From patchwork Mon Mar 15 18:08:55 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27806 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 4023027BC54; Mon, 15 Mar 2021 18:37:59 +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 6FB4D27BC52 for ; Mon, 15 Mar 2021 18:37:58 +0000 (GMT) Received: from localhost ([::1]:56814 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLs6H-0002fQ-Jt for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 14:37:57 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37740) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrfG-0007GQ-Gd for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:53648) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrfG-0003ML-3F 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 1lLrfF-0004oV-TN for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 01/10] gnu: r-limma: Move to (gnu packages bioconductor). References: <20210315180714.8233-1-zimon.toutoune@gmail.com> In-Reply-To: <20210315180714.8233-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 18:10:01 +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=B47171.161583176518359 (code B ref 47171); Mon, 15 Mar 2021 18:10:01 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 18:09:25 +0000 Received: from localhost ([127.0.0.1]:36937 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLree-0004lv-LG for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:25 -0400 Received: from mail-wm1-f53.google.com ([209.85.128.53]:36780) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrec-0004lQ-Tw for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:23 -0400 Received: by mail-wm1-f53.google.com with SMTP id r15-20020a05600c35cfb029010e639ca09eso20856131wmq.1 for <47171@debbugs.gnu.org>; Mon, 15 Mar 2021 11:09:22 -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:mime-version :content-transfer-encoding; bh=sLWcH5zpRMN/aAT99C7DnRKAHbSa/plbeh872SKyrco=; b=aPDKFsunBHcDmafxs0VsS0K92Y3czXLSsj+9pv0DM+6FV+JAMbYU+XhW7flt5zYnCu 2Yj5L7iXgnWUwFg8Np9Gj9HeJObWC79kDZw0LBGrKBsKsFL9+SbbPVoYg5taIXFIFmBu 8Br+FVpL0bFlHGhSlmLOqZK4/HPohujoSkxsLkBQ/K07I/aExohJkl/kR2A/y09Wc//n DdJ6kNMdUbrAAKSm10qbU4jpehQ453NQq3z3ymnNGNmwAmNte9/F4kQzih2lhMHIKnLD IHspO9s6ASqnN4HwV8sS/BJsN+nkrysmigbMeZPutwI8jXt+gowx3X04VHakLyZ/2rsW ZTJQ== 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:mime-version :content-transfer-encoding; bh=sLWcH5zpRMN/aAT99C7DnRKAHbSa/plbeh872SKyrco=; b=fqpuu3qqq/zRHCgnql9ZV+ejeYr8ZKSLQ1fwRcYHMmoK3s+3k+rHU+e0xD68CF5hQR aOU17FH29Zd5kMx35W2o6CstJg+8UtzOEtDMnqoU7NxaUl2FBjmJjdTZJyMlUlr8mz1e l+AFZIKrxuVjp/w3t7dBKYWnrAx1XXnA0f72ZVm4gt/P+HIMlle8+dnGzcFqeehjhapy w4uWqgTOl0ltt5MU7cBip4Zdjz/FP2Fbte+U7vzAMbEHYKsQrI2T+NbO/LziLA2Lubuw bcEN60+lqd7E12NF/sBE1U6WzJ8DhGAhy6m1jFzTsDLWBlRfhpj9y2a3siR8rX0QHHwH /ptw== X-Gm-Message-State: AOAM532XdjC9zA4hjPNnrCKoVKbWfxoXg1/ymij8gYaNNd96gI+fNaKx aKP35g2IO4f+n4KOdN8XXSscMKKAEOY= X-Google-Smtp-Source: ABdhPJxJlzfCdtOM9ClnVopNtF+vLIhv0dV4NURuPoCQtjfNpsAO2WTgT+RH11u01hdB8vkcdasgHA== X-Received: by 2002:a1c:2308:: with SMTP id j8mr907215wmj.45.1615831757071; 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.22.2021.03.15.11.09.16 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:09:16 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 19:08:55 +0100 Message-Id: <20210315180904.8346-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 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-limma): Move from here... * gnu/packages/bioconductor.scm (r-limma): ...to here. --- gnu/packages/bioconductor.scm | 19 +++++++++++++++++++ gnu/packages/bioinformatics.scm | 19 ------------------- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d611f3a491..379b6c30c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1850,6 +1850,25 @@ Enrichment Analysis} (GSEA).") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-limma + (package + (name "r-limma") + (version "3.46.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "limma" version)) + (sha256 + (base32 + "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz")))) + (build-system r-build-system) + (home-page "http://bioinf.wehi.edu.au/limma") + (synopsis "Package for linear models for microarray and RNA-seq data") + (description "This package can be used for the analysis of gene expression +studies, especially the use of linear models for analysing designed experiments +and the assessment of differential expression. The analysis methods apply to +different technologies, including microarrays, RNA-seq, and quantitative PCR.") + (license license:gpl2+))) + (define-public r-rbgl (package (name "r-rbgl") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d9afe2c56f..9774b442a3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,25 +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-limma - (package - (name "r-limma") - (version "3.46.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "limma" version)) - (sha256 - (base32 - "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz")))) - (build-system r-build-system) - (home-page "http://bioinf.wehi.edu.au/limma") - (synopsis "Package for linear models for microarray and RNA-seq data") - (description "This package can be used for the analysis of gene expression -studies, especially the use of linear models for analysing designed experiments -and the assessment of differential expression. The analysis methods apply to -different technologies, including microarrays, RNA-seq, and quantitative PCR.") - (license license:gpl2+))) - (define-public r-xvector (package (name "r-xvector") 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") From patchwork Mon Mar 15 18:08:57 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27808 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 27E3027BC54; Mon, 15 Mar 2021 18:38:16 +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 42D0327BC52 for ; Mon, 15 Mar 2021 18:38:15 +0000 (GMT) Received: from localhost ([::1]:58526 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLs6Y-0003Pb-FI for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 14:38:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37746) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrfH-0007If-DN