJ96dSJCcUbuPh0/h0NXfQ== X-Received: by 2002:a1c:b702:: with SMTP id h2mr10277720wmf.99.1621628805744; Fri, 21 May 2021 13:26:45 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.45 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:45 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 23/50] gnu: r-keggrest: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:55 +0200 Message-Id: <20210521202622.26591-23-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-keggrest): Move from here... * gnu/packages/bioconductor.scm (r-keggrest): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6d60b5884c..5ee670e858 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2634,6 +2634,32 @@ microarray data, using nearest neighbor averaging.") Shiny-based display methods for Bioconductor objects.") (license license:artistic2.0))) +(define-public r-keggrest + (package + (name "r-keggrest") + (version "1.30.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "KEGGREST" version)) + (sha256 + (base32 + "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s")))) + (properties `((upstream-name . "KEGGREST"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-httr" ,r-httr) + ("r-png" ,r-png))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/KEGGREST") + (synopsis "Client-side REST access to KEGG") + (description + "This package provides a package that provides a client interface to the +@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.") + (license license:artistic2.0))) + (define-public r-limma (package (name "r-limma") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b789ecd977..5dacf8a342 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8994,32 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-keggrest - (package - (name "r-keggrest") - (version "1.30.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "KEGGREST" version)) - (sha256 - (base32 - "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s")))) - (properties `((upstream-name . "KEGGREST"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-httr" ,r-httr) - ("r-png" ,r-png))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/KEGGREST") - (synopsis "Client-side REST access to KEGG") - (description - "This package provides a package that provides a client interface to the -@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.") - (license license:artistic2.0))) - (define-public r-gage (package (name "r-gage") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:30 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:30 +0000 Received: from localhost ([127.0.0.1]:37743 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk1-0000HW-TP for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:30 -0400 Received: from mail-wm1-f53.google.com ([209.85.128.53]:51739) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjP-00009v-Mk for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:52 -0400 Received: by mail-wm1-f53.google.com with SMTP id u133so11744900wmg.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:51 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=lPuLYewpgN20jwOxUL7MSEqfXRTrg+VQAJuLQemUoK0=; b=FmnTpyn2gXGIZQgih2hyJpiH/rAa5yvYIb4l+5A1HqpDVm+vgTl8stLOKAeislSSh1 fDPZu7376iO9DZzupPJ8rfMrxnIqoV15ZFylkrMmnhSRs73oZZ0jBRvxj3MjgHSylb2a tnJm/HEExcFmibjd0dhnBcgpjZxtmfLCjChwon0fbcNb8hAQF3zqRJRzwtD6xyFh+juc 8U+mpW1Vgv2s+wATIGlBMkqAKL/5yrJiCiJTNqSnhPl7uzXUHB03dM41uNGTm689izMN GO0EfWhiiE12MBApyQs16pOccNzL79OKOCWtU+DfMHDbky8bYyWLVOVw+ZdYfpta52+b 5lAg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=lPuLYewpgN20jwOxUL7MSEqfXRTrg+VQAJuLQemUoK0=; b=FQZccox8SztW2fsGZVkiJfRZuGqJUuSHE4GY1BNSQQuKw1BxO1zwXw98c7+CQWxDyM lYBs7FeJqpm2nBKCPc5Od83iogTFSJ2M8wYQbScOTPvRYDwextUsdICBl2Kmpmv/31up qE2V9ieOnDq7H952rPt/sRv95MnY3UolWGdsO52Tin3nwbxj/ubAJualRNB9pYm2jZuC 1ING8mCKi66FCkmV7tRREIfMc70qOV7KNyLJOivyRcXaLwch2lGy0yMspmchwE4xu0fk P6huMSzLOaZMBZiJGQJrTZUnVQrSFg+LjA+UbOaUTIerotJeDaVp+wyQuLMHkPLpAqrP APnw== X-Gm-Message-State: AOAM532Kb7U7nEuB0pDEgaptggh2/Y//p8u4XJFgglzaxSgul6B9s9tD jxKSDQs/1yqMZuuq5/SwLkJPaOS+8SI= X-Google-Smtp-Source: ABdhPJxV9/r6i/FA1Rfx4raON20gCZzXyfNt1qwJS7scyEfXkRplznmuP5f0PMLLhOOpDPUR4VCpIA== X-Received: by 2002:a7b:c3d4:: with SMTP id t20mr9932051wmj.13.1621628806170; Fri, 21 May 2021 13:26:46 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.45 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:45 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 24/50] gnu: r-gage: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:56 +0200 Message-Id: <20210521202622.26591-24-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-gage): Move from here... * gnu/packages/bioconductor.scm (r-gage): ...to here. --- gnu/packages/bioconductor.scm | 33 ++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5ee670e858..f6d3ef897a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017 Efraim Flashner -;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu @@ -2294,6 +2294,37 @@ formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.") (license license:lgpl2.0+))) +(define-public r-gage + (package + (name "r-gage") + (version "2.40.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gage" version)) + (sha256 + (base32 + "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-go-db" ,r-go-db) + ("r-graph" ,r-graph) + ("r-keggrest" ,r-keggrest))) + (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" + "articles/10.1186/1471-2105-10-161")) + (synopsis "Generally applicable gene-set enrichment for pathway analysis") + (description + "GAGE is a published method for gene set (enrichment or GSEA) or pathway +analysis. GAGE is generally applicable independent of microarray or RNA-Seq +data attributes including sample sizes, experimental designs, assay platforms, +and other types of heterogeneity. The gage package provides functions for +basic GAGE analysis, result processing and presentation. In addition, it +provides demo microarray data and commonly used gene set data based on KEGG +pathways and GO terms. These functions and data are also useful for gene set +analysis using other methods.") + (license license:gpl2+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5dacf8a342..daf1fb6958 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8994,37 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-gage - (package - (name "r-gage") - (version "2.40.2") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gage" version)) - (sha256 - (base32 - "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-keggrest" ,r-keggrest))) - (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" - "articles/10.1186/1471-2105-10-161")) - (synopsis "Generally applicable gene-set enrichment for pathway analysis") - (description - "GAGE is a published method for gene set (enrichment or GSEA) or pathway -analysis. GAGE is generally applicable independent of microarray or RNA-Seq -data attributes including sample sizes, experimental designs, assay platforms, -and other types of heterogeneity. The gage package provides functions for -basic GAGE analysis, result processing and presentation. In addition, it -provides demo microarray data and commonly used gene set data based on KEGG -pathways and GO terms. These functions and data are also useful for gene set -analysis using other methods.") - (license license:gpl2+))) - (define-public r-genomicfiles (package (name "r-genomicfiles") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:30 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:31 +0000 Received: from localhost ([127.0.0.1]:37745 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk2-0000Hd-Fh for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:30 -0400 Received: from mail-wm1-f45.google.com ([209.85.128.45]:42543) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjQ-0000A1-4O for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:52 -0400 Received: by mail-wm1-f45.google.com with SMTP id f75-20020a1c1f4e0000b0290171001e7329so7779568wmf.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:52 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=inq9neC5ix32A8akE1Q/XEP7EZ3hAz0EhOMcAMgLS4E=; b=dhaVv47tA9Pj7EhizrNQ2QUsJemzISGR/peAPD1MrF2JMnFQhvkln4CqwcT2cDzpMx BU7HAK4sasPN20k2EkRxA1t7qwj9unzRrVRoCs/gLP0YmbAUpuYJe2MWwoNxv0/4xAjX chXplhNiUsxE+VEQt69DRCgnS2ejS5B1Joy/E7LDDu4Yup+Ft7U8l1x+HDZvK0OUoAWv UsYd8KWRmmbTaB763z0C1Wr0kNSdGUbgrRyw+iofKEiJsY/MzSwmeYCNNfaew4jJjAUl pJh5V3tGd/pu9X9dQ5r9X8XiFFc0P3+3/fpzwhL3w2Yp6lqDrgyiJS/IVkx+xtQgDVnO 4hLw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=inq9neC5ix32A8akE1Q/XEP7EZ3hAz0EhOMcAMgLS4E=; b=pGXw/cOpV2MlXTbPmA3O8a4SSJQ7zDXJ/sqUvnHJ0KSxrLZdAZuy+K3N4EJRmucGym qaK4sBoUFexC5wz2flb/ZHXom3Rb26wDLOdvI98iYZCOgCaj0l/VL1mnIA2R+MQft4+o HNaue9b3ELxgYvbbdeiShwz7jtfqBqn6ugHvPbv2TlmDIMD1mPo7FurH2kUXD7rSTbz/ zM2pwx+c7gRA66J/HGf94WhdDzUAznippaz6HFBEVyWEPTA6zHhXXS4DCXegvUAwrW9K LDBE5duFaKB0M3cLfl9woCu7UjnKIEIMoGBJU7DsdmYV5WPSqqkOUy8Lxl6qbWcVqoOH WnAQ== X-Gm-Message-State: AOAM531LG934D6yLs3za3RaAAQ5InfsetUuTvztj6t/1FxDaWyAyE2zX fLo0Veh/YhfYDhmcBQI9UDP4d6FnXGQ= X-Google-Smtp-Source: ABdhPJycj+jsB2OZeYl19jT2wq04GPHYXs2hPDvVikcIF+nPEM588Hb8mmyMkJ9NTdj5H18Ee06hOQ== X-Received: by 2002:a05:600c:4eca:: with SMTP id g10mr10858172wmq.187.1621628806656; Fri, 21 May 2021 13:26:46 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.46 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:46 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 25/50] gnu: r-complexheatmap: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:57 +0200 Message-Id: <20210521202622.26591-25-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-complexheatmap): Move from here... * gnu/packages/bioconductor.scm (r-complexheatmap): ...to here. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 39 --------------------------------- 2 files changed, 39 insertions(+), 39 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f6d3ef897a..92eb5a0906 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2082,6 +2082,45 @@ genome data packages and support for efficient SNP representation.") analysis.") (license license:artistic2.0))) +(define-public r-complexheatmap + (package + (name "r-complexheatmap") + (version "2.6.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ComplexHeatmap" version)) + (sha256 + (base32 + "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x")))) + (properties + `((upstream-name . "ComplexHeatmap"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cairo" ,r-cairo) + ("r-circlize" ,r-circlize) + ("r-clue" ,r-clue) + ("r-colorspace" ,r-colorspace) + ("r-digest" ,r-digest) + ("r-getoptlong" ,r-getoptlong) + ("r-globaloptions" ,r-globaloptions) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-png" ,r-png) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/jokergoo/ComplexHeatmap") + (synopsis "Making Complex Heatmaps") + (description + "Complex heatmaps are efficient to visualize associations between +different sources of data sets and reveal potential structures. This package +provides a highly flexible way to arrange multiple heatmaps and supports +self-defined annotation graphics.") + (license license:gpl2+))) + (define-public r-deseq (package (name "r-deseq") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index daf1fb6958..acaf41acc4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9028,45 +9028,6 @@ distributed by file or by range. User defined mapper and reducer functions provide added flexibility for data combination and manipulation.") (license license:artistic2.0))) -(define-public r-complexheatmap - (package - (name "r-complexheatmap") - (version "2.6.2") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ComplexHeatmap" version)) - (sha256 - (base32 - "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x")))) - (properties - `((upstream-name . "ComplexHeatmap"))) - (build-system r-build-system) - (propagated-inputs - `(("r-cairo" ,r-cairo) - ("r-circlize" ,r-circlize) - ("r-clue" ,r-clue) - ("r-colorspace" ,r-colorspace) - ("r-digest" ,r-digest) - ("r-getoptlong" ,r-getoptlong) - ("r-globaloptions" ,r-globaloptions) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page - "https://github.com/jokergoo/ComplexHeatmap") - (synopsis "Making Complex Heatmaps") - (description - "Complex heatmaps are efficient to visualize associations between -different sources of data sets and reveal potential structures. This package -provides a highly flexible way to arrange multiple heatmaps and supports -self-defined annotation graphics.") - (license license:gpl2+))) - (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:31 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:31 +0000 Received: from localhost ([127.0.0.1]:37747 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk2-0000Hk-Rn for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:31 -0400 Received: from mail-wm1-f50.google.com ([209.85.128.50]:44795) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjQ-0000A6-HP for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:53 -0400 Received: by mail-wm1-f50.google.com with SMTP id y184-20020a1ce1c10000b02901769b409001so7810028wmg.3 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:52 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=4/IyA5GjTj8VBRc6sNBtUWUqFF7zQtZdeCYJyfJb8Yk=; b=dJtW3S/R9waK91eigv3dmZRP1jdM/zC3E441Uh64bhh1Zpza+Wo4nGdlEqXj/tPp72 AR2K0j6P5tVFJwybzq7N/1Ab9/acd9OGntoVzfytt43Mv9FBXqR4VrQb6VJIf3g5Wa6D 4ZguuzTr/9JXJNnRXwW5f/IZ6eei+P2lLKKDgn8BrASmqtfVr4pRF1gHliuh4Dq0N2HA eghv0Hix/u4cCCHbL2rm77Ky4eX4EaO0zEs0s+qeuafAnOFRz4rqDAY29Y2gTynlOAFn xhMz1Js2gy84bodXXPOgtxfttzj5oDXpOf0KtSiB8gEOBWygcyuisP/7Fzw884wSIQSE kg9w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=4/IyA5GjTj8VBRc6sNBtUWUqFF7zQtZdeCYJyfJb8Yk=; b=VTLX1LXYidKXIsDobWOMKDlVfo3QHKDDcsKM34Gygv3x+5BINy+c37WnX3grcELxoL TWJAF9IaXElNRjpy5jDiec/UFzmQW7uPXngEtk9TNdiSJVAifzYHKSUm15VU0cNl7+0f nRgQWCndUfgcWjynd7F3msQqYhc/WBG3NjvBQCtYYnSPR0/7xySsky5u6mmGu7B5Qckr prWbpq4DTmzPMiVlXUPTfPbKUW7YVEHmkmPx8gKiLSiRXczEEFAGadzSL8GbaWrNxzj9 qWM9H9Q4rV0lx49JVu8YzsxfaRJ1xu7FAABQBbHhrGndI6yUToRAjZJ6NrOgXzarJhXy BHaA== X-Gm-Message-State: AOAM531n2l02yRwMqSSp8va9SyIVhgxNFM2/3zOE+oJvi+hZqbPdn8SE Ln5oa05XJTkVF3p+XTjsorAZ1Cjz1h8= X-Google-Smtp-Source: ABdhPJzhtCMAzB3kx59WtROg2BgnPbWtwU+jfiL0gd4bXRd/zRjjd5rOYG6cEsFtBcI30udyoEgDRg== X-Received: by 2002:a05:600c:4f8f:: with SMTP id n15mr2926037wmq.107.1621628807066; Fri, 21 May 2021 13:26:47 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.46 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:46 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 26/50] gnu: r-genomicfiles: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:58 +0200 Message-Id: <20210521202622.26591-26-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-genomicfiles): Move from here... * gnu/packages/bioconductor.scm (r-genomicfiles): ...to here. --- gnu/packages/bioconductor.scm | 34 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 34 --------------------------------- 2 files changed, 34 insertions(+), 34 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 92eb5a0906..e73e78f616 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2546,6 +2546,40 @@ transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.") (license license:artistic2.0))) +(define-public r-genomicfiles + (package + (name "r-genomicfiles") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicFiles" version)) + (sha256 + (base32 + "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz")))) + (properties `((upstream-name . "GenomicFiles"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrixgenerics" ,r-matrixgenerics) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/GenomicFiles") + (synopsis "Distributed computing by file or by range") + (description + "This package provides infrastructure for parallel computations +distributed by file or by range. User defined mapper and reducer functions +provide added flexibility for data combination and manipulation.") + (license license:artistic2.0))) + (define-public r-genomicranges (package (name "r-genomicranges") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index acaf41acc4..4836eee82c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8994,40 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-genomicfiles - (package - (name "r-genomicfiles") - (version "1.26.