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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48575 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48575@debbugs.gnu.org Cc: zimoun Received: via spool by 48575-submit@debbugs.gnu.org id=B48575.1621628833967 (code B ref 48575); Fri, 21 May 2021 20:28:04 +0000 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 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 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+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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")