for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:53650) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrfH-0003Md-02 for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLrfG-0004ok-R6 for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 03/10] gnu: r-genomicranges: 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=B47171.161583177018411 (code B ref 47171); Mon, 15 Mar 2021 18:10:02 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 18:09:30 +0000 Received: from localhost ([127.0.0.1]:36947 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrek-0004ms-0s for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:30 -0400 Received: from mail-wm1-f51.google.com ([209.85.128.51]:33657) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLred-0004lS-Oj for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:24 -0400 Received: by mail-wm1-f51.google.com with SMTP id w203-20020a1c49d40000b029010c706d0642so2718818wma.0 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=xeLBVlZt0/Pn5u7gI2OgMDwB9DVPZwQs3bjdjPUIMq0=; b=PPovfXbTHK/3fpONOSURTyci7633G7nzg8gv4+etH0bA+3XCR/lassdcuVjiGvRu0L rV/SoVi8uzzKcdo4ZZzcbcpAKp+UaFThgT8qeSbekAdo0kqxEFM8qLMAn+uYhAyJuuIj 9yQ0yIlPfzjoexZ83Nys6aW+IMl+44OzLC5dM3BcISL62FhKZa+cjU7Sk9bhcR3CAiJ7 VJOvCcNK4SvZtOgjRlZHPPI5RlIL26Iq56MNDiECt45f2vVzrWRe28RRAumHtgmeiQtj j+JYKi35hvHJlbUK0JXfgF36WMDSkGTnI0dfVokFEgwO/VyjhdmZnhYvZpjpxCZhJ66+ 18Gg== 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=xeLBVlZt0/Pn5u7gI2OgMDwB9DVPZwQs3bjdjPUIMq0=; b=sgon+GqC3KNATKkOUCdRqp1BeB3JoiOyaYvIOS9O4nCdUOwnyKH7ChlDvQMAfgWOHz IX42EXKYKiCf7SrBTzSztgZElNwbZC+6hH+acF6mS3VSkg0BFzBoXyp/7pNskcbXxyd9 Npea+Roods8Y9vWeRhFYd9QlLNZFlEDL4btjQfFdG7e61nEQ2xZQabmOopsdTr4Fv7ay 31UQXM6E0X7HphTaayr2VlTzV6vbSvgF7sPvrGKWXOmlmHmO7E8VNCj7tAxU39R1/87U VmaNKeAFcSfqncnGdSjLgR3ovgTB5wg+CduP3fkx/ABpcFTL3KQ9HtbtWrPk9NDVS4cL u5Pg== X-Gm-Message-State: AOAM531ASHFbDejEk4296OfHlG9ZR1wHKv/fU1IcOAdBSCMZWulAn535 Yavx6/MmQeut2B4NCU5VWKHyxoC1Ei8= X-Google-Smtp-Source: ABdhPJzSVXVmm4YQrZ/v0k2HyoKaqrd0E1LBaGXeWnCUcY2P1+yRSUTGHx2B7AdIlfJiRyEH3sQDaQ== X-Received: by 2002:a1c:318b:: with SMTP id x133mr912251wmx.154.1615831758140; Mon, 15 Mar 2021 11:09:18 -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 19:08:57 +0100 Message-Id: <20210315180904.8346-3-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-genomicranges): Move from here... * gnu/packages/bioconductor.scm (r-genomicranges): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fdb2f7c7ac..ec273cae70 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1770,6 +1770,37 @@ translation between different chromosome sequence naming conventions (e.g., names in their natural, rather than lexicographic, order.") (license license:artistic2.0))) +(define-public r-genomicranges + (package + (name "r-genomicranges") + (version "1.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicRanges" version)) + (sha256 + (base32 + "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) + (properties + `((upstream-name . "GenomicRanges"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GenomicRanges") + (synopsis "Representation and manipulation of genomic intervals") + (description + "This package provides tools to efficiently represent and manipulate +genomic annotations and alignments is playing a central role when it comes to +analyzing high-throughput sequencing data (a.k.a. NGS data). The +GenomicRanges package defines general purpose containers for storing and +manipulating genomic intervals and variables defined along a genome.") + (license license:artistic2.0))) + (define-public r-gostats (package (name "r-gostats") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 65db983461..4889c148e4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,37 +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-genomicranges - (package - (name "r-genomicranges") - (version "1.42.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicRanges" version)) - (sha256 - (base32 - "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) - (properties - `((upstream-name . "GenomicRanges"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/GenomicRanges") - (synopsis "Representation and manipulation of genomic intervals") - (description - "This package provides tools to efficiently represent and manipulate -genomic annotations and alignments is playing a central role when it comes to -analyzing high-throughput sequencing data (a.k.a. NGS data). The -GenomicRanges package defines general purpose containers for storing and -manipulating genomic intervals and variables defined along a genome.") - (license license:artistic2.0))) - (define-public r-biobase (package (name "r-biobase") From patchwork Mon Mar 15 18:08:58 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27809 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 A3DB527BC54; Mon, 15 Mar 2021 18:38:40 +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 14A5F27BC52 for ; Mon, 15 Mar 2021 18:38:40 +0000 (GMT) Received: from localhost ([::1]:59420 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLs6x-0003lO-7u for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 14:38:39 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37754) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrfH-0007Jd-S0 for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:53651) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrfH-0003Mn-HH for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLrfH-0004os-BZ for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 04/10] gnu: r-biobase: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 18:10:03 +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=B47171.161583177118419 (code B ref 47171); Mon, 15 Mar 2021 18:10:03 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 18:09:31 +0000 Received: from localhost ([127.0.0.1]:36949 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrek-0004mu-Eg for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:30 -0400 Received: from mail-wm1-f51.google.com ([209.85.128.51]:56273) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLree-0004lU-75 