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicFiles" version)) - (sha256 - (base32 - "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz")))) - (properties `((upstream-name . "GenomicFiles"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (home-page "https://bioconductor.org/packages/GenomicFiles") - (synopsis "Distributed computing by file or by range") - (description - "This package provides infrastructure for parallel computations -distributed by file or by range. User defined mapper and reducer functions -provide added flexibility for data combination and manipulation.") - (license license:artistic2.0))) - (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:31 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:31 +0000 Received: from localhost ([127.0.0.1]:37749 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk3-0000Ht-AE for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:31 -0400 Received: from mail-wr1-f51.google.com ([209.85.221.51]:33296) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjR-0000AJ-1X for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:53 -0400 Received: by mail-wr1-f51.google.com with SMTP id n2so22297933wrm.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:52 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=+/ohMXZD/XpdR6XwB+BhQJ/VD0IyC0iZqMenxEi1DYI=; b=HTKL7r8EVRER4YCQui4zIFYNGNX4PIRBOLCw+4+vtlWXrGv494IZj1wnzMfktXKSI/ dgVLviLCbGwt02E1hcuAtZ8jHPDSEllWi7rxIfvfcC9JX9d+LKyV1EEd9fy6gAqfnJ3U L0I/uLEjNnYcvbWcCM8rZwq9RDylMQhQpbFICDJl8Pg/uP7dlm4yW6PGt6CaeP7EXxL1 24qGLRZgzOR/9dJ4R9KHXIwmy5gimCd9gZuvOwwmXgun+JGKMD/nleTuXNyRnrl9e2Ux 4lJE7UMeZOyqOiFqMypUWz5y0gPd0aY8tsR1ckUjwUHQ+J7mlhI1Wuiff8Gz0XiaSezh SwEg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=+/ohMXZD/XpdR6XwB+BhQJ/VD0IyC0iZqMenxEi1DYI=; b=ZTbrvnmxCI3Ke+Ls9z6xmovKpdkVkCoT8NslMtR8Rv/5b0leMGQIaEwvq4qVRtZ3EK HLHjf0lblDSlmrMd+pSVzWcufQwadw/CEAeguO4TjYj1YQ39JPkVPrxDLKV6qFHwXREy tfmxb1OjP7l/C/bln03ScbkWOBnElR+XzLU48qZSd7czibgjTUQb5LGD1tZWZxKVPESN c/+7CSyZRL4CYdTIgk/u4dE6MxT4XOHKvZ23qeNqoNmmtFPTzVb3V3fQrVkAys9Hes76 OYE/4UaNw8gD2PYcANAKmrLLHfPDcsG8+RUkBei5z+cxtJ8sKsC/KjLM7q0bMbyId4YY 2YCQ== X-Gm-Message-State: AOAM533Ef/62MUI91A2kQarrND1btC2fozP2c0tRD3er9Pukyul/tUQE qu5NEmjEddrtaLLVffQChHhDpmxZrk0= X-Google-Smtp-Source: ABdhPJwdFF2uIsct0widK3fA+DsZgAO1KJN6zMC0p4EnbkzRs+Crla66G0s+dNDBnL6Zd3OjxR3cSg== X-Received: by 2002:adf:fc91:: with SMTP id g17mr11360709wrr.191.1621628807491; Fri, 21 May 2021 13:26:47 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.47 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:47 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 27/50] gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:59 +0200 Message-Id: <20210521202622.26591-27-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here... * gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e73e78f616..7717c821b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2235,6 +2235,35 @@ testing. The package also provides functions for the visualization and exploration of the results.") (license license:gpl3+))) +(define-public r-dirichletmultinomial + (package + (name "r-dirichletmultinomial") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DirichletMultinomial" version)) + (sha256 + (base32 + "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk")))) + (properties + `((upstream-name . "DirichletMultinomial"))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/DirichletMultinomial") + (synopsis "Dirichlet-Multinomial mixture models for microbiome data") + (description + "Dirichlet-multinomial mixture models can be used to describe variability +in microbial metagenomic data. This package is an interface to code +originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): +1-15.") + (license license:lgpl3))) + (define-public r-edaseq (package (name "r-edaseq") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4836eee82c..0c7b3d602f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8994,35 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-dirichletmultinomial - (package - (name "r-dirichletmultinomial") - (version "1.32.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DirichletMultinomial" version)) - (sha256 - (base32 - "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk")))) - (properties - `((upstream-name . "DirichletMultinomial"))) - (build-system r-build-system) - (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/DirichletMultinomial") - (synopsis "Dirichlet-Multinomial mixture models for microbiome data") - (description - "Dirichlet-multinomial mixture models can be used to describe variability -in microbial metagenomic data. This package is an interface to code -originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): -1-15.") - (license license:lgpl3))) - (define-public r-ensembldb (package (name "r-ensembldb") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:32 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:32 +0000 Received: from localhost ([127.0.0.1]:37751 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk3-0000I0-MN for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:32 -0400 Received: from mail-wr1-f53.google.com ([209.85.221.53]:39714) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjR-0000AV-HD for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:54 -0400 Received: by mail-wr1-f53.google.com with SMTP id v12so22200484wrq.6 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:53 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=9zISe9rFLbchuImfNcM0SnLo2CE31AzSoJPIaCp/pnM=; b=DnPYLMx0hTadBP+Fw9i9E+usH3rplIouF/pgiyPDW0RmT2DWoOEUTXMb34NGrrjo5P xIh17hs+BURo6f2OVNYxwbYwitFUNNNAqxLmKVF1E+FOFdac5+uraw8pHh90DDsDDJj9 AysdLwoa62JTL1DcH7foFJz7RDFjW5KuXpe2iNSYBXibjpMHWZ3OsWPz0BZ7p7hfmRt2 0y/FF+tEezt/X81T6amZyY9fbEw8nbdJ8wxdZtlRrAYJ9n5I9aObjYZkPFkYBlELY7Iu BpBxsy7GEqVpVb+cY2Bbxk6rfvVYwYg/q+zvrWVeYBCXbd+qf0ZPvuEzXwvfpt77xbSR 138g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=9zISe9rFLbchuImfNcM0SnLo2CE31AzSoJPIaCp/pnM=; b=WhfdC9WGoTp9aXFKCFEm4IVcSX5CeccqeZK1a8iRsmHoNRn6XAa2iE3zzPBun+j8Zi A/zIQlGveTSscLtqvtWLWdS/FbQPBys3XpO3AnuVLJ8Rma7Y4LzFdpeIxBlDilMH24vl 2GmD8WKMtIgTaM4z9p44qY9UQqlX98xawWAUzEkPVcYyjUn30KCpGMPgInM+9DrMGuUn PTXqav0Z6rXSmGQBKhSRAPOBhgH8PVJcTndGMxYIo6QOTbOVk2BFJm8LSsALngJV3GGA NtVHhv/5BtmFMNLgl/MCKunThhev4ot1b0YSgPfnjGrZormYALdFjefHkczqNcVZaepD tqSA== X-Gm-Message-State: AOAM532zvKZuZqfCMnnALlvJuU2afr0Oi98vOHsMLBv+Z7qRo7yY7XHM fD1nuh3AsmfSuoGkYbFJYRYZaIvbjjE= X-Google-Smtp-Source: ABdhPJz4sbaumD4bC7PLg4936vsAr/SlQRcD+u+/rA49xumKUVn9cDtRmcnufseb69Yopo+b2p3BYA== X-Received: by 2002:a5d:4c49:: with SMTP id n9mr11037625wrt.417.1621628807912; Fri, 21 May 2021 13:26:47 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.47 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:47 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 28/50] gnu: r-organismdbi: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:00 +0200 Message-Id: <20210521202622.26591-28-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-organismdbi): Move from here... * gnu/packages/bioconductor.scm (r-organismdbi): ...to here. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 32 -------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7717c821b9..c63d39dc9c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2940,6 +2940,38 @@ mzIdentML files with the drawback of having less pretty output than a vendor specific parser.") (license license:gpl2+))) +(define-public r-organismdbi + (package + (name "r-organismdbi") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "OrganismDbi" version)) + (sha256 + (base32 + "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw")))) + (properties `((upstream-name . "OrganismDbi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-dbi" ,r-dbi) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-graph" ,r-graph) + ("r-iranges" ,r-iranges) + ("r-rbgl" ,r-rbgl) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/OrganismDbi") + (synopsis "Software to enable the smooth interfacing of database packages") + (description "The package enables a simple unified interface to several +annotation packages each of which has its own schema by taking advantage of +the fact that each of these packages implements a select methods.") + (license license:artistic2.0))) + (define-public r-pcamethods (package (name "r-pcamethods") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0c7b3d602f..1c90700c95 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9039,38 +9039,6 @@ chromosome region or transcript models of lincRNA genes.") ;; No version specified (license license:lgpl3+))) -(define-public r-organismdbi - (package - (name "r-organismdbi") - (version "1.32.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "OrganismDbi" version)) - (sha256 - (base32 - "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw")))) - (properties `((upstream-name . "OrganismDbi"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-dbi" ,r-dbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-graph" ,r-graph) - ("r-iranges" ,r-iranges) - ("r-rbgl" ,r-rbgl) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/OrganismDbi") - (synopsis "Software to enable the smooth interfacing of database packages") - (description "The package enables a simple unified interface to several -annotation packages each of which has its own schema by taking advantage of -the fact that each of these packages implements a select methods.") - (license license:artistic2.0))) - (define-public r-biovizbase (package (name "r-biovizbase") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:32 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:32 +0000 Received: from localhost ([127.0.0.1]:37753 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk4-0000I8-2v for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:32 -0400 Received: from mail-wr1-f46.google.com ([209.85.221.46]:39709) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjS-0000An-DZ for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:54 -0400 Received: by mail-wr1-f46.google.com with SMTP id v12so22200522wrq.6 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:54 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=kE+FzhGHJKFbog33VGG5pEwrPhxNRKKdEb1FwbBz0Co=; b=FJXahakvG8Ko9RyhAByK0AA+oDo5Rm9Pvpxis0KZ1jGPOn8pSSYXz0YF38DLTpcWk8 80mO8glAqj4Vu+5JGOVBfPBMbSLBYqKaQrvbnTlI+kk8XNk/OddPIZzRqIU1noFua8CC KYQl+atfrx1axHD2VIVab6hB7cgxVjW7qQ7QybuFszeXZArqNS9rcdohYvVsZI4SJfT6 8DF7Z9emAnXtGtuOcbloycaSD0TUvugwPi2tJgkysZEFd/EtMtAs27IJ+PIXF0Z7Vp41 ZmXzJAGJBHMWJmq7ItZ0ssHhzOrSpiKG3UeWgGMJE2Gi/mQLyn5Svsr5qz9TGzaK9ozY 6D9w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=kE+FzhGHJKFbog33VGG5pEwrPhxNRKKdEb1FwbBz0Co=; b=DYyw7xe70YhoQUqRctZryGxCC4V1tSjrncG5k836RNvhUA9HRJfzbM3jV2vaap0mBM f3n/JwoTOzAzqERlg6hXstIWVLcxyQJpz6XQMm5kgTVP8Mu35l4cxukAOB13oBM286qh pxJsaVnOpmVfePVI4qMbL89ve9QLUsyVF6dtGOKTlZuS3qdIgfG7bSW8ad50zGTRaiuT j8Hzaf5p3PjMCAhq6VNLmBQiPILrTXgm1zr2w0rpXrIPYPPfSaJuOmrzyXVMjXuSuwH9 8QEYIxkvgAX9IttR6IQ3mwF/oQ1kuVnbNYUibfEY+DM7RVjNuP/dyK1vdqtLitBM0bn/ 7R+w== X-Gm-Message-State: AOAM533u5HvJfYhFZUn/o6g3Lyq0iIfqHyHMX06LOMZrtP+KMg6MItmt SomD0klhY7F2A4TYc6IFepoaD8infec= X-Google-Smtp-Source: ABdhPJwzJXlZKED7bY0Ec6/SOv7wrb32r6o/pA6mVEd+O4XLwaiq/WWncftRDN7ViengscFfFefofQ== X-Received: by 2002:adf:cd0b:: with SMTP id w11mr10828714wrm.178.1621628808817; Fri, 21 May 2021 13:26:48 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:48 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 30/50] gnu: r-vsn: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:02 +0200 Message-Id: <20210521202622.26591-30-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-vsn): Move from here... * gnu/packages/bioconductor.scm (r-vsn): ...to here. --- gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 36 --------------------------------- 2 files changed, 36 insertions(+), 36 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d0ebcf8481..05c4896276 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3480,6 +3480,42 @@ dependencies between GO terms can be implemented and applied.") coding changes and predict coding outcomes.") (license license:artistic2.0))) +(define-public r-vsn + (package + (name "r-vsn") + (version "3.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "vsn" version)) + (sha256 + (base32 + "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-ggplot2" ,r-ggplot2) + ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") + (synopsis "Variance stabilization and calibration for microarray data") + (description + "The package implements a method for normalising microarray intensities, +and works for single- and multiple-color arrays. It can also be used for data +from other technologies, as long as they have similar format. The method uses +a robust variant of the maximum-likelihood estimator for an +additive-multiplicative error model and affine calibration. The model +incorporates data calibration step (a.k.a. normalization), a model for the +dependence of the variance on the mean intensity and a variance stabilizing +data transformation. Differences between transformed intensities are +analogous to \"normalized log-ratios\". However, in contrast to the latter, +their variance is independent of the mean, and they are usually more sensitive +and specific in detecting differential transcription.") + (license license:artistic2.0))) + (define-public r-xvector (package (name "r-xvector") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7256df3f83..600c2ca81e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8934,42 +8934,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-vsn - (package - (name "r-vsn") - (version "3.58.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "vsn" version)) - (sha256 - (base32 - "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb")))) - (build-system r-build-system) - (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-ggplot2" ,r-ggplot2) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes - (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") - (synopsis "Variance stabilization and calibration for microarray data") - (description - "The package implements a method for normalising microarray intensities, -and works for single- and multiple-color arrays. It can also be used for data -from other technologies, as long as they have similar format. The method uses -a robust variant of the maximum-likelihood estimator for an -additive-multiplicative error model and affine calibration. The model -incorporates data calibration step (a.k.a. normalization), a model for the -dependence of the variance on the mean intensity and a variance stabilizing -data transformation. Differences between transformed intensities are -analogous to \"normalized log-ratios\". However, in contrast to the latter, -their variance is independent of the mean, and they are usually more sensitive -and specific in detecting differential transcription.") - (license license:artistic2.0))) - (define-public r-ensembldb (package (name "r-ensembldb") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:33 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:33 +0000 Received: from localhost ([127.0.0.1]:37755 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk4-0000IF-HJ for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:32 -0400 Received: from mail-wr1-f44.google.com ([209.85.221.44]:39708) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjS-0000Ao-Qx for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:55 -0400 Received: by mail-wr1-f44.google.com with SMTP id v12so22200534wrq.6 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:54 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=Poe2LuMsCnuZtRINjiEp0jYCsrl+xGyc9hxjLq6OOdE=; b=VtoL3XvQvB+lz02tW1QKmhpRW6gN9Fcpj35Tji1OLCjcT4zJM8TiR9IycOrhTzoU5F cFzJvo/JLPw+U2bo7qzENwxijsxk8YlbSdi2ttKvHcd9eX2QhXlzVTVxiUpZEEmlUZh8 ZEBtUi+Q/IsObwISy4GdvDP925z6ji+GK+vHJ0pa8DVBJM7X3opJuAEUpIf2uwyQKJ3b oNivCA5MCJtEt33v12mMmMVoBhncmVS9HfTd6iyCp6aSBt6gY9j1RVDzogosyurEeDoC wn0NnrkIBirpzT+A3m6rO3GVnuym15DRzfqP1TedV9k19LP3Vgf4M2/0m3XqX2gTLJqU uIxA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=Poe2LuMsCnuZtRINjiEp0jYCsrl+xGyc9hxjLq6OOdE=; b=fl0KnCBC3snu6CVxNn4shTYdEqsL3KJvGrYyFpgjtSHGha8bR4KIPOuEY55k2kAhH3 191qoJWEfcx8UcflZ0rGCAERkLH6l537fiMn64RwwRTWofK6yo0vUZWXcRmuu5yGR8V3 H7lbx5nTjpZGwORV30Xey6DsgPN2enZmi6hmajoUE+edfw75ii4vPCcaAsr9AdsLAdK7 uF1biJZtEym7/ponvfvVkP8xC2oja6DIYnOhKDj98nd23I4iMFXB9p4TPmMeymoKFwYN vhyDoihryuK1l8iCEDRWpMhnMbcsEO3yZyi7+OwBMF0ODLajqVd3jxeRUu8PDyUiIYhg 9cXQ== X-Gm-Message-State: AOAM5317/wBEmSPyi6K9tk9vs1WtSkV2OsQloHjueIvg90vzd/rkPpJw 4DupVywyqG+sA6h0mr5tOay1aiLDaTI= X-Google-Smtp-Source: ABdhPJz2yDVQguBrk3AjLSYO8f1XTzASO11WuQVPq88MVDNRkzEu7INj7HmkdJTl0bHmvf/+Gr3G6g== X-Received: by 2002:adf:fc44:: with SMTP id e4mr11317508wrs.23.1621628809274; Fri, 21 May 2021 13:26:49 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:49 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 31/50] gnu: r-biovizbase: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:03 +0200 Message-Id: <20210521202622.26591-31-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-biovizbase): Move from here... * gnu/packages/bioconductor.scm (r-biovizbase): ...to here. --- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 42 --------------------------------- 2 files changed, 42 insertions(+), 42 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 05c4896276..7439ad96da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2044,6 +2044,48 @@ matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.") (license license:artistic2.0))) +(define-public r-biovizbase + (package + (name "r-biovizbase") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biovizBase" version)) + (sha256 + (base32 + "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq")))) + (properties `((upstream-name . "biovizBase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-dichromat" ,r-dichromat) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rlang" ,r-rlang) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/biovizBase") + (synopsis "Basic graphic utilities for visualization of genomic data") + (description + "The biovizBase package is designed to provide a set of utilities, color +schemes and conventions for genomic data. It serves as the base for various +high-level packages for biological data visualization. This saves development +effort and encourages consistency.") + (license license:artistic2.0))) + (define-public r-bsgenome (package (name "r-bsgenome") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 600c2ca81e..e6692ece0c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8979,48 +8979,6 @@ chromosome region or transcript models of lincRNA genes.") ;; No version specified (license license:lgpl3+))) -(define-public r-biovizbase - (package - (name "r-biovizbase") - (version "1.