From patchwork Mon Mar 15 18:08:56 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27807 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id CAC1627BC54; Mon, 15 Mar 2021 18:38:07 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H3, RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id E327227BC52 for ; Mon, 15 Mar 2021 18:38:06 +0000 (GMT) Received: from localhost ([::1]:57670 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLs6Q-00034a-2h for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 14:38:06 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37742) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrfG-0007HM-S5 for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:53649) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrfG-0003MP-HQ for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLrfG-0004od-C5 for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 02/10] gnu: r-xvector: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 18:10:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47171 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47171@debbugs.gnu.org Cc: zimoun Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.161583176918402 (code B ref 47171); Mon, 15 Mar 2021 18:10:02 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 18:09:29 +0000 Received: from localhost ([127.0.0.1]:36940 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLref-0004m4-3v for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:28 -0400 Received: from mail-wr1-f53.google.com ([209.85.221.53]:41090) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLred-0004lR-BY for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:23 -0400 Received: by mail-wr1-f53.google.com with SMTP id f12so9145383wrx.8 for <47171@debbugs.gnu.org>; Mon, 15 Mar 2021 11:09:23 -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=+7sTqLmA4P0R8o4KC/s7BbhNoeiAsAfZjDs1II0/dUw=; b=irNi6Z/pRtb6RaTdWBqhO8115flFQ50dsQJqb8WB/qM2ozsEDNWT12K/QhqwsLQM7M 24efnkmSpha9nkN70RpSWmSW4NfYHXLxo3kXlCjIBvcVlWR3O0J0bRdcXQpGWwNES3RO vDecYHPZKbwGaWBQxS1egIQyromWqdzdFuHW9rFLQ14hc+f5wY+ARvro/uJQg81RO4jJ /UEwzEZzodHEbBi2MH7eTg9w6ZF2QNdqb8aee50q6Vb7bzIL6oQlniAAZkg96SGi+V9w 2GgPEBr1MBDravp+hep72hWw3bim+CC9ngOglSV+IunZ0rAd5gB6lmhIIe46VsQyOoG4 vgPA== 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=+7sTqLmA4P0R8o4KC/s7BbhNoeiAsAfZjDs1II0/dUw=; b=fVgwx/Lx5yg+S97B8izG9A+L3YrPsXGkcEu2n5YdFTjVRXcMwVVhyvf1PQQjUyhiWa 6Hzz+spZr3fSePPsA6smxl4AbylxHdfIQ7C8UnqSBEjp+te8K9sECCvkFBsEBtRZyQAi 0jnA/b2LGBP0oGoIwegdvFh8GNFdpyINoC7zFbQtZyP1IGQyZbeDirPRFfSxoa2+RChy Rt7sLpqNx8KTs45y5nZfAThImLvpxkjpvV7bsLnii/aDL768NSKFZV0POiin++6R3kl1 OgYW4P/BdxPtklQZ3zrQP62IINKxt1caVlf6xzPZ+I9N2XvAb8vShnAfa3WP8nBZm0nP A2dQ== X-Gm-Message-State: AOAM533P4AklIM0veOQUAHzu7R9TauW2/A7L7eXaJJVTSwht2lcUEzWY 2voyJsw/yDPoA70wRMVpYEswCGrayFs= X-Google-Smtp-Source: ABdhPJwDDJd1GvP29XNuU9snYfnkY4/ptqLgNZakb81YVMoOSw19jRPwifY0M+dkOUv/YOHoSuN/fQ== X-Received: by 2002:adf:de92:: with SMTP id w18mr847189wrl.217.1615831757644; Mon, 15 Mar 2021 11:09:17 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id s11sm438851wme.22.2021.03.15.11.09.17 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:09:17 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 19:08:56 +0100 Message-Id: <20210315180904.8346-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210315180904.8346-1-zimon.toutoune@gmail.com> References: <20210315180904.8346-1-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-xvector): Move from here... * gnu/packages/bioconductor.scm (r-xvector): ...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 379b6c30c0..fdb2f7c7ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2108,6 +2108,42 @@ annotation infrastructure.") coding changes and predict coding outcomes.") (license license:artistic2.0))) +(define-public r-xvector + (package + (name "r-xvector") + (version "0.30.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "XVector" version)) + (sha256 + (base32 + "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq")))) + (properties + `((upstream-name . "XVector"))) + (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))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/XVector") + (synopsis "Representation and manpulation of external sequences") + (description + "This package provides memory efficient S4 classes for storing sequences +\"externally\" (behind an R external pointer, or on disk).") + (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 9774b442a3..65db983461 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,42 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-xvector - (package - (name "r-xvector") - (version "0.30.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "XVector" version)) - (sha256 - (base32 - "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq")))) - (properties - `((upstream-name . "XVector"))) - (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))))) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/XVector") - (synopsis "Representation and manpulation of external sequences") - (description - "This package provides memory efficient S4 classes for storing sequences -\"externally\" (behind an R external pointer, or on disk).") - (license license:artistic2.0))) - (define-public r-genomicranges (package (name "r-genomicranges")