for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:24 -0400 Received: by mail-wm1-f51.google.com with SMTP id 12so3647689wmf.5 for <47171@debbugs.gnu.org>; Mon, 15 Mar 2021 11:09:24 -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=2VeeyUjjE5n07uG6P7+EsnurFhU9M2CRJ4yNfwn9KI8=; b=a5xqBp6MukKTnWSSCWsVAdnzdGhG9AjNl11BnCNLbKA1IDHFkJFP4wbhNPV06sFb8s hlfcMYjVKq2858K7ljPUyzkndXWFww+IAhGZhoE7zs7WTI8ElTN6qfUc00UVXg9uoqek NmfbQawv2Nd6k9ad03KJgx4nnnT5ZmkC7COvGfR4BH6ILuz3qR++e9hE7tOtJ7QS6Rz4 ZttRvX+kvg+gSDWJ1pVEdYUIzGhVTw5C5aDyKMj+hJRuKtG/pcRmrA5mskBsZsrXyWok gWGG7QQJHcgqqOQnyx4Vnzaga5XDQ63qCpydk0Ue/8iwrlgZqY6m1rYokIe9AqXIkLla 4sDQ== 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=2VeeyUjjE5n07uG6P7+EsnurFhU9M2CRJ4yNfwn9KI8=; b=myJubeFplltSBZWWtTey+fT9KXXe3EAgcSpbgqXWHSh38teayokMptzId0rdE29NvZ ElpPOYsHHnPx7xY+CBEN6R58LWVRGCG4BKjbwpM4VA8/f/JPwpWAvNLREhVnGwwTYTZ1 EzT/CaCEtquuPcAG7lR9C2MIxYGY7w9CIkDK2pNhfG8J2VK5dK8geRSJ1K7hJrYMcIQ5 rEwGTE9WZWE3BzZ8QW43hV82q1529s+unuQ9MZVe8bvaAmXTpxJIQ25AVhlTH3VPLiV7 SHs/3blFE0MExJ84k40a7IWPJPa1/3AbrPFn0dDp+PwV6EfrSAWDbmaGp+7zDoikzx9J OUBQ== X-Gm-Message-State: AOAM532DpOaMHj+AZ9VCFX5r86/81HGtnl4sUad65mj9IqbEZ6ghkX2z VsTzrWW1laW4TrzG6v9f/v9OTHbC2a4= X-Google-Smtp-Source: ABdhPJxbFqp7sf8mCa5wpEct1Y/E0UTQq9RgyIP7n2/kmEoGLFxemhznFX9B8aFxIZE5ezCjI/hchw== X-Received: by 2002:a7b:c083:: with SMTP id r3mr848480wmh.177.1615831758777; Mon, 15 Mar 2021 11:09:18 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id s11sm438851wme.22.2021.03.15.11.09.18 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:09:18 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 19:08:58 +0100 Message-Id: <20210315180904.8346-4-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-biobase): Move from here... * gnu/packages/bioconductor.scm (r-biobase): ...to here. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 22 ---------------------- 2 files changed, 22 insertions(+), 22 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec273cae70..b7308848c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1570,6 +1570,28 @@ microarrays.") databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-biobase + (package + (name "r-biobase") + (version "2.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Biobase" version)) + (sha256 + (base32 + "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) + (properties + `((upstream-name . "Biobase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "https://bioconductor.org/packages/Biobase") + (synopsis "Base functions for Bioconductor") + (description + "This package provides functions that are needed by many other packages +on Bioconductor or which replace R functions.") + (license license:artistic2.0))) + (define-public r-category (package (name "r-category") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4889c148e4..b73862ff86 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,28 +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-biobase - (package - (name "r-biobase") - (version "2.50.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Biobase" version)) - (sha256 - (base32 - "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) - (properties - `((upstream-name . "Biobase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) - (home-page "https://bioconductor.org/packages/Biobase") - (synopsis "Base functions for Bioconductor") - (description - "This package provides functions that are needed by many other packages -on Bioconductor or which replace R functions.") - (license license:artistic2.0))) - (define-public r-annotationdbi (package (name "r-annotationdbi") From patchwork Mon Mar 15 18:08:59 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27814 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 D859227BC54; Mon, 15 Mar 2021 18:40:11 +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 05EB827BC52 for ; Mon, 15 Mar 2021 18:40:11 +0000 (GMT) Received: from localhost ([::1]:36298 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLs8Q-0005wt-3E for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 14:40:10 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37762) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrfI-0007Kc-AA for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:53652) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrfI-0003NP-07 for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLrfH-0004oz-R2 for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 05/10] gnu: r-annotationdbi: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 18:10:03 +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=B47171.161583177118426 (code B ref 47171); Mon, 15 Mar 2021 18:10:03 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 18:09:31 +0000 Received: from localhost ([127.0.0.1]:36951 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrek-0004n2-Tb for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:31 -0400 Received: from mail-wm1-f54.google.com ([209.85.128.54]:38690) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLree-0004lV-TE for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:26 -0400 Received: by mail-wm1-f54.google.com with SMTP id m20-20020a7bcb940000b029010cab7e5a9fso20827928wmi.3 for <47171@debbugs.gnu.org>; Mon, 15 Mar 2021 11:09:24 -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=j6qoA4rCbZlkriSCPy9bFbT5/GnzcUbNgMlyEaryzhc=; b=OQV5lp4C+0nLqR2aL1NSnypzayn3MSCOmPZJvjVWdsRXPxzKiPjEF/e9LCZy7s+Qxt 0ZfvgVu/zssRO5qBhdwvX7Hq62CqBHkgN21MQzdRTXS3hKSSOwQrQ0pLwSJLY+LcGDxv 2OOevh8OMLIxOqW/0Zc8ukOz26isGbFVJj9cOLysZUnS0MnGPOCUHakkjNSHCUBral0b ixRtQhtmJoEaYkV3y+Df6Qtzo4kYbG5UHSJ/qIBMOKAGLvGaxc0BMESdbikWbUaOqQfH jHBg2idyDRHhRqwT75e6tBKjIk4yNQjJ2CLZGiTEy0/LRLgyQCgN72qV1aopwTEJNPxj cX+g== 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=j6qoA4rCbZlkriSCPy9bFbT5/GnzcUbNgMlyEaryzhc=; b=VQ6oT/V5lRPqaeiS0pyrZ/tYr6XRNI8NmlqvdNI4PivBPJ9HeyifT61NUjYLcMR6h0 OOJ0vkqRFYQspfEkSq0w08BERTNqug1vWkVwCxGwLMPcvmoksdJxOCUKWx9sLoWfbbnw aN5C5uNL3lM4znjYyfr0C6OIJcWJfory+YYhrve0fLix7TRI2skzBCUjOZpEzRzl37ZN stN+RjphjLesQRxrcsvlROBKC7lenZ3QOd16o+VI27h+isJTGYdBj7a2/9KRozrOpXOJ IgW1CEOeH0Xo7gpyvT3zzXUDFxOZZbJzwgY2EpTNT9vLqkJJ4fB7PtXiubh6CIVfNwwu YOeA== X-Gm-Message-State: AOAM531SxKXkIurEhN2TpbRclPGHG/ytdDhXhGz02q7XGMW0ScPDtmhz SNbzWCamNJyixeeuyCa1fRxrUOGlWtc= X-Google-Smtp-Source: ABdhPJy1ORa8MYYSSGoSbO828boCWgz4oRRLiwIFJeGKqNcwAahVrNfBfXl4owIlR+bf7RyKEAr+Yw== X-Received: by 2002:a1c:2049:: with SMTP id g70mr885131wmg.7.1615831759346; Mon, 15 Mar 2021 11:09:19 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id s11sm438851wme.22.2021.03.15.11.09.18 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:09:19 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 19:08:59 +0100 Message-Id: <20210315180904.8346-5-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-annotationdbi): Move from here... * gnu/packages/bioconductor.scm (r-annotationdbi): ...to here. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b7308848c0..2ae212dfac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1538,6 +1538,35 @@ structure.") microarrays.") (license license:artistic2.0))) +(define-public r-annotationdbi + (package + (name "r-annotationdbi") + (version "1.52.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationDbi" version)) + (sha256 + (base32 + "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) + (properties + `((upstream-name . "AnnotationDbi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-dbi" ,r-dbi) + ("r-iranges" ,r-iranges) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/AnnotationDbi") + (synopsis "Annotation database interface") + (description + "This package provides user interface and database connection code for +annotation data packages using SQLite data storage.") + (license license:artistic2.0))) + (define-public r-annotationforge (package (name "r-annotationforge") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b73862ff86..a45196bc5b 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-annotationdbi - (package - (name "r-annotationdbi") - (version "1.52.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "AnnotationDbi" version)) - (sha256 - (base32 - "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) - (properties - `((upstream-name . "AnnotationDbi"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/AnnotationDbi") - (synopsis "Annotation database interface") - (description - "This package provides user interface and database connection code for -annotation data packages using SQLite data storage.") - (license license:artistic2.0))) - (define-public r-biomart (package (name "r-biomart") From patchwork Mon Mar 15 18:09:00 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27817 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 A6CF927BC54; Mon, 15 Mar 2021 18:41:04 +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 B254627BC52 for ; Mon, 15 Mar 2021 18:41:03 +0000 (GMT) Received: from localhost ([::1]:37152 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLs9G-0006Iq-7k for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 14:41:02 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37772) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrfI-0007Lb-PB for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:53653) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrfI-0003Na-FT for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLrfI-0004p7-Ax for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 06/10] gnu: r-biomart: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 18:10:04 +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=B47171.161583177218434 (code B ref 47171); Mon, 15 Mar 2021 18:10:04 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 18:09:32 +0000 Received: from localhost ([127.0.0.1]:36953 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrel-0004n9-Br for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:31 -0400 Received: from mail-wr1-f53.google.com ([209.85.221.53]:46936) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLref-0004lX-Qq for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:26 -0400 Received: by mail-wr1-f53.google.com with SMTP id v4so6158300wrp.13 for <47171@debbugs.gnu.org>; Mon, 15 Mar 2021 11:09:25 -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=ZiOyeAbP8hVWcFWNzy1l+NEXiwferumVNSVS7JSIH8g=; b=N73aXrAV2+UySs3nKF4Y387VCfwYiyrFmPNf8jUkhHdrNj96Ve381xc41pU1VOxNSs 1KGl//1BxeWKUaSH7ePIb43ubaXJnqWj0ufOBzyHBOS6rRNsJ74FfTfOxvGBobvprerd rlEoqgHaGDfViX71Bh8y7CiCFhLmaQAbMcywkI1YdycsEeBcIhLh42mBZGTLHCZYaLOz lL7Q8WONqUIc1ef/lapiLDjPtDVsNVUalWmeZ417BO3tsrJPtN4sYPOYZPRgpFgpZ4HZ IwY0tmz5Ln4YbdT0H7/Bwd3pFMwllWp32KJKweUx2tKQwJ7dcHSfsvOMntv5FQB/t216 fJFw== 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=ZiOyeAbP8hVWcFWNzy1l+NEXiwferumVNSVS7JSIH8g=; b=Q2/KbwFvrkFdzSJcuzxRc8nkTokWIqbgvSXuiRMjkb3mkjMbl/VIpucuRtG5cH2gyq kClpVO6p76+h2zRpXviBDLSL7nQx9HXYG/DqcdDTJsoHHUq+dd+fAWeoXoziUNrRMDjq 4ipus4ve/tk4ywoRmri/mvb4z/PQfmR2tXd/P5W7PqoLiMl7eJhSbitWYSFBOssoZ6f9 N2EsY/pPGBXyIHL+/uDeAHUp3PMAdt5OcpYNCbC4w4hZu7BubB+lxi07dPri3FvfYLam 76xviKAojImVL+VLAz1axj3aCN8COZJyPldzWOxqG4uTnJoNOB8CwYnChIPuoCbBGqAx r8yA== X-Gm-Message-State: AOAM532qTbI0K3KnJ40be4Xei0VJwZVS+kYvxL2U9lqU2vrwrWd0jPjN 6pVUpaCsm1Sw/OAoGemYMAPz4nQt/oU= X-Google-Smtp-Source: ABdhPJys7/MNpjysS0OovD38684EHQcuLX4z+MGyTwjwGtwspP21JQ/2O5juJnwrzGgc/69kpQ8VGg== X-Received: by 2002:a5d:6b50:: with SMTP id x16mr832612wrw.379.1615831759935; Mon, 15 Mar 2021 11:09:19 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id s11sm438851wme.22.2021.03.15.11.09.19 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:09:19 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 19:09:00 +0100 Message-Id: <20210315180904.8346-6-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-biomart): Move from here... * gnu/packages/bioconductor.scm (r-biomart): ...to here. --- gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 38 --------------------------------- 2 files changed, 38 insertions(+), 38 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2ae212dfac..897e85dfe3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1621,6 +1621,44 @@ databases. Packages produced are intended to be used with AnnotationDbi.") on Bioconductor or which replace R functions.") (license