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "biovizBase" version)) - (sha256 - (base32 - "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq")))) - (properties `((upstream-name . "biovizBase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dichromat" ,r-dichromat) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (home-page "https://bioconductor.org/packages/biovizBase") - (synopsis "Basic graphic utilities for visualization of genomic data") - (description - "The biovizBase package is designed to provide a set of utilities, color -schemes and conventions for genomic data. It serves as the base for various -high-level packages for biological data visualization. This saves development -effort and encourages consistency.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:33 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:33 +0000 Received: from localhost ([127.0.0.1]:37757 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk4-0000IM-VH for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:33 -0400 Received: from mail-wm1-f53.google.com ([209.85.128.53]:36550) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjT-0000B0-5B for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:55 -0400 Received: by mail-wm1-f53.google.com with SMTP id n17-20020a7bc5d10000b0290169edfadac9so8084535wmk.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:55 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=b1fQ4jXDRH91NBR1YEwu2AtIWNrQnr2UAXjU+EigkvE=; b=dEFYgRnFA6i8h2yh0rRAHNyKXqad0m/qRMeboIULxK4NuPDvgqHylql+tkcemeEGsB 1Mtch8SW4PO8C0TCx6Vounrl8UZpK9s2PoOsDW84A628+Z8h1cYKMZP5HWOR0pI75lKW j/CLibR+hnN6f1Ma8xK/BSy3gV9aatt4j0rMtrpy0xd2EelkfD6ST2Nc+FcobfvITcHH /YaUAK60FSJ896nxRbnKE+f7PeEVNJhwUOENQ4n8sBjJx00732heXe3TVHaZfC8Oq+Vy RQCOYsnWiZEgN6m+vMMNavh/qZt+GL3ovzyYOe2pZEjsypey55We19PDqFldGWxOJ6fX aVnw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=b1fQ4jXDRH91NBR1YEwu2AtIWNrQnr2UAXjU+EigkvE=; b=K/omwVTyUyP7VHyaRhlczSYstNdCLOQ31aw3BTJ0GSY3acNwLTmOJS3yEuxhwASXMM 8uOqUUPk820QbTPuakDCaZxBjCcRGbzL1HGR2FR1fqhyVm6CtTB7ov5x+8SMq/fNnwaI DYqx4B5VzDNqGpgRLzOPDRwJpx2l8HolMJ7n0Rs8Nid+TotQNDGwpMvDN6I9Q+d6VSgC IEBw6foGjf9ekcn+Rumb4KKPGmRIx1xTboDBEWIVjqHgw0eBin8H61n5Q479szF1+0Ek 3eX3ejIffYyoJnJ7vIN1ytbcAK83cnUBHXZuv4smeSmgElNxmdbMjXpfsMBkCpjYrera 9QDg== X-Gm-Message-State: AOAM5302kunLwRvv+W437ADP5KjaZpYc3CC5tfbqusUVCDxry9HNYKTh v+N9OS7INEymuWlv5CMKFIWkCAFmaRU= X-Google-Smtp-Source: ABdhPJzjmHBVEuBT6sY0d9DYCVr+yZv9fsKajzeGNiW0C/4qYmsD3eJ/JuGcqkWs+vf467y3vD/doA== X-Received: by 2002:a1c:7c03:: with SMTP id x3mr10835339wmc.168.1621628809696; Fri, 21 May 2021 13:26:49 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.49 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:49 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 32/50] gnu: r-ensembldb: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:04 +0200 Message-Id: <20210521202622.26591-32-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-ensembldb): Move from here... * gnu/packages/bioconductor.scm (r-ensembldb): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 --------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7439ad96da..7e86af7d21 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2398,6 +2398,51 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.") (license license:gpl2+))) +(define-public r-ensembldb + (package + (name "r-ensembldb") + (version "2.14.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ensembldb" version)) + (sha256 + (base32 + "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-curl" ,r-curl) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-protgenerics" ,r-protgenerics) + ("r-rsamtools" ,r-rsamtools) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jotsetung/ensembldb") + (synopsis "Utilities to create and use Ensembl-based annotation databases") + (description + "The package provides functions to create and use transcript-centric +annotation databases/packages. The annotation for the databases are directly +fetched from Ensembl using their Perl API. The functionality and data is +similar to that of the TxDb packages from the @code{GenomicFeatures} package, +but, in addition to retrieve all gene/transcript models and annotations from +the database, the @code{ensembldb} package also provides a filter framework +allowing to retrieve annotations for specific entries like genes encoded on a +chromosome region or transcript models of lincRNA genes.") + ;; No version specified + (license license:lgpl3+))) + (define-public r-fastseg (package (name "r-fastseg") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e6692ece0c..baef88cd2e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8934,51 +8934,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-ensembldb - (package - (name "r-ensembldb") - (version "2.14.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ensembldb" version)) - (sha256 - (base32 - "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-protgenerics" ,r-protgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/jotsetung/ensembldb") - (synopsis "Utilities to create and use Ensembl-based annotation databases") - (description - "The package provides functions to create and use transcript-centric -annotation databases/packages. The annotation for the databases are directly -fetched from Ensembl using their Perl API. The functionality and data is -similar to that of the TxDb packages from the @code{GenomicFeatures} package, -but, in addition to retrieve all gene/transcript models and annotations from -the database, the @code{ensembldb} package also provides a filter framework -allowing to retrieve annotations for specific entries like genes encoded on a -chromosome region or transcript models of lincRNA genes.") - ;; No version specified - (license license:lgpl3+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:33 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:34 +0000 Received: from localhost ([127.0.0.1]:37759 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk5-0000IU-Bc for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:33 -0400 Received: from mail-wr1-f45.google.com ([209.85.221.45]:45892) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjT-0000B3-No for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:56 -0400 Received: by mail-wr1-f45.google.com with SMTP id x7so2594125wrt.12 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:55 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=3bzLoBL+wfpmWr0LO51TWODHnKj4fRH43j3EeZGVyqA=; b=OcdUIhqNLFA46MNhI3BQFJKRENNXus6y0Xy4+RMHkG/dRJzM8NTl+k30ik192bC4Eu IoLaF0UEjjJ4Q2rk9RdKfLKNbI7dUDvdg4DLgH2DzzekW2/rMm2R3LyGBOTlg+wl5GDl kjOk+/tZghhjMfxJwLDDw57T36RMXUM+DKgUdJoKAAKM9bkJt2nshrNL2hL6UybuZsd1 o6+gV++eW6DkaZnU7c87FNCic8RXP6CY8810MSX0irz3qBSMxCgf4cb/xHAqO6j5/98N GN2DXAaHE/aKhvvZXfqHWB8NE+tS2W7aC3Z5lUes7WWtF1fiTqJ2QN0UsFz6TkKe0kzE 7R7Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=3bzLoBL+wfpmWr0LO51TWODHnKj4fRH43j3EeZGVyqA=; b=X1EFnPA/rTJhN8fhTvC8AU8v86oKg7UvykpD/Z8nUoFmzGZO1q8816/K5ip2fQTfRZ 1Qp2fa7sqto7dLc2TzUyXYpxChrhDRGCBdXIllJD8rjx6ERv0qr+kneOD6PzVSRrOVmN V/0RxfJCpDBJqacNds3KikOv3chhOc0Zo2QXuuUsCwmBYXwevOcGa1kYQ6e0HUhJCVSU 910OVxz8ec/38gjhStmJpBA+849PkadrV8FXEWF084tS58X5Ugw+Dv/pQSzxW+Rkc3hM ZPMd7D+gR4yrfL+1zHeqS2V4KdpUKXJg4u74u8MjcuE9Enq8bwxhlpH+aYTSWyJcMLsy Ui+g== X-Gm-Message-State: AOAM532bFGG1kh1MUS/tOeqx0woe/knx3dZ8eI5r+OTB1l3UQqUMA967 rGUu8g+17lnAbMwF3rjO94v3xllK2eg= X-Google-Smtp-Source: ABdhPJx+XoGDCyubWXKYbZ30aj4R3eACs4zoiTIcPbqrbHELVlxm1Z/+0SpTy6N8tKHyRrq6HOJmBQ== X-Received: by 2002:adf:f7cf:: with SMTP id a15mr11037611wrq.184.1621628810140; Fri, 21 May 2021 13:26:50 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.49 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:49 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 33/50] gnu: r-mzr: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:05 +0200 Message-Id: <20210521202622.26591-33-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-mzr): Move from here... * gnu/packages/bioconductor.scm (r-mzr): ...to here. --- gnu/packages/bioconductor.scm | 62 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 61 -------------------------------- 2 files changed, 62 insertions(+), 61 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7e86af7d21..5ceffd7b4d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -36,6 +36,7 @@ #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages boost) #:use-module (gnu packages cran) #:use-module (gnu packages compression) #:use-module (gnu packages gcc) @@ -3051,6 +3052,67 @@ mzIdentML files with the drawback of having less pretty output than a vendor specific parser.") (license license:gpl2+))) +(define-public r-mzr + (package + (name "r-mzr") + (version "2.24.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mzR" version)) + (sha256 + (base32 + "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/boost") + #t)))) + (properties `((upstream-name . "mzR"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-boost + (lambda _ + (substitute* "src/Makevars" + (("\\./boost/libs.*") "") + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5_LIBS\\)" match) + (string-append match "/libhdf5.a")) + (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") + (("\\ARCH_OBJS=" line) + (string-append line + "\nBOOST_LIBS=-lboost_system -lboost_regex \ +-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) + #t))))) + (inputs + `(;; Our default boost package won't work here, unfortunately, even with + ;; mzR version 2.24.1. + ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources + ("zlib" ,zlib))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-ncdf4" ,r-ncdf4) + ("r-protgenerics" ,r-protgenerics) + ("r-rcpp" ,r-rcpp) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/sneumann/mzR/") + (synopsis "Parser for mass spectrometry data files") + (description + "The mzR package provides a unified API to the common file formats and +parsers available for mass spectrometry data. It comes with a wrapper for the +ISB random access parser for mass spectrometry mzXML, mzData and mzML files. +The package contains the original code written by the ISB, and a subset of the +proteowizard library for mzML and mzIdentML. The netCDF reading code has +previously been used in XCMS.") + (license license:artistic2.0))) + (define-public r-organismdbi (package (name "r-organismdbi") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index baef88cd2e..a6321a179a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8873,67 +8873,6 @@ trait.") proteomics packages.") (license license:artistic2.0))) -(define-public r-mzr - (package - (name "r-mzr") - (version "2.24.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "mzR" version)) - (sha256 - (base32 - "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg")) - (modules '((guix build utils))) - (snippet - '(begin - (delete-file-recursively "src/boost") - #t)))) - (properties `((upstream-name . "mzR"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-boost - (lambda _ - (substitute* "src/Makevars" - (("\\./boost/libs.*") "") - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5_LIBS\\)" match) - (string-append match "/libhdf5.a")) - (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") - (("\\ARCH_OBJS=" line) - (string-append line - "\nBOOST_LIBS=-lboost_system -lboost_regex \ --lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) - #t))))) - (inputs - `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.24.1. - ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources - ("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-ncdf4" ,r-ncdf4) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/sneumann/mzR/") - (synopsis "Parser for mass spectrometry data files") - (description - "The mzR package provides a unified API to the common file formats and -parsers available for mass spectrometry data. It comes with a wrapper for the -ISB random access parser for mass spectrometry mzXML, mzData and mzML files. -The package contains the original code written by the ISB, and a subset of the -proteowizard library for mzML and mzIdentML. The netCDF reading code has -previously been used in XCMS.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:34 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:34 +0000 Received: from localhost ([127.0.0.1]:37761 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk5-0000Ib-Qg for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:34 -0400 Received: from mail-wr1-f52.google.com ([209.85.221.52]:40724) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjU-0000BF-3L for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:56 -0400 Received: by mail-wr1-f52.google.com with SMTP id z17so22188591wrq.7 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:56 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=kuQ3D3X+U+p8xGwb+z27Hs6bVUlHDygQ+c2xd7wcUGc=; b=f4NEaGV2Rx8X/qkJVKKXOZzO56CegjdsTgxrm/JEvBwkvfGVrTNSeQyBeubSSS0ldj s7/U6o3GOjOe/9IlsBEWyq89MVlTxF8OSXFRtH/1Hqw32ny664JC1e8L9ZexAvcHN5Sd x8Qn+/lgByMQRozd6DCJb6QponxZQMx1L016HIJRE19HLbsveoqDDv0DQfRrdpSH22Hf SNnOZ0epjP8k2ShzMhZ7kEYZe9AbnzzXN17FdpvXj6GCMkSMHqpHacWSxYhWrfUvcnZD La71tmV3Tii7akDjPMwtydmIOuQ0kCeUdRLs/Xg5H3rREzUVEX8mjfjthh+xJunj5RSj zyyQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=kuQ3D3X+U+p8xGwb+z27Hs6bVUlHDygQ+c2xd7wcUGc=; b=jj34DFUohzRl3szfdyakSQCkrhYARbN379LmXWcq6l7lrQEcy202QZe/Yter3qltqQ ICFomTxairQuZX2HuNRgGuYjAQeIryb+bvctPdAKKC6ouwYQnzRMBC5OjlcBu4y4KTyy sAIqDkoYXC1WCZKi9gtSqg/AMoEnF3zt8Qpb+5yapY/teVcOz3SkPdv7do9Sb3plfLzc kKK4nwQINcBbhOQD1Kyyr61+mbmlvOG5EMZcGFIFeaUkrj4lSgAJiqV8tCUUDmDC/Prf se0x+IZV7qfOd1cUZgv7C4vZ1o1Gft+o/SdMDoENxTfQhiKOIP3C98cYSn+KtlWYAwjt d1Fw== X-Gm-Message-State: AOAM532tXwiBBfj8ai9IM2au0UOsntRSOv2eW3wcWUWIKJLCwNIvfSwX jnhvJT7+bRZYdKG2CcXd3AqdPfbEMXI= X-Google-Smtp-Source: ABdhPJztgkodxgVWW2RwtVcoQcpGtwkTn2sP/q8p0jhMTlippZ4uhl/vAQpTWDXHH5iy1M1LBmgp7Q== X-Received: by 2002:adf:e38c:: with SMTP id e12mr11047501wrm.128.1621628810548; Fri, 21 May 2021 13:26:50 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.50 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:50 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 34/50] gnu: r-protgenerics: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:06 +0200 Message-Id: <20210521202622.26591-34-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-protgenerics): Move from here... * gnu/packages/bioconductor.scm (r-protgenerics): ...to here. