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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Received: via spool by 45399-submit@debbugs.gnu.org id=B45399.160874681712622 (code B ref 45399); Wed, 23 Dec 2020 18:07:08 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:57 +0000 Received: from localhost ([127.0.0.1]:54104 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XI-0003HQ-Nt for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:57 -0500 Received: from mail-wr1-f42.google.com ([209.85.221.42]:36056) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XB-0003FF-KY for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:50 -0500 Received: by mail-wr1-f42.google.com with SMTP id t16so73211wra.3 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:49 -0800 (PST) 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=yiPYQ4gH0qWC9Hizov0oQITO4DIkZSfqJFlBXahYh7M=; b=l4g9pnxpAPN5UU2Vrpapb41OJVFwyD6PGdcY2eColA8rrXKDWIoRwtGm6BB1uMPKQB aEKOTXfF2Qei8J7nJosHJ0+dSmibs7C5LgZDfnCTpm5FP1suJf6HtSbuhPZJLjQvYuxj bm/ZlOS/l1gQnb3IcwMOi6m4YCc0+kQMgnR3fSfVGy9t31vQIwMFeRgiWmAzq3yFCTye +07KJdlCVp/Hyy1ogjXlDgAKWQ2mLg1pAyg/1LwmPOIvQQ9ACq+CpRFAFRfRmTxv/dwR e/mT+AvRaL1WpkG+UK2sdBj3mrkpC0zDok/SB1dBuEOiwG1ta9LgFV/Mhi3bKHphAAkJ jgBw== 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=yiPYQ4gH0qWC9Hizov0oQITO4DIkZSfqJFlBXahYh7M=; b=MCOAea3IUaKo3djmThy9VxLoo3RgvNNqPouLFi8X563FhZnE/lpC2b0Hxnzgdcsmq1 HMN9lNFU5y9NhNZD/uuSY/is9zFSti44btLNsV9KF+LdlvVFNroaD1LIVB8NIUM1/oYf XwrWUiGmErpJ8I30fZcCCahZYiLQ/jI1N8NMnR/ydM+4x/lICbj6pcOf/rZRP9BfN5C+ 9oVWfKvXYucjP9cZh03ov8ODf13ZxzIoXumM+YAqXYmH2AoGCYkZDcHcbUxAfm9Kj3RC brwE6ZxlytPp6QBXg91m1yYPhJcVCG0sBz7p7+QbRYHzFE34ta/TIv5Pb4p8MxBYWxyE n1Ug== X-Gm-Message-State: AOAM531zv3BYfGJ1FUMru5WwUmNDRSJYxNcTexIaUjYpxI+HouC92c24 RBI5gvm3uE0XPADaiC0IClJ1As9rrgk= X-Google-Smtp-Source: ABdhPJztjMt4gk+zoj1LBYqB9njKO1Gj75FwqjplOv+Fi2Y2wWdHDWlpDqITBWWoPl8sixJWBeQRzQ== X-Received: by 2002:a05:6000:cc:: with SMTP id q12mr31161735wrx.335.1608746804215; Wed, 23 Dec 2020 10:06:44 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:43 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:35 +0100 Message-Id: <20201223180635.58647-11-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com> References: <20201223180635.58647-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN X-Migadu-Spam-Score: 2.77 Authentication-Results: aspmx1.migadu.com; dkim=fail (headers rsa verify failed) header.d=gmail.com header.s=20161025 header.b=l4g9pnxp; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: EF1C29404C5 X-Spam-Score: 2.77 X-Migadu-Scanner: scn0.migadu.com X-TUID: T/9hfBmX6XbM * gnu/packages/bioinformatics.scm (r-ggbio): Move from here... * gnu/packages/bioconductor.scm (r-ggbio): ...to here. --- gnu/packages/bioconductor.scm | 65 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 65 --------------------------------- 2 files changed, 65 insertions(+), 65 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a3dd93e763..55df9bf7d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9308,6 +9308,71 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines by Ernst and Kellis.") (license license:artistic2.0))) +(define-public r-ggbio + (package + (name "r-ggbio") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ggbio" version)) + (sha256 + (base32 + "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; See https://github.com/tengfei/ggbio/issues/117 + ;; This fix will be included in the next release. + (add-after 'unpack 'fix-typo + (lambda _ + (substitute* "R/GGbio-class.R" + (("fechable") "fetchable")) + #t))))) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-biovizbase" ,r-biovizbase) + ("r-bsgenome" ,r-bsgenome) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggally" ,r-ggally) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gtable" ,r-gtable) + ("r-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-organismdbi" ,r-organismdbi) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://www.tengfei.name/ggbio/") + (synopsis "Visualization tools for genomic data") + (description + "The ggbio package extends and specializes the grammar of graphics for +biological data. The graphics are designed to answer common scientific +questions, in particular those often asked of high throughput genomics data. +All core Bioconductor data structures are supported, where appropriate. The +package supports detailed views of particular genomic regions, as well as +genome-wide overviews. Supported overviews include ideograms and grand linear +views. High-level plots include sequence fragment length, edge-linked +interval to data view, mismatch pileup, and several splicing summaries.") + (license license:artistic2.0))) + (define-public r-gqtlbase (package (name "r-gqtlbase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bc483e6f13..512abcd8fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10484,71 +10484,6 @@ high-level packages for biological data visualization. This saves development effort and encourages consistency.") (license license:artistic2.0))) -(define-public r-ggbio - (package - (name "r-ggbio") - (version "1.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ggbio" version)) - (sha256 - (base32 - "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; See https://github.com/tengfei/ggbio/issues/117 - ;; This fix will be included in the next release. - (add-after 'unpack 'fix-typo - (lambda _ - (substitute* "R/GGbio-class.R" - (("fechable") "fetchable")) - #t))))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-organismdbi" ,r-organismdbi) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "http://www.tengfei.name/ggbio/") - (synopsis "Visualization tools for genomic data") - (description - "The ggbio package extends and specializes the grammar of graphics for -biological data. The graphics are designed to answer common scientific -questions, in particular those often asked of high throughput genomics data. -All core Bioconductor data structures are supported, where appropriate. The -package supports detailed views of particular genomic regions, as well as -genome-wide overviews. Supported overviews include ideograms and grand linear -views. High-level plots include sequence fragment length, edge-linked -interval to data view, mismatch pileup, and several splicing summaries.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.29.2