From patchwork Mon Mar 15 13:01:30 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27703 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 6A1F327BC54; Mon, 15 Mar 2021 13:02:27 +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 AE28527BC52 for ; Mon, 15 Mar 2021 13:02:26 +0000 (GMT) Received: from localhost ([::1]:37738 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLmrZ-0002bR-T3 for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 09:02:25 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:59810) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLmrE-0002Zr-Kj for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51730) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLmrE-0006lN-Cv for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLmrE-00069l-8L for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47156] [PATCH 05/10] gnu: r-s4vectors: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:02:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47156 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47156@debbugs.gnu.org Cc: zimoun Received: via spool by 47156-submit@debbugs.gnu.org id=B47156.161581332323650 (code B ref 47156); Mon, 15 Mar 2021 13:02:04 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:02:03 +0000 Received: from localhost ([127.0.0.1]:35036 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr8-00068a-Tk for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:02 -0400 Received: from mail-wm1-f52.google.com ([209.85.128.52]:53131) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr4-00067l-D9 for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:01:55 -0400 Received: by mail-wm1-f52.google.com with SMTP id d191so8048848wmd.2 for <47156@debbugs.gnu.org>; Mon, 15 Mar 2021 06:01:54 -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=/+6AunnG0DDWTKnpRJDXXd345iWPkWrSTnkN3r6Mbq8=; b=HfAVPX9hFzdabgi2ZqDAnF/w1tVbK2Omx2aF6Ptfr7bpoVLTrUr9teJ2/XBTslBK6Y 0xh8KWs0/jo21HugJTIBxkcJheWx7kZRHm77MXFqgIXtDnIJI/L/z8HJRNze3jNIPjXJ juDuCjG7PlI/KyJ5GIx9I6iqqPWl9tX1EaGGuMojUgz43dOuQKjB1kvKcPNCElPGVwJn Eh8DPCqhbncgLRNaKdKwQ4/hrVtWsafM6rxz3CH5we0xmeMfwyjuxMwpD6hrP7ul+nHW aHRJyENAu65EwA+bGMf6mAjzjue0lvsRSJxKlZ7dX0V4ubaGDF+TpfBK43tzewybclKF Q4zQ== 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=/+6AunnG0DDWTKnpRJDXXd345iWPkWrSTnkN3r6Mbq8=; b=UyKrseElwYtgKNvpdENxlY3ipjZbYzF71qUHlmQ9zPO775HDR9kNRxHD3kbogRzYFC 0uD89bQOR/tkWAwYJx3FhO8ZfTJuUtwE9VtgEzulHI3O78DDDw9ZwOls2mrTmXENUJBX WCKL2zf0tqlvzn78sCfLjbNkJOwcYhfmRs/OjjQiKD7uydTHuC43BQrkWt3ahUUof8GP NYvjvTjo5CmPPs5Uu8DuiV/VvvpBaA94JtXDiolnIKQ8o0ybL87ACvBneJ+ysFZ8raFM UHQuvlTLRWavRpJvKIlDKdGdl/cCdV3TdBqyA8wYXQneVFyKCNV8NoFPx17SCAXBMtyc sknQ== X-Gm-Message-State: AOAM531d/fXe0ZxXYS4oRtneAlgZ3QGIwP3CKV81Li97detXPpwsoHj/ RO9OqDDw03lIwjffTx6fvxlTM2yVL9M= X-Google-Smtp-Source: ABdhPJxYDam4/QBMkNTpte0slzS0vdCWVVIrFI2u7LVpSBUbx2/w6aBRDxc82VXv7tUCqONrfA51HA== X-Received: by 2002:a1c:7f84:: with SMTP id a126mr26411827wmd.151.1615813308552; Mon, 15 Mar 2021 06:01:48 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id f16sm18344646wrt.21.2021.03.15.06.01.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 06:01:48 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 14:01:30 +0100 Message-Id: <20210315130134.30302-5-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210315130134.30302-1-zimon.toutoune@gmail.com> References: <20210315130134.30302-1-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-s4vectors): Move from here... * gnu/packages/bioconductor.scm (r-s4vectors): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 28 insertions(+), 27 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7c97e52312..ed34a9308a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen +;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo @@ -9154,6 +9155,33 @@ generated.") routines.") (license license:lgpl2.0+))) +(define-public r-s4vectors + (package + (name "r-s4vectors") + (version "0.28.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "S4Vectors" version)) + (sha256 + (base32 + "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh")))) + (properties + `((upstream-name . "S4Vectors"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "https://bioconductor.org/packages/S4Vectors") + (synopsis "S4 implementation of vectors and lists") + (description + "The S4Vectors package defines the @code{Vector} and @code{List} virtual +classes and a set of generic functions that extend the semantic of ordinary +vectors and lists in R. Package developers can easily implement vector-like +or list-like objects as concrete subclasses of @code{Vector} or @code{List}. +In addition, a few low-level concrete subclasses of general interest (e.g. +@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the +S4Vectors package itself.") + (license license:artistic2.0))) + ;; This is a CRAN package, but it depends on preprocessorcore, which is a ;; Bioconductor package. (define-public r-wgcna diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d8d64818d2..1fcb436f0d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,33 +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-s4vectors - (package - (name "r-s4vectors") - (version "0.28.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "S4Vectors" version)) - (sha256 - (base32 - "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh")))) - (properties - `((upstream-name . "S4Vectors"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) - (home-page "https://bioconductor.org/packages/S4Vectors") - (synopsis "S4 implementation of vectors and lists") - (description - "The S4Vectors package defines the @code{Vector} and @code{List} virtual -classes and a set of generic functions that extend the semantic of ordinary -vectors and lists in R. Package developers can easily implement vector-like -or list-like objects as concrete subclasses of @code{Vector} or @code{List}. -In addition, a few low-level concrete subclasses of general interest (e.g. -@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the -S4Vectors package itself.") - (license license:artistic2.0))) - (define-public r-iranges (package (name "r-iranges")