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ gnu/packages/bioinformatics.scm | 20 -------------------- 2 files changed, 20 insertions(+), 20 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5ceffd7b4d..a9365a4018 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3175,6 +3175,26 @@ the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) +(define-public r-protgenerics + (package + (name "r-protgenerics") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ProtGenerics" version)) + (sha256 + (base32 + "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz")))) + (properties `((upstream-name . "ProtGenerics"))) + (build-system r-build-system) + (home-page "https://github.com/lgatto/ProtGenerics") + (synopsis "S4 generic functions for proteomics infrastructure") + (description + "This package provides S4 generic functions needed by Bioconductor +proteomics packages.") + (license license:artistic2.0))) + (define-public r-rbgl (package (name "r-rbgl") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a6321a179a..6120cb6804 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8853,26 +8853,6 @@ for analyzing gene-level association tests in meta-analyses for binary trait.") (license license:gpl3))) -(define-public r-protgenerics - (package - (name "r-protgenerics") - (version "1.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ProtGenerics" version)) - (sha256 - (base32 - "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz")))) - (properties `((upstream-name . "ProtGenerics"))) - (build-system r-build-system) - (home-page "https://github.com/lgatto/ProtGenerics") - (synopsis "S4 generic functions for proteomics infrastructure") - (description - "This package provides S4 generic functions needed by Bioconductor -proteomics packages.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:34 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:34 +0000 Received: from localhost ([127.0.0.1]:37763 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk6-0000Ii-6o for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:34 -0400 Received: from mail-wm1-f44.google.com ([209.85.128.44]:44793) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjU-0000BG-I3 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:57 -0400 Received: by mail-wm1-f44.google.com with SMTP id y184-20020a1ce1c10000b02901769b409001so7810109wmg.3 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:56 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=AxB0i+TeHMRnPIZO77vQwEsAWsixThXNCMxsZu1rb8U=; b=KafGRQZs6UPxGalxGaX01wjWo4pjP1feW0e/eBE3dnbgyF0j/gx/WNNplYthb/+Alb C/aJJi9s8baXHsG7tecYDpMKJh/1A1RW3+fl6uLetjKtTdpwwQMYekcN2TRO0QeEevJ8 mpVAebhIb1U0y/N8+5to2RBYiIUJS3TrzPlby2p3FuSqKmAQWKuHcfcd4xhredExSSDR dCuPB8M8bAya15QTuG1dKJTFkW9xPSmHEJELsflPwAG7OAZpAiLxMCk0uUFfGDeNHavz SciwJxQ5rB4gPcoC9C6rGx0H9SDUMrPlsji5JDegq5LOgs10HYX/Jj99xASI4fPGM7rJ uyMQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=AxB0i+TeHMRnPIZO77vQwEsAWsixThXNCMxsZu1rb8U=; b=gllbbcX/aNA8TuguaqIgYGW4mQ2G+Vaqc0etksaghNSVLyyLnEOr3yhZgPITGJe/r8 ueezBAi6g8/X5RUL9dlmheCn/iTfpqFWYOkYkuNE9/KuPZEfIZ9Uso7U6ozQIetJylNO kXoJ9bsdhvZEUHB/K7OIPdx4094Ylh4k0nSpAY9kFXvpRn/mlZCzx9K4kbpzi9etXqEh Ecw1GdS++/2MU68kq5XLDtnaTC6GkT4zVDiOH+weZ3uzZNV9ouRT6OT7dDiJ65mOylS6 AmgsRHkR8Uopmctyp5zhV7Vw44Wo/GWKdxdV4nn8L7gRdhz6pgR8qNuTXAjsEDz5LMp+ hYkA== X-Gm-Message-State: AOAM530Sw/4D6Ls9HidICPEqHnOViWZYx73blqTK8D3VTp39fgIF3dKZ eBnvfk3cfLv/NDNU6mjzxEPIe2QUSxg= X-Google-Smtp-Source: ABdhPJzNUPIRIKeNQhrZORAbZ4x6nhJihsNnQiO0mgv2emfORsufyzi5tPl3zLJ/T9pS/Al/UZa6pg== X-Received: by 2002:a7b:c5cd:: with SMTP id n13mr10317859wmk.97.1621628810951; Fri, 21 May 2021 13:26:50 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.50 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:50 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 35/50] gnu: r-sva: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:07 +0200 Message-Id: <20210521202622.26591-35-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-sva): Move from here... * gnu/packages/bioconductor.scm (r-sva): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a9365a4018..a7b1c63b56 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3524,6 +3524,37 @@ typically represent genomic ranges of interest and the columns represent samples.") (license license:artistic2.0))) +(define-public r-sva + (package + (name "r-sva") + (version "3.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "sva" version)) + (sha256 + (base32 + "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy")))) + (build-system r-build-system) + (propagated-inputs + `(("r-edger" ,r-edger) + ("r-genefilter" ,r-genefilter) + ("r-mgcv" ,r-mgcv) + ("r-biocparallel" ,r-biocparallel) + ("r-matrixstats" ,r-matrixstats) + ("r-limma" ,r-limma))) + (home-page "https://bioconductor.org/packages/sva") + (synopsis "Surrogate variable analysis") + (description + "This package contains functions for removing batch effects and other +unwanted variation in high-throughput experiment. It also contains functions +for identifying and building surrogate variables for high-dimensional data +sets. Surrogate variables are covariates constructed directly from +high-dimensional data like gene expression/RNA sequencing/methylation/brain +imaging data that can be used in subsequent analyses to adjust for unknown, +unmodeled, or latent sources of noise.") + (license license:artistic2.0))) + (define-public r-systempiper (package (name "r-systempiper") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6120cb6804..2cc41b7e98 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8790,37 +8790,6 @@ resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.") (license license:artistic2.0))) -(define-public r-sva - (package - (name "r-sva") - (version "3.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "sva" version)) - (sha256 - (base32 - "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy")))) - (build-system r-build-system) - (propagated-inputs - `(("r-edger" ,r-edger) - ("r-genefilter" ,r-genefilter) - ("r-mgcv" ,r-mgcv) - ("r-biocparallel" ,r-biocparallel) - ("r-matrixstats" ,r-matrixstats) - ("r-limma" ,r-limma))) - (home-page "https://bioconductor.org/packages/sva") - (synopsis "Surrogate variable analysis") - (description - "This package contains functions for removing batch effects and other -unwanted variation in high-throughput experiment. It also contains functions -for identifying and building surrogate variables for high-dimensional data -sets. Surrogate variables are covariates constructed directly from -high-dimensional data like gene expression/RNA sequencing/methylation/brain -imaging data that can be used in subsequent analyses to adjust for unknown, -unmodeled, or latent sources of noise.") - (license license:artistic2.0))) - (define-public r-raremetals2 (package (name "r-raremetals2") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:35 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:35 +0000 Received: from localhost ([127.0.0.1]:37765 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk6-0000Iq-Ko for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:35 -0400 Received: from mail-wr1-f53.google.com ([209.85.221.53]:36371) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjU-0000BR-TZ for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:57 -0400 Received: by mail-wr1-f53.google.com with SMTP id c14so20429585wrx.3 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:56 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=GNE7B5p9yFT2jKkL0Wi0iSOeeBRpdM4BYuuDctd4u8U=; b=Iz/A0duSAM6KARw0FBrLWKEQGV3mhc9Otq4SNkBs9DqI/gtCztbZjaKYEYvVjSeITA iQ3P4WRiGDQnFZjkmZtY4a6+IpWc/1DsbZRBd66Y6YfsQ2B80QeFvhO7fE0WM0gqO4qM zZod6FRup60/FccKDxW5Lw+GhHv49x3w+o1ljry16DwmecywQa0jB2tttfpEn/5JMcfC hpnDw/U0fdu43HxDVyeJVnEI69eJxMlRqTN2138ULy8p5sLiqPr3C7R/Smb7Sy8xrFgz UjJzPdB3HFifP+GYnAH5QWl9kn56o7QrY4KGc7HtNC8v0c2EVvsYBW+38FmSkEaL3T4l DuZA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=GNE7B5p9yFT2jKkL0Wi0iSOeeBRpdM4BYuuDctd4u8U=; b=TNqJDAgPaGNU2pi7rQiZRTNJ+lQQvLaBh15qHACwxEgeuCK5JH6Y0jfybBBA56ik+6 rWEERGxoGlDmKovojEA11yqviLe5gQAQ2/aiUNMHAD/rT986j6ZUAugnWb0v1UwVJbO5 4Dl2ZmQTLB4mQCifmNYFsY0sdBNRLvlphTb+Hz+9H09OeihegcDB4KyYBkGux09VkOYD zc0qaCyrfyJLHBA/8LKUqAnaLVG7M1PGmOe0ORp90+TPtSuSUxGNYkZFpmQjEVpaODsu vGHexYL3B6/GNuAVEaqle60O2HeQQWQ0gBqFXMdfnoMs8ReQX7bpuZEC4WqzXH7QNEcE fejA== X-Gm-Message-State: AOAM530sANgTbTc7Lu+xkvG9DB/SaPNWNU5SENVc8S1fgL341rM5nJdA lV+XZt4SK26PScmW0vDS0cdGlWHbQ5E= X-Google-Smtp-Source: ABdhPJyn22LKIE7ubs3c9Evun+F9gtPSFBSZbjIjXbVYFvXbDL0LXEErYWr2VbCoBZZWO/PsdXKbHA== X-Received: by 2002:a5d:64a6:: with SMTP id m6mr11384233wrp.425.1621628811421; Fri, 21 May 2021 13:26:51 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.51 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:51 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 36/50] gnu: r-motifrg: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:08 +0200 Message-Id: <20210521202622.26591-36-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-motifrg): Move from here... * gnu/packages/bioconductor.scm (r-motifrg): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a7b1c63b56..47a245b4f5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2924,6 +2924,33 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-motifrg + (package + (name "r-motifrg") + (version "1.31.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "motifRG" version)) + (sha256 + (base32 + "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn")))) + (properties `((upstream-name . "motifRG"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-iranges" ,r-iranges) + ("r-seqlogo" ,r-seqlogo) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/motifRG") + (synopsis "Discover motifs in high throughput sequencing data") + (description + "This package provides tools for discriminative motif discovery in high +throughput genetic sequencing data sets using regression methods.") + (license license:artistic2.0))) + (define-public r-msnbase (package (name "r-msnbase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2cc41b7e98..e2000ccb68 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7872,33 +7872,6 @@ plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).") (license license:lgpl2.0+))) -(define-public r-motifrg - (package - (name "r-motifrg") - (version "1.31.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "motifRG" version)) - (sha256 - (base32 - "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn")))) - (properties `((upstream-name . "motifRG"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-iranges" ,r-iranges) - ("r-seqlogo" ,r-seqlogo) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/motifRG") - (synopsis "Discover motifs in high throughput sequencing data") - (description - "This package provides tools for discriminative motif discovery in high -throughput genetic sequencing data sets using regression methods.") - (license license:artistic2.0))) - (define-public r-zlibbioc (package (name "r-zlibbioc") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:35 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:35 +0000 Received: from localhost ([127.0.0.1]:37767 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk7-0000Ix-23 for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:35 -0400 Received: from mail-wm1-f47.google.com ([209.85.128.47]:51739) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjV-0000BY-Ai for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:57 -0400 Received: by mail-wm1-f47.google.com with SMTP id u133so11745002wmg.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:57 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=LqQ4QlvybZaQTA9fY/j8dC94vBwgekc+gsPfPvzDf1o=; b=XsfE/CnMmrGX3C/OJn0yFsjIx4gi2KdNZDH9+D9aVlqL/4Zw+iZMKZYoFQPANUk3x5 2Z4LenvgqMKE5pqoNk51JllV49/k/0GSPAe8wIfcDjilG3JHewtFy0+A1/HN3/xA4/I2 AzUu6SSB3V50jSBsWd2SP7rTJHxG9PuXaYz+1QOodUFjGuZnNpjcCMmaxt6b2Vl1eEg0 qrN5uxOIHHHlHR56xQE0gp/b6so4wjdAuxbsmLgkBu0Y+bYacGtNXhopm8agSyxxgMCf aYUY1RpAhBIV6p37N7kUnpd48ZyVZgVCCwIipUsPny66VB2Ce1zaBlJzfRKd9BrZqcb7 j7AA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=LqQ4QlvybZaQTA9fY/j8dC94vBwgekc+gsPfPvzDf1o=; b=JOUZsBAHCOnTKfF/SHftKEhgmudEI2p4IwsFvRT+0xB2fT6dnYl8rh9HnefN5rLM1P TWMa/3X2buO6ZuqbBjIeWLlTIZkgmrf5m96+EdRrg9h8saDii93VVdWgyALkH6TDeMxj zwcnpdybSQrlX81qPTeUlWk0WsnaTztAksd7exm36s6yXHnkA16v39CKlY7YKSY/XwRR d6zvg4StdeW4WZEtrk+e3DdUEzA9QysgYSc5N4dOOO1xRK2yurHas1nc4L0eWzji/SLN 60kcAMwLqTNBjreLQTV5gXRMoZypjw2dDd0c9vqdh25xYNG6mexMrPxyR1Rf3IIiM6mO FWWA== X-Gm-Message-State: AOAM532hn7hSN7YNGEcRILPhaST0mMva2nfAr36nDDuTfpprKL+EzCpR 2AkOtfIvJVTVwFDmLroKKa9Yw1hpWS0= X-Google-Smtp-Source: ABdhPJzLsRy6R92RTkV2GyumPqCMXVhxg1zkgd54wYPRVYY8/l4wxHRtCYGKDoZsnn1pVflT4NHk+g== X-Received: by 2002:a7b:c405:: with SMTP id k5mr10423810wmi.133.1621628811885; Fri, 21 May 2021 13:26:51 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.51 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:51 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 37/50] gnu: r-seqlogo: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:09 +0200 Message-Id: <20210521202622.26591-37-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-seqlogo): Move from here... * gnu/packages/bioconductor.scm (r-seqlogo): ...to here. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 23 ----------------------- 2 files changed, 23 insertions(+), 23 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 47a245b4f5..c58c5af5d6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3447,6 +3447,29 @@ differential expression analysis, RNAseq data and related problems.") ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-seqlogo + (package + (name "r-seqlogo") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "seqLogo" version)) + (sha256 + (base32 + "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1")))) + (properties `((upstream-name . "seqLogo"))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/seqLogo") + (synopsis "Sequence logos for DNA sequence alignments") + (description + "seqLogo takes the position weight matrix of a DNA sequence motif and +plots the corresponding sequence logo as introduced by Schneider and +Stephens (1990).") + (license license:lgpl2.0+))) + (define-public r-seqpattern (package (name "r-seqpattern") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e2000ccb68..9ba818d581 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7849,29 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-seqlogo - (package - (name "r-seqlogo") - (version "1.56.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "seqLogo" version)) - (sha256 - (base32 - "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1")))) - (properties `((upstream-name . "seqLogo"))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/seqLogo") - (synopsis "Sequence logos for DNA sequence alignments") - (description - "seqLogo takes the position weight matrix of a DNA sequence motif and -plots the corresponding sequence logo as introduced by Schneider and -Stephens (1990).") - (license license:lgpl2.0+))) - (define-public r-zlibbioc (package (name "r-zlibbioc") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:35 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:35 +0000 Received: from localhost ([127.0.0.1]:37769 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk7-0000J5-DS for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:35 -0400 Received: from mail-wr1-f54.google.com ([209.85.221.54]:40729) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjV-0000Be-SY for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:58 -0400 Received: by mail-wr1-f54.google.com with SMTP id z17so22188653wrq.7 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:57 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=VOnrUDDdhYIyZ/Ayu3WwM46H5rqFV4TN2tLaIkcakCA=; b=C7yqyIxoUqgXWXPHzbwDUad57WzKeByDg3btL+owXXGBkpiSrwgF4NlBdwXvEeeImH PcxlDYV8lZHYBHbZNl9+0R/aPNoN4Ld2OW8fk8PG7/AORaiOcgqPr8TDYgL4uCOltgQ6 0zstRJJuEJAoY+wv+hu2NTY8BEPMyIm3ttqt9XWJKrlFpIIq3j2tdj5kl0a+u8uztnwI WqTSBHE59xg/hsR0Esh7P+nUfdrdd2+lfAmPZjG3oreBhbbmmBKJsCuXQTcvNtoWWFHR oIEGq91v0sb6mA1qis9BI6AIUmCNzlUU4BSPo8TKR43vXrtors74l26WisJYct6wv3mM pN/Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=VOnrUDDdhYIyZ/Ayu3WwM46H5rqFV4TN2tLaIkcakCA=; b=Crmsr9vGYG+TRElqB9xHddy5uJdk/qNkncwodsmVCY50FFKMEBxtuNzmDMNclC7AjT f/alQFXOApDUjRMV1sODf0NskVl06O8YOxabpcfW6WflzAhDjEqEtP/E/uNw9QpXUp/I CIKJsEdLDTWBdQ9maKmEJOfm0cgDBx0lFLX2wmwly/ibPD/VCahwFBodOqCQRdPiy6ck fFU9KI3CY+HflAuS/IzwU/pUDoWs09tptnvgjAnSnTkvj22ukQRGbPxT4U7w+3iUxvU9 s02a2LNc62/URyrpL5Q1CkdUxDi/2MLgpNqcRq+YL/27UUMrcoeni/MNZNyKNNKYrDdR 7cUA== X-Gm-Message-State: AOAM53252a8BsZmJmU+Qd2LS16wrtFAHbveZ9N3Fs3/k4UKEkGhjAOF8 mIBk2FGzVji5+7YnjpNLOTsDvi22GU8= X-Google-Smtp-Source: ABdhPJwdmUfbX3Coy3HS98UktEhqcI9Aoxh5pREBjzVSfUi7Or8aFJBCrv77acSedDqSHMX5UAcnSA== X-Received: by 2002:adf:d1e1:: with SMTP id g1mr11446601wrd.401.1621628812299; Fri, 21 May 2021 13:26:52 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.51 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:52 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 38/50] gnu: r-zlibbioc: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:10 +0200 Message-Id: <20210521202622.26591-38-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here... * gnu/packages/bioconductor.scm (r-zlibbioc): ...to here. --- gnu/packages/bioconductor.scm | 19 +++++++++++++++++++ gnu/packages/bioinformatics.scm | 19 ------------------- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c58c5af5d6..e720d7bf6a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3802,6 +3802,25 @@ and specific in detecting differential transcription.") \"externally\" (behind an R external pointer, or on disk).") (license license:artistic2.0))) + (define-public r-zlibbioc + (package + (name "r-zlibbioc") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "zlibbioc" version)) + (sha256 + (base32 + "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg")))) + (properties + `((upstream-name . "zlibbioc"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/zlibbioc") + (synopsis "Provider for zlib-1.2.5 to R packages") + (description "This package uses the source code of zlib-1.2.5 to create +libraries for systems that do not have these available via other means.