license:artistic2.0))) +(define-public r-biomart + (package + (name "r-biomart") + (version "2.46.3") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "biomaRt" version)) + (sha256 + (base32 + "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) + (properties + `((upstream-name . "biomaRt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) + ("r-httr" ,r-httr) + ("r-openssl" ,r-openssl) + ("r-progress" ,r-progress) + ("r-rappdirs" ,r-rappdirs) + ("r-stringr" ,r-stringr) + ("r-xml" ,r-xml) + ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/biomaRt") + (synopsis "Interface to BioMart databases") + (description + "biomaRt provides an interface to a growing collection of databases +implementing the @url{BioMart software suite, http://www.biomart.org}. The +package enables retrieval of large amounts of data in a uniform way without +the need to know the underlying database schemas or write complex SQL queries. +Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, +Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt +users direct access to a diverse set of data and enable a wide range of +powerful online queries from gene annotation to database mining.") + (license license:artistic2.0))) + (define-public r-category (package (name "r-category") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a45196bc5b..289a96f572 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,44 +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-biomart - (package - (name "r-biomart") - (version "2.46.3") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "biomaRt" version)) - (sha256 - (base32 - "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) - (properties - `((upstream-name . "biomaRt"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-httr" ,r-httr) - ("r-openssl" ,r-openssl) - ("r-progress" ,r-progress) - ("r-rappdirs" ,r-rappdirs) - ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/biomaRt") - (synopsis "Interface to BioMart databases") - (description - "biomaRt provides an interface to a growing collection of databases -implementing the @url{BioMart software suite, http://www.biomart.org}. The -package enables retrieval of large amounts of data in a uniform way without -the need to know the underlying database schemas or write complex SQL queries. -Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, -Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt -users direct access to a diverse set of data and enable a wide range of -powerful online queries from gene annotation to database mining.") - (license license:artistic2.0))) - (define-public r-biocparallel (package (name "r-biocparallel") From patchwork Mon Mar 15 18:09:01 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27826 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 7D52627BC54; Mon, 15 Mar 2021 18:49:39 +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 B443527BC52 for ; Mon, 15 Mar 2021 18:49:38 +0000 (GMT) Received: from localhost ([::1]:40746 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLsHZ-00033x-Tp for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 14:49:37 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37780) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrfJ-0007Mx-9U for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:53654) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrfI-0003Nl-Tb for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLrfI-0004pE-Oz for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 07/10] gnu: r-biocparallel: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 18:10:04 +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=B47171.161583177218441 (code B ref 47171); Mon, 15 Mar 2021 18:10:04 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 18:09:32 +0000 Received: from localhost ([127.0.0.1]:36955 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrel-0004nH-UZ for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:32 -0400 Received: from mail-wr1-f45.google.com ([209.85.221.45]:45708) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLref-0004lY-Ve for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:26 -0400 Received: by mail-wr1-f45.google.com with SMTP id 61so6156058wrm.12 for <47171@debbugs.gnu.org>; Mon, 15 Mar 2021 11:09:25 -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=9tvzkp2H5GD3lS7uHSfS5tHmwqBWS2qgCunwFKXr+m0=; b=io0VYz1TEByLQcQ4e6ZDiHfZpgZ4gFzfuviknmwrKGlUoD9iMNs6HKG/iscnIbl1jl c4Nhabv2bKcPMa3Whnt5hIQzdq7LTPpnnEDGLP8rOsme9XXWrp6dWogDk3bQolmJjSy0 dvWTWHy9+4fLh2SKXzrd/or8f8Vrr2EhubAnvHJTx9W221cqQ5wqHDr5AodmHe3CPF+9 QSE3owdh9ij1dGXNgA5eOah7AVSWBqvqKPxf/UdMwWq7QTk/YTalQ8tUqGmxsa/8YR9u 4P24+/BDHLjuQsPGLyXaSZSVeliQpOi3j62nxiWeBlPvIzuLT5fXvLt0/pPGI8DLH1By HNpA== 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=9tvzkp2H5GD3lS7uHSfS5tHmwqBWS2qgCunwFKXr+m0=; b=iVw3pcqsTghxgfQYUEtjsQXwdxTtnd/AXri6jAOKlMXtRLNMW5yS+uZTrL1ts1Yhtz ymwENSTUkq8ynaEuJ7FH3qLXeCYSeJ5aDac6Oz7TVYjVwm4JbTpyZemCx47uIC5K10Yb DyNYvDYvSzDgOkeiChuWaevgUC2xQaGFlTzwIV8oQ8IdUeiQwH+M0Y2eiZe5D+sKTBM9 yPyNHfRf7C8/aDYWi3vVfvduM3LALgZQ5PWPDCIei84jwW6sYMEtr+LR1Yyox90OW9G8 o5JIHa50kkXgSOvS/gdV0jfnJHhAXmCW37o6glsULRr4HB+Fy8L/LiXgn7qOAZIGVT3c VCcA== X-Gm-Message-State: AOAM5334GeFYRyHGPWkA9F8dyqG+MAvHQ5lnInk+vyuiTxaEjbL0thaC SsI0c1bdnzOLayGt6r9JrOefChcdRJs= X-Google-Smtp-Source: ABdhPJxia1A5pd3205dI9NMuXuVVd5HboAJhlAKSkuZY/L1OLa56K1ei1YL3EGunh8dha1TYzuSfDQ== X-Received: by 2002:adf:b345:: with SMTP id k5mr949383wrd.14.1615831760440; Mon, 15 Mar 2021 11:09:20 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id s11sm438851wme.22.2021.03.15.11.09.19 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:09:20 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 19:09:01 +0100 Message-Id: <20210315180904.8346-7-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-biocparallel): Move from here... * gnu/packages/bioconductor.scm (r-biocparallel): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 897e85dfe3..6482d8e4c1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1659,6 +1659,33 @@ users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.") (license license:artistic2.0))) +(define-public r-biocparallel + (package + (name "r-biocparallel") + (version "1.24.