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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:03:03 +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=B47156.161581332723715 (code B ref 47156); Mon, 15 Mar 2021 13:03:03 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:02:07 +0000 Received: from localhost ([127.0.0.1]:35051 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrG-0006AL-R5 for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:07 -0400 Received: from mail-wr1-f47.google.com ([209.85.221.47]:42738) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr9-000683-HH for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:00 -0400 Received: by mail-wr1-f47.google.com with SMTP id x13so5646106wrs.9 for <47156@debbugs.gnu.org>; Mon, 15 Mar 2021 06:01:59 -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=eqc+9cvsgDprbsNpPrLnaDaAZehsN4tKi8aEh4epFBc=; b=P0iBUy8gwaWxNtDieWdjpoIiAUe5jbo7v8JDyfGR4JBxRUroV1XkHjxbMDA719HtGM 6Wu34EWzdnj6irc9c+hqJ4q+44RdZL981BeAY5xVHHH8wuK4priZMyfJFXZeZR+WQgO3 RDFz3jkDb/5jXn30xoegbLEz6+V3LKLubhkdX2/m0OCfJSXSFyF+il+/5N97+c4ZkRx8 2Twh8zNXR9en2/ww8p7VH8rCC6/Y78dDGRyGzKhjBLXL5ZPg7l4q7QsbHyPNYY8CvLbd 6lUVgmSxHY2DOpZAq34bCnhP9ljPpAN0euIhB3FSGjRbD0sOSwryEzoP17Ny/ddOY5hA sISg== 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=eqc+9cvsgDprbsNpPrLnaDaAZehsN4tKi8aEh4epFBc=; b=Dia2n7ZXtiOpUaekoFrSx/6qK9ASxfiiJSuOi08A6WV/AnyKrZ8M2V03FMxckZfynV l0arVG1Ljp5qiWK3FK935NcRRZNUJpVRkHsrTNsJHW6t8ykrz1CI7a/QQqMiOwFLcFCy R8imtrRfdGcX9MdPA7LGG2C1IwZSC97N2VvYH5wAAPlqjyx5ezgPwBKfMXbKxMfmHvuv 5acaXMho1ovOQ+B9sCQMXkEAn6rL5LviUObZAVP6bhzuYKul6e8sKlIPeHPBmg8HhijK xtG/wKWhO/F4rAKV1TmKfFed95D9jhA7Hvyam1Z4229iOJAXLe8ByVD8/7grQ7TCGodF k5Lw== X-Gm-Message-State: AOAM5312Y9RAL8N2BnsQYga/ZoAAL45q+FyakcDjcL6qgJkCqD9vs7Tk gOrRMnJnwb/5UuZN1GXNnNfs36aGIiE= X-Google-Smtp-Source: ABdhPJwxJLkULV/FSVLRmXoaEnT4JGMp1L7J6/KhmMgJUrFhyTcmWLyKLeCBuj3OoCeJIlz1Hv5azg== X-Received: by 2002:a5d:6ca6:: with SMTP id a6mr26870834wra.179.1615813309118; Mon, 15 Mar 2021 06:01:49 -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 14:01:31 +0100 Message-Id: <20210315130134.30302-6-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-iranges): Move from here... * gnu/packages/bioconductor.scm (r-iranges): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 30 insertions(+), 29 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ed34a9308a..68c5ed7768 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2016 Pjotr Prins +;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo @@ -1244,6 +1245,35 @@ and evaluate clustering results.") arbitrary genomic intervals along chromosomal ideogram.") (license license:gpl2))) +(define-public r-iranges + (package + (name "r-iranges") + (version "2.24.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "IRanges" version)) + (sha256 + (base32 + "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52")))) + (properties + `((upstream-name . "IRanges"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/IRanges") + (synopsis "Infrastructure for manipulating intervals on sequences") + (description + "This package provides efficient low-level and highly reusable S4 classes +for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more +generally, data that can be organized sequentially (formally defined as +@code{Vector} objects), as well as views on these @code{Vector} objects. +Efficient list-like classes are also provided for storing big collections of +instances of the basic classes. All classes in the package use consistent +naming and share the same rich and consistent \"Vector API\" as much as +possible.") + (license license:artistic2.0))) + ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 ;; from Bioconductor. (define-public r-deconstructsigs diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1fcb436f0d..36ecf47467 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,35 +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-iranges - (package - (name "r-iranges") - (version "2.24.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "IRanges" version)) - (sha256 - (base32 - "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52")))) - (properties - `((upstream-name . "IRanges"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/IRanges") - (synopsis "Infrastructure for manipulating intervals on sequences") - (description - "This package provides efficient low-level and highly reusable S4 classes -for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more -generally, data that can be organized sequentially (formally defined as -@code{Vector} objects), as well as views on these @code{Vector} objects. -Efficient list-like classes are also provided for storing big collections of -instances of the basic classes. All classes in the package use consistent -naming and share the same rich and consistent \"Vector API\" as much as -possible.") - (license license:artistic2.0))) - (define-public r-genomeinfodbdata (package (name "r-genomeinfodbdata")