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9ba818d581..39c437f4a2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7849,25 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-zlibbioc - (package - (name "r-zlibbioc") - (version "1.36.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "zlibbioc" version)) - (sha256 - (base32 - "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg")))) - (properties - `((upstream-name . "zlibbioc"))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/zlibbioc") - (synopsis "Provider for zlib-1.2.5 to R packages") - (description "This package uses the source code of zlib-1.2.5 to create -libraries for systems that do not have these available via other means.") - (license license:artistic2.0))) - (define-public r-r4rna (package (name "r-r4rna") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:36 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:36 +0000 Received: from localhost ([127.0.0.1]:37771 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk7-0000JC-Q3 for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:36 -0400 Received: from mail-wr1-f51.google.com ([209.85.221.51]:42585) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjR-0000Ad-QJ for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:07 -0400 Received: by mail-wr1-f51.google.com with SMTP id x8so22193552wrq.9 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:53 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=RU452Q1zmzpGVME6dqq576fIYB4sfqPUGhPKFL8Dypc=; b=JYNqG9+O3CUierfef2JrD4tZm/818Q64IcDTEViFiy7BiSbPxXkkHjF40iWkLsY8/C wQqFgcy0k42BAqQkzg6RkVpoG4HcLYpe+V2szsW9EBG5VksJ1I8iOqK3QIR6l6FITqZo 4CQ6/9RSfStxdyt4S9pE4t4Gc3r3B0+ffpn24FBjOEwV95UxBT1RoYsCn2cp9FKfBaqJ UIJrC7Gc1+i5ranKkFOo9z4KkBzS/b5hMFklWaN7gjY8fJzFH0EuLwhSG1AEzZ7lbJ6O 3mVJJoBDhA04JgYw6rx5K/VdpMKONapCOxJ96o6k/gyabGKApLGKF2mW6w/ab9EkAgYp lDRQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=RU452Q1zmzpGVME6dqq576fIYB4sfqPUGhPKFL8Dypc=; b=NT8VSY4oJ06IhIrcW2kAmKd4BuzIgmX7Q1djLbKiEuP+nh3Vgtquavhjd+2h6peroY F06k212k9l0F4hstNKpjr+EDrC+LoqK8ewG2hf8TUt1W9qh8+00jsQpUfh+LrAnG1BiO ScRfd/LVaduQiMw6V+4hWnreOYzuctHC88XeeKsZjUg73XRPcp5MByFgulO7CVvbaUce EQ+pTe21B37kwjeenjyGCeI2zxHoANPgLiAFxVG18RyBGMNlrwKITBb5i8j6LNM1ZYkP /AnYT+m5ShklkXWrHY5gVySACLzNihLuZrLWqJFP1w6CgOG+EzI5C0g8t5JoQeXYIWbt U92A== X-Gm-Message-State: AOAM530baOYKUTCj3GfHHyQMTnu5JEQk1uYxWTrsj3wUYmRoy1OYqFro V+fdnniDsXiwiYPfgd8We3v/PYduIFo= X-Google-Smtp-Source: ABdhPJzsQQn9eLwJNcOTEMhoSPhjmvKsV4C2xwchzHxMwjf8R1myWE2JbdFT//zWIGlipW1zzsrhKg== X-Received: by 2002:a5d:59a4:: with SMTP id p4mr11657924wrr.248.1621628808380; Fri, 21 May 2021 13:26:48 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:48 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 29/50] gnu: r-affyio: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:01 +0200 Message-Id: <20210521202622.26591-29-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-affyio): Move from here... * gnu/packages/bioconductor.scm (r-affyio): ...to here. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 24 insertions(+), 24 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c63d39dc9c..d0ebcf8481 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1694,6 +1694,30 @@ problems in CEL-level data to help evaluate performance of quality metrics.") to streamline the more common analyses that a Biostatistician might see.") (license license:artistic2.0))) +(define-public r-affyio + (package + (name "r-affyio") + (version "1.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affyio" version)) + (sha256 + (base32 + "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h")))) + (build-system r-build-system) + (propagated-inputs + `(("r-zlibbioc" ,r-zlibbioc))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/bmbolstad/affyio") + (synopsis "Tools for parsing Affymetrix data files") + (description + "This package provides routines for parsing Affymetrix data files based +upon file format information. The primary focus is on accessing the CEL and +CDF file formats.") + (license license:lgpl2.0+))) + (define-public r-affxparser (package (name "r-affxparser") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1c90700c95..7256df3f83 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8934,30 +8934,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-affyio - (package - (name "r-affyio") - (version "1.60.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "affyio" version)) - (sha256 - (base32 - "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h")))) - (build-system r-build-system) - (propagated-inputs - `(("r-zlibbioc" ,r-zlibbioc))) - (inputs - `(("zlib" ,zlib))) - (home-page "https://github.com/bmbolstad/affyio") - (synopsis "Tools for parsing Affymetrix data files") - (description - "This package provides routines for parsing Affymetrix data files based -upon file format information. The primary focus is on accessing the CEL and -CDF file formats.") - (license license:lgpl2.0+))) - (define-public r-vsn (package (name "r-vsn") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:36 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:36 +0000 Received: from localhost ([127.0.0.1]:37773 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk8-0000JJ-4Z for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:36 -0400 Received: from mail-wm1-f41.google.com ([209.85.128.41]:55106) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjY-0000By-DO for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:07 -0400 Received: by mail-wm1-f41.google.com with SMTP id o127so11748717wmo.4 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:00 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=PZLbfIvxLq/mL2OJh+TE+U0x2EZDlIdOz60SG+/jzmY=; b=Kw/WiLO701QvTdsRAd7kafxJq8Zf8ml2+ADA32oN4JXTbslCS0sz291v5umHrT4ff5 nOlz19mEqOtAxqfLxIsxdUet2szaaKkeJmfevJbXiCAU6ZoZx6TtqDziEcpjSIg85wlU pPu497IXQHDBL1r1DMLBRipVuyRO2QNjp+k0ygpyTzYxcje5qpGfwuKd4yun1zETilBA gXv7c2munhqWxl4QeV65bMVBlXadKZVEWF7r3crDdxxUeHQEQOrnO9SF6z6pI2PQL8Ao gK8uWA632qGA7YxnCK3UV2pBUR8BvHwQ36zYpLUElhKYkTUiDQfVbLu6lm7rzq1KeXct 4twA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=PZLbfIvxLq/mL2OJh+TE+U0x2EZDlIdOz60SG+/jzmY=; b=l4w0qaaMWHxKk1ZmF5PxbjRWNarnQ6KlPlH5rRMWOEuG+7XAkcjT0TdopI7aCpDRor aEpUyS/N8T80ltanyJeQsv+edwzsCTAu4wx9rHeL9iqQpOHg+fGUjg22KAIVc9O4ZAVu /kBn4GZ6/RKU8G/yzQKoN+SC03M3BJE/RF+2hmGvI9lqVT6bIaxU0IMB5/PZW4PiRBQ3 0IAYGKUtNbNE5yoYilC/MErIdhCit66uY+7q4OsSFnInj8NEBO0PMwuUd3dROrIGY9Kx FhyNrNJ7dY72E1SKavjXC23sfw6CXG7FDv4Gv335PUCT0pF0rxNFBnVYyUFVfc6Igcrd yHmg== X-Gm-Message-State: AOAM5332rqSVWVxH/Y035yDkGsIonOGVIDnSDt7qElRImobgHlW6UraJ /9Ac7v9JWGI44pnz3wxb5t/cvsUBk+k= X-Google-Smtp-Source: ABdhPJwfZSvxFXfwr1NfZoiOQlG0I2nBTsd4STGusgGPg8BEBFZOc1Tpr1Nk9LRvbRMJ9fbjUCVoUw== X-Received: by 2002:a7b:c446:: with SMTP id l6mr10424299wmi.75.1621628813742; Fri, 21 May 2021 13:26:53 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.53 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:53 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 41/50] gnu: r-rcas: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:13 +0200 Message-Id: <20210521202622.26591-41-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-rcas): Move from here... * gnu/packages/bioconductor.scm (r-rcas): ...to here. --- gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 49 --------------------------------- 2 files changed, 49 insertions(+), 49 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 99607ba564..1d38fa1c05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3307,6 +3307,55 @@ proteomics packages.") the graph algorithms contained in the Boost library.") (license license:artistic2.0))) +(define-public r-rcas + (package + (name "r-rcas") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "RCAS" version)) + (sha256 + (base32 + "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m")))) + (properties `((upstream-name . "RCAS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-cowplot" ,r-cowplot) + ("r-data-table" ,r-data-table) + ("r-dt" ,r-dt) + ("r-genomation" ,r-genomation) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-ggseqlogo" ,r-ggseqlogo) + ("r-gprofiler2" ,r-gprofiler2) + ("r-iranges" ,r-iranges) + ("r-pbapply" ,r-pbapply) + ("r-pheatmap" ,r-pheatmap) + ("r-plotly" ,r-plotly) + ("r-plotrix" ,r-plotrix) + ("r-proxy" ,r-proxy) + ("r-ranger" ,r-ranger) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rmarkdown" ,r-rmarkdown) + ("r-s4vectors" ,r-s4vectors) + ("pandoc" ,pandoc))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (synopsis "RNA-centric annotation system") + (description + "RCAS aims to be a standalone RNA-centric annotation system that provides +intuitive reports and publication-ready graphics. This package provides the R +library implementing most of the pipeline's features.") + (home-page "https://github.com/BIMSBbioinfo/RCAS") + (license license:artistic2.0))) + (define-public r-regioner (package (name "r-regioner") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ae61ecae74..a1ee4b6772 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7872,55 +7872,6 @@ including VCF header and contents in RDF and JSON.") secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-rcas - (package - (name "r-rcas") - (version "1.16.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "RCAS" version)) - (sha256 - (base32 - "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m")))) - (properties `((upstream-name . "RCAS"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-dt" ,r-dt) - ("r-genomation" ,r-genomation) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggseqlogo" ,r-ggseqlogo) - ("r-gprofiler2" ,r-gprofiler2) - ("r-iranges" ,r-iranges) - ("r-pbapply" ,r-pbapply) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-plotrix" ,r-plotrix) - ("r-proxy" ,r-proxy) - ("r-ranger" ,r-ranger) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-s4vectors" ,r-s4vectors) - ("pandoc" ,pandoc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (synopsis "RNA-centric annotation system") - (description - "RCAS aims to be a standalone RNA-centric annotation system that provides -intuitive reports and publication-ready graphics. This package provides the R -library implementing most of the pipeline's features.") - (home-page "https://github.com/BIMSBbioinfo/RCAS") - (license license:artistic2.0))) - (define-public rcas-web (package (name "rcas-web") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:37 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:37 +0000 Received: from localhost ([127.0.0.1]:37775 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk8-0000JR-Ih for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:36 -0400 Received: from mail-wm1-f44.google.com ([209.85.128.44]:38828) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjY-0000C5-Of for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:07 -0400 Received: by mail-wm1-f44.google.com with SMTP id u4-20020a05600c00c4b02901774b80945cso8061514wmm.3 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:00 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=f/xVXtBaE5gloM4h+iHW0NAvupaR04NPZxnb6aSXxEM=; b=IDu/nMkSm0r90gMflyQthrg9kDGN9XYl0g1JTqR+qaanBEFJ2Z5QDZiQTTT5AHzZoJ qQsQsRjILmNyLWpb+j8Qku5OzxEJ31v4zRO1hAAqOAYesAMY+gOjcMMjBUXSzrMIXn2e A73Ft6e/1VN1Q9jaAgvx/jQp8QoXpgB/ZgbdfTd5sg5GG2mRMRKJkusWl6x0lQ9zViDz oK8C35qBlHMC2CAi+4YbAW9tIUAMr9+Hh52CzJmIK2K/ZSB3734rIIE3/bTqKObnpyX4 4KVgKNeHCsZKPmkt+K7ZQvGkAoBCA8HwBrSXvSEMc/3XPo8PhDYu5aPIWM16NUfWCbab FCEQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=f/xVXtBaE5gloM4h+iHW0NAvupaR04NPZxnb6aSXxEM=; b=Zhbd+Xg4un/D/KrqaQ/PB0wSXLpJCs59uTmwz4466IszBGF0cenqQEHQrL8yRo/asi P+B3AVPLxOWQbqW32GVS1G8lx60AmkDfURytWHEXIor0A7OLK1U43VS2L83cqp8r/UZh STUMjz3P64eCUPlEYaJeiZMeOKFWqkThblByyFoFw0yjZt31TxUcZzbpWyHmWPYtOHH4 9sSmpmBSN5zyE4aZJEXrOSifEcvR7xw3DfyjGf5cnp2hyLdr5enri755VzmHj11VdPpA bRZcF4MfFDm1lSWtVxlljEvkAJNuvZ8feKfdlxhFDv6fWAkVBtQVDU6lSHkM36pQsR6x U2Pw== X-Gm-Message-State: AOAM530W0GAlvqGSX/2+aPKefOyFaavo1izpnfSI544pLIT13p5DpiUW /gnHC8Wj2ZJaLsg7bLWPy8UzqyTrUio= X-Google-Smtp-Source: ABdhPJyOTe8u3PBoilELeb9KS0E/KJV/5XpolmfTHAQS9AKPNPr5eKm0iCbkPx7XV9t/ggTvqyyltQ== X-Received: by 2002:a05:600c:410a:: with SMTP id j10mr10586846wmi.5.1621628814268; Fri, 21 May 2021 13:26:54 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.53 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:53 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 42/50] gnu: r-mutationalpatterns: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:14 +0200 Message-Id: <20210521202622.26591-42-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here... * gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 --------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1d38fa1c05..7c471c7375 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3013,6 +3013,51 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) +(define-public r-mutationalpatterns + (package + (name "r-mutationalpatterns") + (version "3.0.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MutationalPatterns" version)) + (sha256 + (base32 + "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ;; These two packages are suggested packages + ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggalluvial" ,r-ggalluvial) + ("r-ggdendro" ,r-ggdendro) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-magrittr" ,r-magrittr) + ("r-nmf" ,r-nmf) + ("r-pracma" ,r-pracma) + ("r-purrr" ,r-purrr) + ("r-s4vectors" ,r-s4vectors) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/MutationalPatterns/") + (synopsis "Extract and visualize mutational patterns in genomic data") + (description "This package provides an extensive toolset for the +characterization and visualization of a wide range of mutational patterns +in SNV base substitution data.") + (license license:expat))) + (define-public r-msnbase (package (name "r-msnbase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a1ee4b6772..b5b2cc2f6b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7923,51 +7923,6 @@ secondary structure and comparative analysis in R.") @dfn{RNA-centric annotation system} (RCAS).") (license license:agpl3+))) -(define-public r-mutationalpatterns - (package - (name "r-mutationalpatterns") - (version "3.0.