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocParallel" version)) + (sha256 + (base32 + "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) + (properties + `((upstream-name . "BiocParallel"))) + (build-system r-build-system) + (propagated-inputs + `(("r-futile-logger" ,r-futile-logger) + ("r-snow" ,r-snow) + ("r-bh" ,r-bh))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocParallel") + (synopsis "Bioconductor facilities for parallel evaluation") + (description + "This package provides modified versions and novel implementation of +functions for parallel evaluation, tailored to use with Bioconductor +objects.") + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-category (package (name "r-category") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 289a96f572..af3fa36b19 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-biocparallel - (package - (name "r-biocparallel") - (version "1.24.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BiocParallel" version)) - (sha256 - (base32 - "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) - (properties - `((upstream-name . "BiocParallel"))) - (build-system r-build-system) - (propagated-inputs - `(("r-futile-logger" ,r-futile-logger) - ("r-snow" ,r-snow) - ("r-bh" ,r-bh))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/BiocParallel") - (synopsis "Bioconductor facilities for parallel evaluation") - (description - "This package provides modified versions and novel implementation of -functions for parallel evaluation, tailored to use with Bioconductor -objects.") - (license (list license:gpl2+ license:gpl3+)))) - (define-public r-biostrings (package (name "r-biostrings") From patchwork Mon Mar 15 18:09:02 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27810 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 C467727BC54; Mon, 15 Mar 2021 18:39:13 +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 A7B1D27BC52 for ; Mon, 15 Mar 2021 18:39:12 +0000 (GMT) Received: from localhost ([::1]:60242 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLs7T-00048b-Sr for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 14:39:11 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37782) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrfJ-0007Nk-Kd for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:53655) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrfJ-0003OP-BU for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLrfJ-0004pL-6w for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 08/10] gnu: r-biostrings: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 18:10:05 +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=B47171.161583177318449 (code B ref 47171); Mon, 15 Mar 2021 18:10:05 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 18:09:33 +0000 Received: from localhost ([127.0.0.1]:36957 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrem-0004nO-Dv for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:32 -0400 Received: from mail-wm1-f47.google.com ([209.85.128.47]:40920) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLreg-0004la-HX for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:27 -0400 Received: by mail-wm1-f47.google.com with SMTP id y124-20020a1c32820000b029010c93864955so20841181wmy.5 for <47171@debbugs.gnu.org>; Mon, 15 Mar 2021 11:09:26 -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=otTvMbzCjF4OUXVG6oBNNk0gRs6Rc4aA20VxSqHVjC4=; b=lLddbQXwoNcmR4nSwh/kpeJfzMzL4Ojsgur+LAwpPazRot6Gtdibmq9Du439B37JPX 4GkoUIPB4zdC0GR3bryNnU8DCnPYZkpzP8Bw7knnn2L1UtCJ5uOyaTB5oJghQgaMPPLq VXCGPNUxpLuU5ItBT/YzDYZvML8+GQfAdsL+5wHHg1m528Ird3XXOXL6nDU6Gh8xQRdz 3+jz7XBI7RwR6iq1zftGh34Grr8j5PASbVGVbN8A06uSqyEaVR7ETzK7KQGXBLfZ0zfS QtiMc3Nea7lXfM+LNJ6uwNGA3Fjsv0ZA2mTdw9D7Ztna0e7hcIXQh4IEBByUXN5dQkF7 BRuQ== 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=otTvMbzCjF4OUXVG6oBNNk0gRs6Rc4aA20VxSqHVjC4=; b=tj2DHSyp9SedO4nVZMilRKjX8FJ0uuhcA3/J7jf3eVy8+ADNzg5GAC6IDiWZRW/uCS l6nBispG+g2CFbJTFq3UJcOfiWQgUt/3y32RAUYQaupX7+kFGZ5mQUZakM3TaArv25vK ajo1mdE8Rbl+inSvmctPwfPjaxQdcO/yaIknbWgT2ztcG00j/9fJnZrfbolVZ9Rn/sFa zsLth38ZkRHaoq0nDa9s5EoE6EfSYN2gIE2M+zrXlY5XDmLAzaVgR1MLCko4eCDN1WSe FPtDDod7tNmV38kMW3P39KybWTHRVWiJ7EEa9D9O8jYN6YXvCgGr8qNTFIFLkT9/E/9v J0Tg== X-Gm-Message-State: AOAM530xsZjCOfPK0UCrNbV7ZyWVu4DmY4Mh8dfdSYt9Ysi46LjH+NzS d0xmKwuDMJ359O0QiAk1PVHBa41Rq+0= X-Google-Smtp-Source: ABdhPJxaH3RuRnVYqntcCDZKdS1ApRKn/aJNHerKsy6VIkrQo+Z63uSUl4FRzlMQ4DyzHnDIK2GYQw== X-Received: by 2002:a1c:7e82:: with SMTP id z124mr878483wmc.51.1615831760982; Mon, 15 Mar 2021 11:09:20 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id s11sm438851wme.22.2021.03.15.11.09.20 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:09:20 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 19:09:02 +0100 Message-Id: <20210315180904.8346-8-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-biostrings): Move from here... * gnu/packages/bioconductor.scm (r-biostrings): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6482d8e4c1..2b7d65023d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1686,6 +1686,33 @@ functions for parallel evaluation, tailored to use with Bioconductor objects.") (license (list license:gpl2+ license:gpl3+)))) +(define-public r-biostrings + (package + (name "r-biostrings") + (version "2.58.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Biostrings" version)) + (sha256 + (base32 + "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5")))) + (properties + `((upstream-name . "Biostrings"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-crayon" ,r-crayon) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/Biostrings") + (synopsis "String objects and algorithms for biological sequences") + (description + "This package provides memory efficient string containers, string +matching algorithms, and other utilities, for fast manipulation of large +biological sequences or sets of sequences.") + (license license:artistic2.0))) + (define-public r-category (package (name "r-category") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index af3fa36b19..415210085e 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-biostrings - (package - (name "r-biostrings") - (version "2.58.