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "MutationalPatterns" version)) - (sha256 - (base32 - "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35")))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ;; These two packages are suggested packages - ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggalluvial" ,r-ggalluvial) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-nmf" ,r-nmf) - ("r-pracma" ,r-pracma) - ("r-purrr" ,r-purrr) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-variantannotation" ,r-variantannotation))) - (home-page "https://bioconductor.org/packages/MutationalPatterns/") - (synopsis "Extract and visualize mutational patterns in genomic data") - (description "This package provides an extensive toolset for the -characterization and visualization of a wide range of mutational patterns -in SNV base substitution data.") - (license license:expat))) - (define-public r-chipkernels (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372") (revision "1")) -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:37 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:37 +0000 Received: from localhost ([127.0.0.1]:37777 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk9-0000JY-0Y for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:37 -0400 Received: from mail-wm1-f44.google.com ([209.85.128.44]:36545) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjZ-0000C8-5a for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:08 -0400 Received: by mail-wm1-f44.google.com with SMTP id n17-20020a7bc5d10000b0290169edfadac9so8084617wmk.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:01 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=+aUpZ7qeOszYGOmbx43gW9RTRCPVnaq5aj0LzDV3Xy0=; b=kDEIRBKuAILKwUGJKPOZRAmAX5c6VbmzwfB4v1sWqKcWsPZbKUGr4QDKdiCRFcHXa/ 5dGt+uYNzf9T+ZIWYodruT1C5OLsUXoEzUrB6gr/OWkYqhJoCIUOPBbiff8FAGjneqj8 o6ILrKb5oRBRXtcbzLLchayoLnxPjbmvI20uewnQppwnDoncfKQvDW/qqZHCeshMVW5M 4ar81EGuOJ9S4keItQsM5BtrKrF/mGqxK5vcAc/Ml7Qo2PBgp2S8urtOyyz2CC8EA3HE 5bH99XcfPqgMQIc6taxJ0QWKC2Esh0hi1EG3Dq1a+3+5IArCoadUS9IDMW2dsVcS1swU k4EQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=+aUpZ7qeOszYGOmbx43gW9RTRCPVnaq5aj0LzDV3Xy0=; b=AJpQoRjhbzO5dzbL3J6WzDFVmxD7chWT99keDFM8dAAAzKx4dXxPMX7znMw3jdtZd7 L1ZXD5cFBZ1e+MWENCehly4acXPH5Vsp1usD8ETk8BnxEL8cx7Gz3rFjfcJU4msU5tsz IBMTgU5tqhjUKsV0yn5WFY1BAn1Wm6Cx4qItEPCfHXS4DIJ0+J7TZsaFCPwPY5RCFXt/ suHo0rdHVHU8o6EZK9RL60E8nDb/B08B7zM0RY5unj5Z11IkSCgCJX7jt5F0dbzBHyAG P26LRRka9r6W6F+TfqTlKFgJ4mSelyocGxIKPgz5vbHNkUuQ/PsnIho+w4d3gZ51x62u ifzQ== X-Gm-Message-State: AOAM5301wG4+JF9ds/7/iq/LvGyQ50tmy4njtgSbEUnOLRttbkX8DTbz CsyssGLxkUiT5Lx3VAqUU9HFDhPNetw= X-Google-Smtp-Source: ABdhPJyAx3JJVgpJNxvXiU5Xjx5mTaUEzND+4LxVXBcrs6f8viZ2imxl6TU4cGq76e8DpsB2RG3bNA== X-Received: by 2002:a05:600c:2219:: with SMTP id z25mr10289924wml.78.1621628814713; Fri, 21 May 2021 13:26:54 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.54 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:54 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 43/50] gnu: r-tximport: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:15 +0200 Message-Id: <20210521202622.26591-43-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-tximport): Move from here... * gnu/packages/bioconductor.scm (r-tximport): ...to here. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 24 insertions(+), 24 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7c471c7375..30d4844ae4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3848,6 +3848,30 @@ dependencies between GO terms can be implemented and applied.") ;; Any version of the LGPL applies. (license license:lgpl2.1+))) +(define-public r-tximport + (package + (name "r-tximport") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tximport" version)) + (sha256 + (base32 + "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/tximport") + (synopsis "Import and summarize transcript-level estimates for gene-level analysis") + (description + "This package provides tools to import transcript-level abundance, +estimated counts and transcript lengths, and to summarize them into matrices +for use with downstream gene-level analysis packages. Average transcript +length, weighted by sample-specific transcript abundance estimates, is +provided as a matrix which can be used as an offset for different expression +of gene-level counts.") + (license license:gpl2+))) + (define-public r-variantannotation (package (name "r-variantannotation") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b5b2cc2f6b..83d6797809 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7990,30 +7990,6 @@ bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.") (license license:gpl2+))) -(define-public r-tximport - (package - (name "r-tximport") - (version "1.18.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "tximport" version)) - (sha256 - (base32 - "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34")))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/tximport") - (synopsis "Import and summarize transcript-level estimates for gene-level analysis") - (description - "This package provides tools to import transcript-level abundance, -estimated counts and transcript lengths, and to summarize them into matrices -for use with downstream gene-level analysis packages. Average transcript -length, weighted by sample-specific transcript abundance estimates, is -provided as a matrix which can be used as an offset for different expression -of gene-level counts.") - (license license:gpl2+))) - (define-public r-rhdf5filters (package (name "r-rhdf5filters") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:37 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:38 +0000 Received: from localhost ([127.0.0.1]:37779 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk9-0000Jh-GV for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:37 -0400 Received: from mail-wm1-f50.google.com ([209.85.128.50]:35357) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjZ-0000CE-K1 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:08 -0400 Received: by mail-wm1-f50.google.com with SMTP id z19-20020a7bc7d30000b029017521c1fb75so8083171wmk.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:01 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=BJbtryq3YhLCmqQPkqA9v0snCtQsUTKzqUtFY2r2O24=; b=Rhxn7+MGJC/AfSPgIcDC48X7FhncD3XXkdrKR5H3cclq6IZQ7BqPRxCayAO2wgWUVI wDbt+pPd6a0x4CX+87E0eAiqKaIxwN0dIA71Pri0TEFByRT1o0L8cuD8JV4hkgXRDm+S dVbigmQwuvnUhedTfBiNpoSFFT4P1KyLzWdgHLyA7wo+w5mY0jComxgmgp6HifyLU1JE /xvgNjccyQnK3f2AOAJ9f5096GSLjc7teAANCPZmKHG1TNM7CZII4HR5RsdNMItTsvJz BFLfUur1S6CwDZL6wA6gPhOMvL8GzrEJYJsSQfYHJz6QHW6AP5tuzXmPw0nXJ8z0RVQe pTHQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=BJbtryq3YhLCmqQPkqA9v0snCtQsUTKzqUtFY2r2O24=; b=gxgFYs5sl+nDnrqyUNZGTaGIQNIAGmkMHhxCugSsyAE5SY31I7l82cdkFNnPKJBkEu NsnZAMuwp/saZmsLXBDDwFfQr3fHAapOXzWca7Zz6ViVF3UTvavgO4e2rBFNygnt0ioz OsFs3IQiTpi1ghKkg5gUgUB2H4HsGswjnNTGTCylR1BDIZCXtK4YsYD6ySexL6JR48+W 9hRS/uF1epit8Ip4V4yyp6UByhZ/+sHGxk8i4boXnnO6+9TSQBqtO0EfGCbXJaN02PxA DSq4vNf1MLpkV/jK/H9WR6uSIjo58BMwQL3MPDJ+sNcy852gfKUM5DEaGgA2HzLdoLN0 QqtQ== X-Gm-Message-State: AOAM5302A5wzxXWk2eyHnNWlP3XRXDUtaipbmHV5TMOVWtf4vkogrbHz keU1wItNytcoTWY9wPeQPoQy2SeSjqI= X-Google-Smtp-Source: ABdhPJzHGeq5dGtwv3M5vJ/3ghmHpDmwehnBf/HfIY/UHnwAncgc6gkMJ44faDDFKX/Pmge8cTaE9Q== X-Received: by 2002:a1c:c90f:: with SMTP id f15mr10711403wmb.142.1621628815129; Fri, 21 May 2021 13:26:55 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.54 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:54 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 44/50] gnu: r-rhdf5filters: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:16 +0200 Message-Id: <20210521202622.26591-44-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 30d4844ae4..8695f13ed8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3482,6 +3482,32 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-rhdf5filters + (package + (name "r-rhdf5filters") + (version "1.2.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "rhdf5filters" version)) + (sha256 + (base32 + "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz")))) + (properties `((upstream-name . "rhdf5filters"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rhdf5lib" ,r-rhdf5lib))) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/grimbough/rhdf5filters") + (synopsis "HDF5 compression filters") + (description + "This package provides a collection of compression filters for use with +HDF5 datasets.") + (license license:bsd-2))) + (define-public r-rsamtools (package (name "r-rsamtools") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 83d6797809..2907d65b38 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7990,32 +7990,6 @@ bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.") (license license:gpl2+))) -(define-public r-rhdf5filters - (package - (name "r-rhdf5filters") - (version "1.2.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "rhdf5filters" version)) - (sha256 - (base32 - "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz")))) - (properties `((upstream-name . "rhdf5filters"))) - (build-system r-build-system) - (propagated-inputs - `(("r-rhdf5lib" ,r-rhdf5lib))) - (inputs - `(("zlib" ,zlib))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/grimbough/rhdf5filters") - (synopsis "HDF5 compression filters") - (description - "This package provides a collection of compression filters for use with -HDF5 datasets.") - (license license:bsd-2))) - (define-public r-rhdf5 (package (name "r-rhdf5") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:38 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:38 +0000 Received: from localhost ([127.0.0.1]:37781 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk9-0000Jp-T3 for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:38 -0400 Received: from mail-wm1-f52.google.com ([209.85.128.52]:44804) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBja-0000CP-3f for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:08 -0400 Received: by mail-wm1-f52.google.com with SMTP id y184-20020a1ce1c10000b02901769b409001so7810193wmg.3 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:02 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=jADkjOcECaxKaVMHW1v5oI4SxtTDJxJxXTNJ9A7zISI=; b=WiVfUHaG3giMdEvTNHS16EXOZzQbKmS0GKVGUqg+OfLAotBpXReZxTM3WEcNgxqut1 8Fw2UVSZkh2bTrfDDcc5SQJyo4c6ZVpuAZdocmL3X4oPZxFPYoVF2I2X/7ESWhRdBfmV dYCmacemttBc5yZ4P/Xq/PXziHy2E3niBFe7vpgxmSAt9HTobDRI7p2BW3xpePWHJJNF kaHmxWiTpqOHSS0949uERjVsLnrLVVV5JOojoJhL5nwpcX3zUjeMD6J8VyEJTfy6PvLg rInqDo7UI+8+4VG2np/rgQ6IL/7L1TZSwHGj4389uZIKkgm05Z4pjjoYqNm9YzsR6lzu tfhA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=jADkjOcECaxKaVMHW1v5oI4SxtTDJxJxXTNJ9A7zISI=; b=lds6a+PoEiDkNkaCcTO16CZ79LRqPQFIiQPq449tKr/UZm9SYbaCh5Pg/Vce4M6lAq W7NC7qWuPRnhiTw4E0gJbr8w6J0mpYPgUcYSfYhMXWRA6pBAS2M5EF7IjcF1ZTx8QhD3 D/7geW1oMEyGtzgrlRpIcuXzR7PqbMF6szlgyVdhJdIEiBXVNrFwOj6Nb7FSnsHHrGrp mf/l6WQyfTOKRcdAcSBggZOVBYLe/AnMsYPjvHfGQopNhamO5lEAwZUQxa9v1Mb7jrvY R4Ubsma3nYvsPlaFobzU3fx8Dkd/RfGVu8iIyqiHKOgHFraam1tn7BQZnYWG7lLkQZe4 jbsw== X-Gm-Message-State: AOAM5334B7a3Q0urvoO8hZ5+ZLbJkO9V34xcmOG8a2gjqxD/1Im3Vs/t 7GdsE3R3S6jfuqZunP0WqWH8+DtfduQ= X-Google-Smtp-Source: ABdhPJwNGX8lKVkVTpbXm4tZ+H9spArajvQIUpHHHU6V+vWV/B5lbQIMQtWmap8ei83/K8hHaZCI0A== X-Received: by 2002:a05:600c:8a9:: with SMTP id l41mr10626387wmp.73.1621628815542; Fri, 21 May 2021 13:26:55 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.55 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:55 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 45/50] gnu: r-annotationfilter: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:17 +0200 Message-Id: <20210521202622.26591-45-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here... * gnu/packages/bioconductor.scm (r-annotationfilter): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8695f13ed8..87b879ad94 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1804,6 +1804,32 @@ microarrays.") annotation data packages using SQLite data storage.") (license license:artistic2.0))) +(define-public r-annotationfilter + (package + (name "r-annotationfilter") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationFilter" version)) + (sha256 + (base32 + "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9")))) + (properties + `((upstream-name . "AnnotationFilter"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicranges" ,r-genomicranges) + ("r-lazyeval" ,r-lazyeval))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/Bioconductor/AnnotationFilter") + (synopsis "Facilities for filtering Bioconductor annotation resources") + (description + "This package provides classes and other infrastructure to implement +filters for manipulating Bioconductor annotation resources. The filters are +used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") + (license license:artistic2.0))) + (define-public r-annotationforge (package (name "r-annotationforge") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2907d65b38..7ad51d3518 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8029,32 +8029,6 @@ package, and for letting R applications work on datasets that are larger than the available RAM.") (license license:artistic2.0))) -(define-public r-annotationfilter - (package - (name "r-annotationfilter") - (version "1.14.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "AnnotationFilter" version)) - (sha256 - (base32 - "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9")))) - (properties - `((upstream-name . "AnnotationFilter"))) - (build-system r-build-system) - (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-lazyeval" ,r-lazyeval))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/Bioconductor/AnnotationFilter") - (synopsis "Facilities for filtering Bioconductor annotation resources") - (description - "This package provides classes and other infrastructure to implement -filters for manipulating Bioconductor annotation resources. The filters are -used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") - (license license:artistic2.0))) - (define-public emboss (package (name "emboss") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:38 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:38 +0000 Received: from localhost ([127.0.0.1]:37783 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBkA-0000Jw-9G for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:38 -0400 Received: from mail-wm1-f52.google.com ([209.85.128.52]:39514) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBja-0000CW-IN for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:09 -0400 Received: by mail-wm1-f52.google.com with SMTP id l18-20020a1ced120000b029014c1adff1edso8058261wmh.4 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:02 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=rXeBKamx5hl0Jia8wbBBgjZVhZy3c5K6zPPfs6MDPh8=; b=UEm6MP+r+yanSu+R6EUBnvnM5GH1CKuhHR1g3j10zmFzCSNItt9N6wL/SuqQ46yUN7 ExQvCGZcvWGMG0DhmYL2YeEUXch5jccfrKto7OqkD57MfBwW4SsiRRNjLON8t6ltfomw oEhFzyk7qGGmPvJb1weIe9AVIfzz/w913QJ6iOKEYTqR1zk+oYl/Mv0ow2H86qLVA4PA yFPvv/aBssTFjrkktVbf+NCb6HJmvgQ7B7V61RotjvhdaS3fhvEhzSo1s+OJm+83nAGh /pxBslzgQOq22tfa77G9qDhR7PHUssjYCP4E3wiopt4RLZFjZ0te+wxj0fM53Uc+Tzxz NKCg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=rXeBKamx5hl0Jia8wbBBgjZVhZy3c5K6zPPfs6MDPh8=; b=TTcSmJKHasREk6qLxOtLzzQ8qp7/S7WYXZRFftWAyL2jYLfwmPUtPweNZ89Db/fJ0v 2W2lxjUjS6Rf/FpfHzSF7Zd/ySD8y97IEXDG1fLa5zwkNeAPxOL0Zj6T2r7KUoFGS02K 0z9YBLxMOWSAky4O1STF0xKv9J+IPyaF/5mXb9DMbqhZYjUMIKvuAB5PDqWBCg6PeZuD U0a8p8M4rLJi17hQFpdQi2mdO9pSiL50vLcNtiyjIdJrdHOaHHBtXSiWslrh2fbS0uvJ aHydnCQN25NpsK9/XXDiobEI7KTheTJBrEQ96LjkDR7Ci3fgZt5LGsO8Q3X+NLpVK6TF u0Pw== X-Gm-Message-State: AOAM533tB4HSdoHJAO0rsNNgPhpk0BtibfksXF1i5Z8JpAclldlkMKZq B7qIVk82bVZIQA4qJAeyHzh4VCsBfik= X-Google-Smtp-Source: ABdhPJz3mgwfRfi6XN+lpgrANLRTmItUepjfOnQt5ftpbPbdjggPildGSqsmtZW6odZ+wxqv3+y8Ig== X-Received: by 2002:a1c:c911:: with SMTP id f17mr10438767wmb.45.1621628816033; Fri, 21 May 2021 13:26:56 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.55 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:55 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 46/50] gnu: r-rhdf5: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:18 +0200 Message-Id: <20210521202622.26591-46-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-rhdf5): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5): ...to here. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 39 --------------------------------- 2 files changed, 39 insertions(+), 39 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 87b879ad94..d027a24bf3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3508,6 +3508,45 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-rhdf5 + (package + (name "r-rhdf5") + (version "2.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "rhdf5" version)) + (sha256 + (base32 + "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-linking + (lambda _ + (substitute* "src/Makevars" + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5_LIBS\\)" match) + (string-append match "/libhdf5.a"))) + #t))))) + (propagated-inputs + `(("r-rhdf5filters" ,r-rhdf5filters) + ("r-rhdf5lib" ,r-rhdf5lib))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/rhdf5") + (synopsis "HDF5 interface to R") + (description + "This R/Bioconductor package provides an interface between HDF5 and R. +HDF5's main features are the ability to store and access very large and/or +complex datasets and a wide variety of metadata on mass storage (disk) through +a completely portable file format. The rhdf5 package is thus suited for the +exchange of large and/or complex datasets between R and other software +package, and for letting R applications work on datasets that are larger than +the available RAM.") + (license license:artistic2.0))) + (define-public r-rhdf5filters (package (name "r-rhdf5filters") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7ad51d3518..ef0d7b3007 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7990,45 +7990,6 @@ bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.") (license license:gpl2+))) -(define-public r-rhdf5 - (package - (name "r-rhdf5") - (version "2.34.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "rhdf5" version)) - (sha256 - (base32 - "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5_LIBS\\)" match) - (string-append match "/libhdf5.a"))) - #t))))) - (propagated-inputs - `(("r-rhdf5filters" ,r-rhdf5filters) - ("r-rhdf5lib" ,r-rhdf5lib))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/rhdf5") - (synopsis "HDF5 interface to R") - (description - "This R/Bioconductor package provides an interface between HDF5 and R. -HDF5's main features are the ability to store and access very large and/or -complex datasets and a wide variety of metadata on mass storage (disk) through -a completely portable file format. The rhdf5 package is thus suited for the -exchange of large and/or complex datasets between R and other software -package, and for letting R applications work on datasets that are larger than -the available RAM.") - (license license:artistic2.0))) - (define-public emboss (package (name "emboss") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:42 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:42 +0000 Received: from localhost ([127.0.0.1]:37785 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBkA-0000K4-Mz for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:42 -0400 Received: from mail-wm1-f48.google.com ([209.85.128.48]:43644) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjb-0000Cd-1F for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:09 -0400 Received: by mail-wm1-f48.google.com with SMTP id z85-20020a1c7e580000b029017a76f3afbaso5255032wmc.2 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:02 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=iaH+3sal2krXTGH2XpmYQLHIK0r2pEqsyUwvzT1KVyo=; b=iZdRj8zAUI7o6OwWdrmX3aOPdKIaTLIqMlaY4R9iRG5A9qtdfIjtKGSU7cb88HLVXR jbksJeKQi9lFiHQ2XjT7IJoTFeEhrLOPu9w/jm6rfXxM5hLHsR7CDRprtBDc0U1HhcR4 uBEtHOEpKGXF75QU4riPGM7O1OY5ugjc/oxxEXQeNcBNI0zW+rXPa3N4yO/xwuNYDDrK YswAaldqf9WiIntssft904Wfrv1UFzfWD07IqgW8Gh5m2xQ/yVE3vtWLlwP066Z8WVjm 0Eyj7XquQC6AMWdxqJykYlPHSP9IOEreogDiSZvpnTweVQl7GAChrEgPB6eJnD5OSJh9 G7jg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=iaH+3sal2krXTGH2XpmYQLHIK0r2pEqsyUwvzT1KVyo=; b=V9/bHkfUOQ+Q1hutzpcHY2bRYLi4RQXMMmN0d0wxktEUtiLnj7hauqnmb8VEkjyT8E cHweVr3OTYqI+zh0oOc7ZjXMi9B2Hwp6Kl4DcImm58uZXpHeyQZmctLm0XxyQg/7iDpl /ZT+xoKTxwebA2WrKRTMsEe/rFdda752I8/lqzyKSHfuWtBjYDatTWgr9z+TxhwpB9LI kahqdEsVs7VIC3t2h2ntzmFarcyVitiwn8q1LjWJsIKpEGVXPKJOQdxnd5bcWzQgkFnZ piZn7K25qN13xMD7RKoybDFsbinj9Sa/ZGJ/XxctbfM8xpgkLgL/zoVQe0MiuUq2VCm9 P39w== X-Gm-Message-State: AOAM530DzkHJ8/pH0hKNlLhqUhx+inLhBCaUFl/zZcCCVvvcAz0hwVt3 VVkYMuVKH6Q+Hhi2tBKys1WUPwCRAkE= X-Google-Smtp-Source: ABdhPJxAFYv+YKQKHeJkYUtV0Q2/YuuUbCMOunXN59pFUJOnbb5HPVQ7HXMxSsoNCUXzFd6YCwIjPQ== X-Received: by 2002:a1c:e912:: with SMTP id q18mr10856343wmc.59.1621628816514; Fri, 21 May 2021 13:26:56 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.56 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:56 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 47/50] gnu: r-chipseq: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:19 +0200 Message-Id: <20210521202622.26591-47-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-chipseq): Move from here... * gnu/packages/bioconductor.scm (r-chipseq): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d027a24bf3..f224a5ecb4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2206,6 +2206,32 @@ genome data packages and support for efficient SNP representation.") analysis.") (license license:artistic2.0))) +(define-public r-chipseq + (package + (name "r-chipseq") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "chipseq" version)) + (sha256 + (base32 + "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-s4vectors" ,r-s4vectors) + ("r-shortread" ,r-shortread))) + (home-page "https://bioconductor.org/packages/chipseq") + (synopsis "Package for analyzing ChIPseq data") + (description + "This package provides tools for processing short read data from ChIPseq +experiments.") + (license license:artistic2.0))) + (define-public r-complexheatmap (package (name "r-complexheatmap") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ef0d7b3007..3ee3d9d4f3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8312,32 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-chipseq - (package - (name "r-chipseq") - (version "1.40.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "chipseq" version)) - (sha256 - (base32 - "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread))) - (home-page "https://bioconductor.org/packages/chipseq") - (synopsis "Package for analyzing ChIPseq data") - (description - "This package provides tools for processing short read data from ChIPseq -experiments.") - (license license:artistic2.0))) - (define-public r-copyhelper (package (name "r-copyhelper") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:42 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:42 +0000 Received: from localhost ([127.0.0.1]:37787 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBkE-0000KE-9S for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:42 -0400 Received: from mail-wm1-f45.google.com ([209.85.128.45]:44799) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjb-0000Cj-HI for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:10 -0400 Received: by mail-wm1-f45.google.com with SMTP id y184-20020a1ce1c10000b02901769b409001so7810227wmg.3 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:03 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=DcGOzSgQkR2g22Nixp75eN8pMoCurmXHwafY9ehZgaU=; b=Oo+WVjOU8Gw+qDFMJi4ew0yTy+0R1M3QtLUV2OupCL9wMOhjeQ4A3P4Wcwof2Sz/Ud Ats84u87+nLkMOCBXn++nMb1EfzGekcwrYydyRk1ABZftP1srKqi7+73KkQ/khZJJn+d aLwGzR5xPiELpsd6+lwK3+O2VO9fyWDZIarGcpbO4uKTAZq9eJ7oM+4KQ70H2CmjGBoP npxkp3Y5tRq28lBjypvrBmNK0JfhmptmwKwLXJvZWOJjaM2IqbTlRiokRKqYcyIuym4r +MsvK05OSCwzyLt2Io6b/iKSOMj+cewYu1yvfxrJ7f1l5kDwDJVXk7mP8eIb0uIDN7Zr 2Wqw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=DcGOzSgQkR2g22Nixp75eN8pMoCurmXHwafY9ehZgaU=; b=nvaW5YnuTAIuzxM9HSTOC5YxJKdN8LEacvBIxeWGdQELA1pCFZPhKjIQx2gHbpRMAG OtEdqza47ak461zbs81PVAnyiyr6uZST3XX24XjzVUY2i0SMfc+YwKjPxXG1hRUQKirj NGHHgHsBPROsvtN8WabQDAY2EQUuqBbbT4uuEZ+GvQgUAiCsPbjwSK4SBuMqMCSTX2FJ 3+DlBxc+Fx5/EHhf+khYGVkXeZfS+p3Pk9L3O6Sy+qO9jpPCLPoGbc3giKEgOvFAaB+f HKv3ReZXeXIpm6NFyXzoS+Qi7nR/SQzNJCV1+pB/jtww0f39gVuJmR4ePUgy8yT7f3Wh /reA== X-Gm-Message-State: AOAM531YZiYlDYYXSaHezWVOctCdlCEhCDhitTFHz3MqV/UBlw7Gl0fI jxi+cUzbauiUn4Lk2/MuXb0fvsWx+HE= X-Google-Smtp-Source: ABdhPJxqy38qqPD+gcg493Sy60TWMyhCqCeIbIwOLmQbosCSoiMZaG9lePlJfoLQ8/MzPoSeWK0WjA== X-Received: by 2002:a05:600c:19c8:: with SMTP id u8mr10555534wmq.25.1621628816978; Fri, 21 May 2021 13:26:56 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.56 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:56 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 48/50] gnu: r-copyhelper: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:20 +0200 Message-Id: <20210521202622.26591-48-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-copyhelper): Move from here... * gnu/packages/bioconductor.scm (r-copyhelper): ...to here. [source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 24 insertions(+), 26 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f224a5ecb4..eee1561c1b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -999,6 +999,30 @@ from Illumina 450k methylation arrays.") chromstaR package.") (license license:gpl3))) +(define-public r-copyhelper + (package + (name "r-copyhelper") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CopyhelpeR" version 'experiment)) + (sha256 + (base32 + "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) + (properties `((upstream-name . "CopyhelpeR"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/CopyhelpeR/") + (synopsis "Helper files for CopywriteR") + (description + "This package contains the helper files that are required to run the +Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content +and mappability files for the reference genomes hg18, hg19, hg38, mm9 and +mm10. In addition, it contains a blacklist filter to remove regions that +display copy number variation. Files are stored as GRanges objects from the +GenomicRanges Bioconductor package.") + (license license:gpl2))) + (define-public r-genelendatabase (package (name "r-genelendatabase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3ee3d9d4f3..2acca0c055 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8312,32 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-copyhelper - (package - (name "r-copyhelper") - (version "1.6.0") - (source - (origin - (method url-fetch) - (uri (string-append "https://bioconductor.org/packages/release/" - "data/experiment/src/contrib/CopyhelpeR_" - version ".tar.gz")) - (sha256 - (base32 - "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) - (properties `((upstream-name . "CopyhelpeR"))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/CopyhelpeR/") - (synopsis "Helper files for CopywriteR") - (description - "This package contains the helper files that are required to run the -Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content -and mappability files for the reference genomes hg18, hg19, hg38, mm9 and -mm10. In addition, it contains a blacklist filter to remove regions that -display copy number variation. Files are stored as GRanges objects from the -GenomicRanges Bioconductor package.") - (license license:gpl2))) - (define-public r-copywriter (package (name "r-copywriter") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:43 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:43 +0000 Received: from localhost ([127.0.0.1]:37789 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBkE-0000KL-MF for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:43 -0400 Received: from mail-wr1-f54.google.com ([209.85.221.54]:42601) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjc-0000Cz-HM for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:10 -0400 Received: by mail-wr1-f54.google.com with SMTP id x8so22193819wrq.9 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:04 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=WTJ0QKwfkRwMUejAmpqr+O0CLj6EkllRvJX9rei3i0w=; b=WKFR21DO7KlMgwuCIOVQDFbiHZxqRr0lEKp4SNxLGF7K5JZqbJA8XJpLSzOg7yzGzF n/e0Jx3WbWODAWKzPT7UcyITg7Sc9Pz1aR+e9vZ0QqpAoZhvz/ByGEjPGZ/IDAyiQaAQ VLbUE/iIxQhkFrmVC1PoZO5UySSQJUEEJtgo/4n4TNBDqqeD/S6p9mjycoC7HP+0YeFm tgk9o83HGvLQGITc7VTIzDskTEB7ONigU+niH3rCewvx9FG96X0zDt05f79ZMYfXd/VJ eVH2CWZnZQsluBZ79MSnORJkocCDc7VFhkfFZ568SPHu9uIW0C1Wyhbcu5IOTQpPUFOa KyTw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=WTJ0QKwfkRwMUejAmpqr+O0CLj6EkllRvJX9rei3i0w=; b=nyfh4GEkbhgyTDYQMPJ4O7DmCNf680coJMTgttt6k6D2vycrFXsMs5LUxjnvUHggXw iiQtM1VhpGROn8FCY8SPxtk7pme1Hgsp2Awr8Dx2ADMZ5xkz4XSQuVSdmEk0ipmsuOQt YGIeoiTanzNnAO5PJB3WKfyzKvrbYiYWabV2QvoYSdxcnDTcbpkyyutXX10hdbFOGHfu GbeHHkoFIhqPrwkubtbWdFSe6mT7thKCh8WYncOwufH2nHeXby2s8BgBYz+/6d1oOjdg bgMQOjDlJTNA7Iew5LJBgQRROca+8SGdqb/u+hTmJvPDpohQGDLa1AYUNNLFPYs9d+YU ckuQ== X-Gm-Message-State: AOAM533b2cKJCuHehYyK2RAu/eaP60hdaZVFuMATc+G7Ze2OMosmpKz0 cuDMBMz6XTun2/tFkibjC3/8AlaPsjI= X-Google-Smtp-Source: ABdhPJzB4ffS4QtsmsD1u+kMcy9Jgjw1AMyvbz/ESowmgd0cX5z3uoLFn1kLjimE1hoXZfoTcIjjTQ== X-Received: by 2002:a5d:5052:: with SMTP id h18mr11082812wrt.365.1621628817984; Fri, 21 May 2021 13:26:57 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.57 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:57 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 50/50] gnu: r-methylkit: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:22 +0200 Message-Id: <20210521202622.26591-50-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-methylkit): Move from here... * gnu/packages/bioconductor.scm (r-methylkit): ...to here. --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 47 --------------------------------- 2 files changed, 47 insertions(+), 47 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe91fd486f..54a6afcf3d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3102,6 +3102,53 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-methylkit + (package + (name "r-methylkit") + (version "1.16.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "methylKit" version)) + (sha256 + (base32 + "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3")))) + (properties `((upstream-name . "methylKit"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-emdbook" ,r-emdbook) + ("r-fastseg" ,r-fastseg) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) + ("r-limma" ,r-limma) + ("r-mclust" ,r-mclust) + ("r-mgcv" ,r-mgcv) + ("r-qvalue" ,r-qvalue) + ("r-r-utils" ,r-r-utils) + ("r-rcpp" ,r-rcpp) + ("r-rhtslib" ,r-rhtslib) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://github.com/al2na/methylKit") + (synopsis + "DNA methylation analysis from high-throughput bisulfite sequencing results") + (description + "MethylKit is an R package for DNA methylation analysis and annotation +from high-throughput bisulfite sequencing. The package is designed to deal +with sequencing data from @dfn{Reduced representation bisulfite +sequencing} (RRBS) and its variants, but also target-capture methods and whole +genome bisulfite sequencing. It also has functions to analyze base-pair +resolution 5hmC data from experimental protocols such as oxBS-Seq and +TAB-Seq.") + (license license:artistic2.0))) + (define-public r-motifrg (package (name "r-motifrg") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 79146f915f..48b521f755 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8312,53 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-methylkit - (package - (name "r-methylkit") - (version "1.16.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "methylKit" version)) - (sha256 - (base32 - "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3")))) - (properties `((upstream-name . "methylKit"))) - (build-system r-build-system) - (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-emdbook" ,r-emdbook) - ("r-fastseg" ,r-fastseg) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-limma" ,r-limma) - ("r-mclust" ,r-mclust) - ("r-mgcv" ,r-mgcv) - ("r-qvalue" ,r-qvalue) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes - (home-page "https://github.com/al2na/methylKit") - (synopsis - "DNA methylation analysis from high-throughput bisulfite sequencing results") - (description - "MethylKit is an R package for DNA methylation analysis and annotation -from high-throughput bisulfite sequencing. The package is designed to deal -with sequencing data from @dfn{Reduced representation bisulfite -sequencing} (RRBS) and its variants, but also target-capture methods and whole -genome bisulfite sequencing. It also has functions to analyze base-pair -resolution 5hmC data from experimental protocols such as oxBS-Seq and -TAB-Seq.") - (license license:artistic2.0))) - (define-public r-raremetals2 (package (name "r-raremetals2") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:43 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:43 +0000 Received: from localhost ([127.0.0.1]:37791 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBkF-0000KT-3G for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:43 -0400 Received: from mail-wm1-f54.google.com ([209.85.128.54]:50830) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjc-0000Cr-2e for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:10 -0400 Received: by mail-wm1-f54.google.com with SMTP id t206so11771448wmf.