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Biostrings" version)) - (sha256 - (base32 - "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5")))) - (properties - `((upstream-name . "Biostrings"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-crayon" ,r-crayon) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/Biostrings") - (synopsis "String objects and algorithms for biological sequences") - (description - "This package provides memory efficient string containers, string -matching algorithms, and other utilities, for fast manipulation of large -biological sequences or sets of sequences.") - (license license:artistic2.0))) - (define-public r-rsamtools (package (name "r-rsamtools") From patchwork Mon Mar 15 18:09:03 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27827 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 B740827BC54; Mon, 15 Mar 2021 18:49:51 +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 D769427BC52 for ; Mon, 15 Mar 2021 18:49:50 +0000 (GMT) Received: from localhost ([::1]:41608 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLsHl-0003RP-TM for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 14:49:49 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37784) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrfK-0007O3-2E for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:53656) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrfJ-0003OW-Pv for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLrfJ-0004pU-LL for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 09/10] gnu: r-rsamtools: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 18:10:05 +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=B47171.161583177318456 (code B ref 47171); Mon, 15 Mar 2021 18:10:05 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 18:09:33 +0000 Received: from localhost ([127.0.0.1]:36959 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrem-0004nV-Vu for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:33 -0400 Received: from mail-wr1-f41.google.com ([209.85.221.41]:36145) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLreh-0004lc-4D for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:27 -0400 Received: by mail-wr1-f41.google.com with SMTP id y16so9183123wrw.3 for <47171@debbugs.gnu.org>; Mon, 15 Mar 2021 11:09:27 -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=D6JehzIlOTQUoVLz4lMMYKkMox6+bUZVl33d8isFOQo=; b=EzQCRZhnT2Pr+bpUZuoIZba209tAUVt35a+F68li4nP+R7TEzn4LheFkM7J1YDRwe4 Lr3Y4LG3750UUGfOVnJirMNMH76Yc/JtBWmgFHnpkIHIm+GaLpbva/XZwNmXORGeEQt0 yDhMIgksw3s4YUvCe+vkYZTYUDeg0Se74PJ5ubfojeqtGVAGunDAEX2S/kCBSeWB8C25 Licw+YlO4gtA65Kca7HfC8W+rB8uObBbVi31VxUunO9KZ7zoqDbjWkgrBAv9q71jWdjA 2CPPB31KORoixmA9weo33yTEPb08GayK/Ir+sUYDeIeLmvgQ55M2IPYc5BFyr6nNjwLL fBjw== 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=D6JehzIlOTQUoVLz4lMMYKkMox6+bUZVl33d8isFOQo=; b=JNhaLE/wx+wJUeQa7fmqx0uD0+1F+o4WhkK/YlsPgGTwelzWUoSSimyEeHlpNfaF1F cbxsuEgssPV+Uiqt4f8PMdWDay6QFZvdYFRvhA1TtnSyjhm9bEKMRmSnA9MBCsjWoQv7 hvK0djOs5Vva0uGgytIZH22u+5O3jEb9q8XMcK7+MR1lP0kgJ8Jrdh80TI6+LEtULh5W iynU7JvUmxjhKSbmDfkcXo+eGLm5MP/XnHqzEfbeNu+HmLftFN5kljg3sdbGXRFE5HgV RvuDSpUjlO6zw9G6kyxuGaJOZjKQPnfdCp1fbr/inqkAeyZb9M+d956sPevVPyofxHIB q5VQ== X-Gm-Message-State: AOAM531aN8aZgbNq6eJASfriRQjXUU+X0uTPyHXtMpivgZvfgJWTPFJS V+8m9qg7zRll67Qlh+yAe6ba60u2p2s= X-Google-Smtp-Source: ABdhPJyTvoTQhWO7SpRYejaZUg3/cj9psNeH4krBWYijn3HzcoIIY9Hid8wJIwAgmHsdlL9jo2t+Ug== X-Received: by 2002:adf:f44b:: with SMTP id f11mr860316wrp.345.1615831761634; Mon, 15 Mar 2021 11:09:21 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id s11sm438851wme.22.2021.03.15.11.09.21 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:09:21 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 19:09:03 +0100 Message-Id: <20210315180904.8346-9-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-rsamtools): Move from here... * gnu/packages/bioconductor.scm (r-rsamtools): ...to here. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 --------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2b7d65023d..c659bdd09e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2147,6 +2147,49 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-rsamtools + (package + (name "r-rsamtools") + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Rsamtools" version)) + (sha256 + (base32 + "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) + (properties + `((upstream-name . "Rsamtools"))) + (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))))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bitops" ,r-bitops) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rhtslib" ,r-rhtslib) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") + (synopsis "Interface to samtools, bcftools, and tabix") + (description + "This package provides an interface to the @code{samtools}, +@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence +Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed +tab-delimited (tabix) files.") + (license license:expat))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 415210085e..05805d1a8b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,49 +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-rsamtools - (package - (name "r-rsamtools") - (version "2.6.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Rsamtools" version)) - (sha256 - (base32 - "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) - (properties - `((upstream-name . "Rsamtools"))) - (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))))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bitops" ,r-bitops) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rhtslib" ,r-rhtslib) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") - (synopsis "Interface to samtools, bcftools, and tabix") - (description - "This package provides an interface to the @code{samtools}, -@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence -Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed -tab-delimited (tabix) files.") - (license license:expat))) - (define-public r-delayedarray (package (name "r-delayedarray") From patchwork Mon Mar 15 18:09:04 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27811 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 9C15F27BC54; Mon, 15 Mar 2021 18:39:25 +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 BE24027BC52 for ; Mon, 15 Mar 2021 18:39:24 +0000 (GMT) Received: from localhost ([::1]:32914 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLs7f-0004YP-Up for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 14:39:23 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37788) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrfK-0007OI-Ga for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:53657) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrfK-0003Od-8u for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLrfK-0004pb-4V for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 10/10] gnu: r-delayedarray: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 18:10:06 +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=B47171.161583177418462 (code B ref 47171); Mon, 15 Mar 2021 18:10:06 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 18:09:34 +0000 Received: from localhost ([127.0.0.1]:36961 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLren-0004nd-Fk for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:33 -0400 Received: from mail-wr1-f51.google.com ([209.85.221.51]:41093) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLreh-0004ld-Qd for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:28 -0400 Received: by mail-wr1-f51.google.com with SMTP id f12so9145506wrx.8 for <47171@debbugs.gnu.org>; Mon, 15 Mar 2021 11:09:27 -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=nfj2rilQWJptQ5L9ZCZZc0numSUsh61ELXk+rityVDE=; b=qIulp7vGIici0cwRbFA1PuxsRCQtZQMyUfwNMAaLTH2OHAbNLBq6MyS0tZbcI/XSvL B+iWzHunhXxfuCZtebN08Eh9y3Zu6s2Evo2TIio+MGfa2iaF2k3QsZsYg6r8VjCoxwEV BgmTIOjRqLt5Dvd1leaOGP//38VsKUPvwUs1MPeRgRpO5hIfgenA9sOSLg7FyUAzYMA8 qngiGaCrhXHrqOOZwBA4X1BLCaujE73M/rR8Z3vvnlXlUurhHRjwBuDfzS+99DQ3igEX O//roDE7O8JIkTnY6+984aikC68mH2Kl1aYVXssEVtSYoXVHevLynXmmQV4gF7rO3T2m BHAw== 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=nfj2rilQWJptQ5L9ZCZZc0numSUsh61ELXk+rityVDE=; b=ZgUClj7qjbYntbMNakIC03jc6DLBmv7SY2N5T9AQxepm40d8c0JQxNNARRn1NZqIH4 3RL8NEIK0Kj9wadnxQK3CTxpt8bc403Ot0S7N6DpMsA9lsB3n+KqJzcxTXM7+1EwqNGG 6/ynz4+yL9xMRKwz30Fd2sfXyIur1s/Ttyz5bhX4Ju12LbgqeM3SIvSdEu8rYTYjk7Wx zsFohYsGWN6Ls3uktFWXXkgWvi6KHqiD5AKevzg2mpm3iCjJNEZUzr17om3paxroC+I/ pGcwYj3BI2h8ybot/jBIg65kQUEaa+drffjhWqBOn5s4Bej2CH5S+AOLGwmtzZUFjLoW jgzw== X-Gm-Message-State: AOAM533yNLjwK8TRAl16y7Is7sBHob+/3QI2sDQwY+9+ZK0Rn4Q700UC juG+AEIZVWsZSEcEGeqO2+OZw+qUtwU= X-Google-Smtp-Source: ABdhPJzLVKteQKX0y3EsKcbBnyo/+WhH6G+1UiTvTm8aoPKUitbVAr5VfQMw+P8RuzCGEqDIrGkBFw== X-Received: by 2002:a5d:6406:: with SMTP id z6mr893328wru.264.1615831762282; Mon, 15 Mar 2021 11:09:22 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id s11sm438851wme.22.2021.03.15.11.09.21 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:09:21 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 19:09:04 +0100 Message-Id: <20210315180904.8346-10-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-delayedarray): Move from here... * gnu/packages/bioconductor.scm (r-delayedarray): ...to here. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 33 --------------------------------- 2 files changed, 33 insertions(+), 33 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c659bdd09e..9212165706 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1212,6 +1212,39 @@ data. In addition, provides numerous plotting functions for commonly used visualizations.") (license license:artistic2.0))) +(define-public r-delayedarray + (package + (name "r-delayedarray") + (version "0.16.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DelayedArray" version)) + (sha256 + (base32 + "09lpj951v1afxkrnjvnhzp4qgklq23ykdwlny7k1lyfcdy9q6wm0")))) + (properties + `((upstream-name . "DelayedArray"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-matrixgenerics" ,r-matrixgenerics))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/DelayedArray") + (synopsis "Delayed operations on array-like objects") + (description + "Wrapping an array-like object (typically an on-disk object) in a +@code{DelayedArray} object allows one to perform common array operations on it +without loading the object in memory. In order to reduce memory usage and +optimize performance, operations on the object are either delayed or executed +using a block processing mechanism. Note that this also works on in-memory +array-like objects like @code{DataFrame} objects (typically with Rle columns), +@code{Matrix} objects, and ordinary arrays and data frames.") + (license license:artistic2.0))) + (define-public r-bluster (package (name "r-bluster") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 05805d1a8b..bc342b5de8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,39 +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-delayedarray - (package - (name "r-delayedarray") - (version "0.16.2") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "DelayedArray" version)) - (sha256 - (base32 - "09lpj951v1afxkrnjvnhzp4qgklq23ykdwlny7k1lyfcdy9q6wm0")))) - (properties - `((upstream-name . "DelayedArray"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/DelayedArray") - (synopsis "Delayed operations on array-like objects") - (description - "Wrapping an array-like object (typically an on-disk object) in a -@code{DelayedArray} object allows one to perform common array operations on it -without loading the object in memory. In order to reduce memory usage and -optimize performance, operations on the object are either delayed or executed -using a block processing mechanism. Note that this also works on in-memory -array-like objects like @code{DataFrame} objects (typically with Rle columns), -@code{Matrix} objects, and ordinary arrays and data frames.") - (license license:artistic2.0))) - (define-public r-summarizedexperiment (package (name "r-summarizedexperiment")