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:04 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=4gFq4aqVkdYOI6WYtCBq/XIu0aKJKA1AIXkcYFbWkaM=; b=Z4mBLo31P+ItGlcnRTu1YHbwWC8JgDkspEQNWdmA8BEsrQTWuPZ0QrWZF+WvTR8xLF WDv09CLlnW8SxtgLmnk736KsemWFumQxoGscK2jIFemftOrApsU0uCsIU3ZUOckCsv88 uBnmN7u7Z0n9QyGN72vI5w+MeopBXMWtECh3b5y5vd7KsbPgWh8rgpfXXtLw9nm4tFV3 yDJnUDDgJOwnfcErfYS7b+Yuw5eQ5vQ4MtpEL7UBeg4fZ+KjhhEf+ZkgHNLU/EKKrl/M 93o2ZabvL/BXa5BJcv0GhTBr5I92dVdUmJhAbutaUl+YA5FLFjpZw4fV2R/kT6AMBV+M mFqA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=4gFq4aqVkdYOI6WYtCBq/XIu0aKJKA1AIXkcYFbWkaM=; b=q63zsbhX2lUVUaUUccDfJyDGqlsjjBkbMc2BKhvit1wsgOA08hT3JgD3ANjSoDHMJy o4/Rz8/TSL0ZFpcyjkRB84/mVMsTJhcftGmtq1iLYkoCICQB9/aRB/onkNHf/0LDqpMH caFb6W3Fz0bQvLQTGqmXYE+7uQ9syd/BCI0OReDhpFfD8ao90kX+tp1XLevpAfJma7Hv es4V1LRFrnvvjtVqscfmnnSYvVncD+F1hpmn1dTPWF1BdTuUISYvrcx8vUSiUQYXctjd wmawJMxGk9NcIk6UZG+ohJD0rLeUGwK9ayRcV7z+5eLTA+Ar/chIJUp9VIcTvydcvefK 22fw== X-Gm-Message-State: AOAM530AMf1K5num/+VxbZ6bOinsdV3hFJmxHY4+jTKR1e+Wb0MNs1kV la/LN9qb4yr3XpMOepME5QbEDZ/wFFM= X-Google-Smtp-Source: ABdhPJzdhb6PgdncYedqBGmcgb4d8wvo+1GyMYqHpVbAVy2ylHuc8Q7THY7R6xFymOrvydF+mKsTcA== X-Received: by 2002:a7b:c7ca:: with SMTP id z10mr10584604wmk.185.1621628817510; Fri, 21 May 2021 13:26:57 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.57 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:57 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 49/50] gnu: r-copywriter: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:21 +0200 Message-Id: <20210521202622.26591-49-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-copywriter): Move from here... * gnu/packages/bioconductor.scm (r-copywriter): ...to here. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 40 --------------------------------- 2 files changed, 40 insertions(+), 40 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eee1561c1b..fe91fd486f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2295,6 +2295,46 @@ provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.") (license license:gpl2+))) +(define-public r-copywriter + (package + (name "r-copywriter") + (version "2.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CopywriteR" version)) + (sha256 + (base32 + "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f")))) + (properties `((upstream-name . "CopywriteR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-chipseq" ,r-chipseq) + ("r-copyhelper" ,r-copyhelper) + ("r-data-table" ,r-data-table) + ("r-dnacopy" ,r-dnacopy) + ("r-futile-logger" ,r-futile-logger) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/PeeperLab/CopywriteR") + (synopsis "Copy number information from targeted sequencing") + (description + "CopywriteR extracts DNA copy number information from targeted sequencing +by utilizing off-target reads. It allows for extracting uniformly distributed +copy number information, can be used without reference, and can be applied to +sequencing data obtained from various techniques including chromatin +immunoprecipitation and target enrichment on small gene panels. Thereby, +CopywriteR constitutes a widely applicable alternative to available copy +number detection tools.") + (license license:gpl2))) + (define-public r-deseq (package (name "r-deseq") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2acca0c055..79146f915f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8312,46 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-copywriter - (package - (name "r-copywriter") - (version "2.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "CopywriteR" version)) - (sha256 - (base32 - "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f")))) - (properties `((upstream-name . "CopywriteR"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-chipseq" ,r-chipseq) - ("r-copyhelper" ,r-copyhelper) - ("r-data-table" ,r-data-table) - ("r-dnacopy" ,r-dnacopy) - ("r-futile-logger" ,r-futile-logger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://github.com/PeeperLab/CopywriteR") - (synopsis "Copy number information from targeted sequencing") - (description - "CopywriteR extracts DNA copy number information from targeted sequencing -by utilizing off-target reads. It allows for extracting uniformly distributed -copy number information, can be used without reference, and can be applied to -sequencing data obtained from various techniques including chromatin -immunoprecipitation and target enrichment on small gene panels. Thereby, -CopywriteR constitutes a widely applicable alternative to available copy -number detection tools.") - (license license:gpl2))) - (define-public r-methylkit (package (name "r-methylkit") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:44 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:44 +0000 Received: from localhost ([127.0.0.1]:37793 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBkF-0000Kc-Ha for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:43 -0400 Received: from mail-wm1-f45.google.com ([209.85.128.45]:43638) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjW-0000Bo-95 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:14 -0400 Received: by mail-wm1-f45.google.com with SMTP id z85-20020a1c7e580000b029017a76f3afbaso5254968wmc.2 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:58 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=GjjPXYSiS+BefP9e4AIkdMmcWJKldfr6UalG2dfVP6s=; b=IpZA3Y3QYDciZj7vTgUT4b1bzMSXUSP+Ke2VqEs1z08NOi5r5MHzYuk9rjUY9bpQ6I KlCgjOSAE238DA604C58BSDm2RyxLX2W60CAgxwDpeos02silOl/F7P8RjieQftxG1BB VH0I/M+miWa51cEBAifmX5MLErS700u6lXjsLmk6HMdRk+uTaUlPHTWzoCyGw37a4ylj QAKLvk7L5wwuj3tEbsmXZZWgxmKbqg/N4lJTizxEKwscpmjdACz6LXd3wCpKfibZZEbX iCz0r6/4fSJNRTQr+WwbdeuclbqBnAravPhPN/vW7Emn2VNEXbWxtyR9lB8/IB9YyrKN Nz4A== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=GjjPXYSiS+BefP9e4AIkdMmcWJKldfr6UalG2dfVP6s=; b=LT54YxYANVjQV9tl4I0cBl0qZ8fNGztrVE1yVSG02WrVbwa9w/6I3+Hvgilk+AS5pe 5A79zbVNEmfSPNom9MUSnCZRbSbcM1welVTf17hITdufjIdbmh9ennJW6erzGhkKAxhW s47Qot9mXhP02U/w+QeAzzIuYP97BXUdHoHeU+2vlUEw2e0KqHEEYdT0LkiAvsTdfvYc tIjUIFi6c0uHUiWdMDDJwjFbnisjFL5aTNh1aRcPtkNeFzyidl9dmALlQp3IlEI8L5EO EQtBLjQL+u6axMe+kWuCkfBCHbX3FPw3yt0mHW/HQJ7xqRecLol5eGEktq0lRq58MJMG sRWg== X-Gm-Message-State: AOAM532br2PGTG+R9mfs5Ms5ibTvu6AvYXQbwEj9ysGcMb89PCPVSndN iYNwQ/QwKUNghuvlCONcLwnA8A6uC5g= X-Google-Smtp-Source: ABdhPJzLjzXDb1UoO675KkZBTK7z8LhPM0txLA6N551d06bm83FC97rw1kM3gKeuEf4Nc71jP1bR8Q== X-Received: by 2002:a1c:7fd0:: with SMTP id a199mr10226636wmd.161.1621628812804; Fri, 21 May 2021 13:26:52 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.52 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:52 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 39/50] gnu: r-rhtslib: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:11 +0200 Message-Id: <20210521202622.26591-39-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-rhtslib): Move from here... * gnu/packages/bioconductor.scm (r-rhtslib): ...to here. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 31 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e720d7bf6a..8e78a2a0ca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -39,6 +39,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages cran) #:use-module (gnu packages compression) + #:use-module (gnu packages curl) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz) @@ -2832,6 +2833,37 @@ Enrichment Analysis} (GSEA).") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-rhtslib + (package + (name "r-rhtslib") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Rhtslib" version)) + (sha256 + (base32 + "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4")))) + (properties `((upstream-name . "Rhtslib"))) + (build-system r-build-system) + ;; Without this a temporary directory ends up in the Rhtslib.so binary, + ;; which makes R abort the build. + (arguments '(#:configure-flags '("--no-staged-install"))) + (propagated-inputs + `(("curl" ,curl) + ("zlib" ,zlib) ; packages using rhtslib need to link with zlib + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/nhayden/Rhtslib") + (synopsis "High-throughput sequencing library as an R package") + (description + "This package provides the HTSlib C library for high-throughput +nucleotide sequence analysis. The package is primarily useful to developers +of other R packages who wish to make use of HTSlib.") + (license license:lgpl2.0+))) + (define-public r-impute (package (name "r-impute") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 39c437f4a2..586efcf21e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7872,37 +7872,6 @@ including VCF header and contents in RDF and JSON.") secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-rhtslib - (package - (name "r-rhtslib") - (version "1.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Rhtslib" version)) - (sha256 - (base32 - "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4")))) - (properties `((upstream-name . "Rhtslib"))) - (build-system r-build-system) - ;; Without this a temporary directory ends up in the Rhtslib.so binary, - ;; which makes R abort the build. - (arguments '(#:configure-flags '("--no-staged-install"))) - (propagated-inputs - `(("curl" ,curl) - ("zlib" ,zlib) ; packages using rhtslib need to link with zlib - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) - (home-page "https://github.com/nhayden/Rhtslib") - (synopsis "High-throughput sequencing library as an R package") - (description - "This package provides the HTSlib C library for high-throughput -nucleotide sequence analysis. The package is primarily useful to developers -of other R packages who wish to make use of HTSlib.") - (license license:lgpl2.0+))) - (define-public r-bamsignals (package (name "r-bamsignals") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:44 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:44 +0000 Received: from localhost ([127.0.0.1]:37795 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBkF-0000Kj-Vq for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:44 -0400 Received: from mail-wm1-f51.google.com ([209.85.128.51]:35356) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjX-0000Bs-Pa for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:15 -0400 Received: by mail-wm1-f51.google.com with SMTP id z19-20020a7bc7d30000b029017521c1fb75so8083132wmk.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:59 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=sgyZSgGVQSrug9mBK3zh5vJAeo/82uG6r8r7MBgi8jM=; b=MVFF+Z0UIoJn1/js3s+UAoMuZtIzxG1o0NVGnMgJgZzNh9AXxGt5I/T1aXpLaXuPcN QTLde/lGjnh7kO6dXO3YgdjPmju/f/Kj4NQgaKLetDrB/AzqQnHpaNM6hNHo3Bsd7N+n udzaHMBwHFfm1lPY620NoUlnvIf/Y1evacSCj/nckDKehgEwvEIagN4SrRCz+V48Oxv4 hOQgxZcbqfRqOKpkOKxgVkhEXJdf7wUyTWNV4zk/5RmLtyjKrA+SGrN9DynJcqzQeJZN noopyjYgPFO0dQtOkiklcEozyXBlwvsty+WlYOnSpY6OXCstvXXNfKJPaPnCWB5uBKP3 Q0mg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=sgyZSgGVQSrug9mBK3zh5vJAeo/82uG6r8r7MBgi8jM=; b=Wyi9B9aIpo2nJP8q4AftHcSquZh3fVCWhE9cSukc8+LIUIG+Xlxl/3Cz/VKMQhbk+T +hFPspWw3EkpTnpT2fM0TV89GbsseiplhVQj+F/jYMPsWDDHnp1OE05V+ntW051seEix 7l+oKZvpKTy62BlnPfZ93ineTvs7hY6pZbjXPHJxLiyFObq2Kr+8hq2jSewOC3DEuwFn WvTsAeeMzakfgP+dTIOKdKvCUzVxpmNYE2hC3aPwBRQzatnFMB7iy8nNi1Eumteu3AKL Y2iT2HGltFt/l7oBSvn469LG6fCCwdAkYT+hAusbP1LGsJ4Ypr/1QjMiMsS6jpzH+oVt FaNQ== X-Gm-Message-State: AOAM531vh8Qh6n2DFLxnokCRt2t03/192RvVGp5ZK9Z5hPS+O5YnT4LB DBVOiVrfamZqhUljZNbwwX+v55o5WWs= X-Google-Smtp-Source: ABdhPJxrJCH/pNds8rqX4TRx2B0xywCdSlrvSCN/jTHY3aqrAQNjNsnTNmcQ+afeQTjRXTzf8R1YXQ== X-Received: by 2002:a05:600c:49a2:: with SMTP id h34mr10862986wmp.64.1621628813246; Fri, 21 May 2021 13:26:53 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.52 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:52 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 40/50] gnu: r-bamsignals: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:12 +0200 Message-Id: <20210521202622.26591-40-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 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: -1.0 (-) * gnu/packages/bioinformatics.scm (r-bamsignals): Move from here... * gnu/packages/bioconductor.scm (r-bamsignals): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e78a2a0ca..99607ba564 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1904,6 +1904,36 @@ standalone, be utilized in other packages, or be wrapped up in higher-level classes.") (license license:gpl2+))) +(define-public r-bamsignals + (package + (name "r-bamsignals") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bamsignals" version)) + (sha256 + (base32 + "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcpp" ,r-rcpp) + ("r-rhtslib" ,r-rhtslib) + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/bamsignals") + (synopsis "Extract read count signals from bam files") + (description + "This package efficiently obtains count vectors from indexed bam +files. It counts the number of nucleotide sequence reads in given genomic +ranges and it computes reads profiles and coverage profiles. It also handles +paired-end data.") + (license license:gpl2+))) + (define-public r-biobase (package (name "r-biobase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 586efcf21e..ae61ecae74 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7872,36 +7872,6 @@ including VCF header and contents in RDF and JSON.") secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-bamsignals - (package - (name "r-bamsignals") - (version "1.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "bamsignals" version)) - (sha256 - (base32 - "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/bamsignals") - (synopsis "Extract read count signals from bam files") - (description - "This package efficiently obtains count vectors from indexed bam -files. It counts the number of nucleotide sequence reads in given genomic -ranges and it computes reads profiles and coverage profiles. It also handles -paired-end data.") - (license license:gpl2+))) - (define-public r-rcas (package (name "r-rcas") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Mon May 31 10:08:12 2021 Received: (at 48575-done) by debbugs.gnu.org; 31 May 2021 14:08:12 +0000 Received: from localhost ([127.0.0.1]:34563 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lniaS-0003bt-5G for submit@debbugs.gnu.org; Mon, 31 May 2021 10:08:12 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21134) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lniaP-0003bh-CL for 48575-done@debbugs.gnu.org; Mon, 31 May 2021 10:08:10 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1622470083; cv=none; d=zohomail.com; s=zohoarc; b=Ry8PDd1QNAIzcnM4fbp9gbYFzdlZIDesJB21YqH4B46+jxRBxjsAQ7QW7+qpAI/+XepJn+pfSpKn4gESgF+UZnK/1J/zcTzfnzVEXvNw/QOjIDS6Ew6LbJSYCusgXrvhZf2Ld1GnTi6NH9ZnEJhP8ScefNI9GNztMs93IvAXQkc= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1622470083; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=y737To7yBXUAujVAy2/0alJHq27r7nuE7Z/ufwmS3Sw=; b=aM9AJdQtCTqC6Pt3MkoJcMeKT18oVOGFkF1KdrJgSaP0cfUQLQO4SfiJb22AG9NP96EF9LqKP+JRJlE8ABiWayvaPOYwUruSgsOarZgAJfdKnB4YkSM17Q918v2yVkVIB3unkM5X9sUWCF9XCkTzWBgRaRJTDiVXKNVkoh2INLQ= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1622470083; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Subject:Date:Message-ID:MIME-Version:Content-Type; bh=y737To7yBXUAujVAy2/0alJHq27r7nuE7Z/ufwmS3Sw=; b=fcsE1QOJRreuqW8uvNyYveTBzk+C9aXRU9OO9T4Sem7znjxvEYUUDl7bbwN0to9x Z8FiFPsAWDHDMp5AbGsFitSyfUnopeulVgtkiqD85sfV5frGQFHfMhS6jKpk5mdyxdq oxi0n0St5NCC+X6N/Y9i1TebHGIbFv5E9k0pXojE= Received: from localhost (p4fd5aa7f.dip0.t-ipconnect.de [79.213.170.127]) by mx.zohomail.com with SMTPS id 1622470081688884.4081138692293; Mon, 31 May 2021 07:08:01 -0700 (PDT) User-agent: mu4e 1.4.15; emacs 27.2 From: Ricardo Wurmus To: 48575-done@debbugs.gnu.org Subject: [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor). X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Mon, 31 May 2021 16:07:55 +0200 Message-ID: <87o8crvvwk.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; format=flowed X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 48575-done 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 (-) Thank you for working on this! I have just applied these patches. -- Ricardo From unknown Fri Aug 15 15:36:36 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 29 Jun 2021 11:24:08 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator