From unknown Mon Aug 18 11:25:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 18:08:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 47171 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47171@debbugs.gnu.org Cc: zimoun , X-Debbugs-Original-To: guix-patches@gnu.org X-Debbugs-Original-Xcc: Received: via spool by submit@debbugs.gnu.org id=B.161583165618146 (code B ref -1); Mon, 15 Mar 2021 18:08:02 +0000 Received: (at submit) by debbugs.gnu.org; 15 Mar 2021 18:07:36 +0000 Received: from localhost ([127.0.0.1]:36928 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrcu-0004ib-6w for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:07:36 -0400 Received: from lists.gnu.org ([209.51.188.17]:43084) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrct-0004iV-8M for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:07:35 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:36884) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrct-0005Mu-1R for guix-patches@gnu.org; Mon, 15 Mar 2021 14:07:35 -0400 Received: from mail-wr1-x432.google.com ([2a00:1450:4864:20::432]:40323) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrco-0002QG-JM for guix-patches@gnu.org; Mon, 15 Mar 2021 14:07:34 -0400 Received: by mail-wr1-x432.google.com with SMTP id l11so9164941wrp.7 for ; Mon, 15 Mar 2021 11:07:30 -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=6HrJQngxNuiMpqot/4zbKQYcw7bvMh1MyWYT0eo9frE=; b=iuFHAUJwcLLMyxBK5d2TKjo1RXNpd7On8H41AC4MMPgcrgYXug7LwT+Tf3o2g3qh+s wIxngVFGplHIorDrT71t1BhUxVTidXXzRk6GDQCTfgu1tDfE44nE/oAIfmipLwwAfKGr 2GUEDN5WRcL+p2H1GAosK2aofu85nSHuqO7Q6jyTY5pabcfHzxoUHyWT19Hq28FVUh6+ oDwGb/Bs4odii0NYroewECnDfV6yADUK6JkPDgDOPCSk/mkgazsf1DiqSOYbus1SHQo0 m6zf6WiF1uvKYEiYLgnPB98/ljLx1F1rPCjwyHzC3qPFCSit+A8Il3i9wMNyWQCAo9kq gL3A== 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=6HrJQngxNuiMpqot/4zbKQYcw7bvMh1MyWYT0eo9frE=; b=MG0usJXq0vo9hNH0PP4Q5S4RITEBK6KMKSvHdjOUlC1TwhTXnBMX/7xaTxPnyrIdvD 33UKe/5+GBUQMR1+WKo/85yqsRracuKG77GpQKzd8CaFC4REvuyyuS1LMLD6sb99l+u1 ezT37pDGAWRuKj5sJyjOq3mWaniBKmdpOnEg4WpaXluCF/rYec6IKyE0+wzHQTPrhXhe FToKON7j5X0JnV527rKslVYkFmL5EwOJLXeu3M29Jx1UuHWCty57T9l+fm65d0LiRWBw 42jLuxfdrB45qa0AP9QHttutlxuLx2J3B2a91/k28ZRodOmwoj2RjNh1NItdE5TRJLuF ++9g== X-Gm-Message-State: AOAM530vX6+u8nOBpilLYzzqMxCau7yCYL9NoQu0P+rciBRKjIc6EAUy tKbVVvbeDawbehzrQbcztpAioSGBDJk= X-Google-Smtp-Source: ABdhPJySxu56C2Aani1aNPRG4vS/LRzkgMhjtpc/Tq4RNxXA4uxqtzdgE+3GQtCI1RgKidjT2W5X+g== X-Received: by 2002:a5d:538d:: with SMTP id d13mr915295wrv.92.1615831649059; Mon, 15 Mar 2021 11:07:29 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id p17sm336613wmq.47.2021.03.15.11.07.27 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:07:27 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 19:07:14 +0100 Message-Id: <20210315180714.8233-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::432; envelope-from=zimon.toutoune@gmail.com; helo=mail-wr1-x432.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) Hi, Janitor [1] patch set. It moves Bioconductor packages from (gnu packages bioinformatics) to (gnu packages bioconductor). Far to be complete; still 4 pacth set like this one are coming... 1: To transfer the Copyright, I use: git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r- Then, after the move, I run: ./pre-inst-env guix build r- --no-grafts ./pre-inst-env guix build r- --no-grafts --check and at the end of the series, I run: make as-derivation to check that "guix pull" is not broken; just in case. Last, I have not carefully checked the imported modules, so it could be possible to perhaps remove couple of #:use-module (gnu packages ) in gnu/packages/bioinformatics.scm. All the best, simon zimoun (10): gnu: r-limma: Move to (gnu packages bioconductor). gnu: r-xvector: Move to (gnu packages bioconductor). gnu: r-genomicranges: Move to (gnu packages bioconductor). gnu: r-biobase: Move to (gnu packages bioconductor). gnu: r-annotationdbi: Move to (gnu packages bioconductor). gnu: r-biomart: Move to (gnu packages bioconductor). gnu: r-biocparallel: Move to (gnu packages bioconductor). gnu: r-biostrings: Move to (gnu packages bioconductor). gnu: r-rsamtools: Move to (gnu packages bioconductor). gnu: r-delayedarray: Move to (gnu packages bioconductor). gnu/packages/bioconductor.scm | 305 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 305 -------------------------------- 2 files changed, 305 insertions(+), 305 deletions(-) base-commit: 266d55dc3080475544bf45e72359c9b9bbcecd53 -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 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 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 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 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 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 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 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 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 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 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 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 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 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 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 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 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 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 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 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 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#47171: closed (Re: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).) Message-ID: References: <87pn00m4ig.fsf@elephly.net> <20210315180714.8233-1-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 47171 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 47171@debbugs.gnu.org Date: Mon, 15 Mar 2021 22:34:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1615847642-12689-1" This is a multi-part message in MIME format... ------------=_1615847642-12689-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #47171: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioc= onductor). which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 47171@debbugs.gnu.org. --=20 47171: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D47171 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1615847642-12689-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 47171-done) by debbugs.gnu.org; 15 Mar 2021 22:33:23 +0000 Received: from localhost ([127.0.0.1]:37484 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLvm7-0003Hi-24 for submit@debbugs.gnu.org; Mon, 15 Mar 2021 18:33:23 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21122) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLvm5-0003Ha-Ff for 47171-done@debbugs.gnu.org; Mon, 15 Mar 2021 18:33:21 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1615847598; cv=none; d=zohomail.com; s=zohoarc; b=msrFBm/Wzr5zUmAMm+dLy3xYCCLF/KPgb0BD+zQiaAJ3aYLVbxHONGGGE2i3Bneq6rPuhTc+NKz29e1DBCYbTbztGCq7VlZmoc0xQVR6BtxWQnGaZ2oAgjCc6p7ga9Zu1Ya0WaPB7Zf8xWZ2jPxpocjQ9q83tEXzCl4i/BO8tuo= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1615847598; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=pbECEJLBdqD9XhG10xE2ynTtPjUv/p+/yngjW1USpV4=; b=j95NVzWOzG2xGCq7pU0axWi3PdJlspS6wPC+u1zFJ+uv9SNxaXjtbGcpo0xmG2qcRhgG/BVXlo80vg6g1lS8piVTzKrEr6oWqgUJxbz7l6zoBlbL7l+WSlip97noArZL4fFB8ySJjt5rG2VKxW6BpZykmpxwHc1mAc+InTCfmA8= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1615847598; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=pbECEJLBdqD9XhG10xE2ynTtPjUv/p+/yngjW1USpV4=; b=bDGmeSy3cD4/hlrK1srEoybgDurGRiGVq9sGmfqR5Bad+ulF40th8ZNJOExQjfHv GQU4aUwZsSlkG4puGMu3Hzu4ul5/fC+kX7ywUqJJwykB6TcEluYAetW+XUAoIHkjzFv mZOGHfE9/cT2hi4UyKol25gXrzwfv+DWcHRWewzo= Received: from localhost (p54ad469f.dip0.t-ipconnect.de [84.173.70.159]) by mx.zohomail.com with SMTPS id 1615847595161378.6259578667474; Mon, 15 Mar 2021 15:33:15 -0700 (PDT) References: <20210315180714.8233-1-zimon.toutoune@gmail.com> User-agent: mu4e 1.4.14; emacs 27.1 From: Ricardo Wurmus To: zimoun Subject: Re: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). In-reply-to: <20210315180714.8233-1-zimon.toutoune@gmail.com> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Mon, 15 Mar 2021 23:33:11 +0100 Message-ID: <87pn00m4ig.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 47171-done Cc: 47171-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi, > zimoun (10): > gnu: r-limma: Move to (gnu packages bioconductor). > gnu: r-xvector: Move to (gnu packages bioconductor). > gnu: r-genomicranges: Move to (gnu packages bioconductor). > gnu: r-biobase: Move to (gnu packages bioconductor). > gnu: r-annotationdbi: Move to (gnu packages bioconductor). > gnu: r-biomart: Move to (gnu packages bioconductor). > gnu: r-biocparallel: Move to (gnu packages bioconductor). > gnu: r-biostrings: Move to (gnu packages bioconductor). > gnu: r-rsamtools: Move to (gnu packages bioconductor). > gnu: r-delayedarray: Move to (gnu packages bioconductor). Thanks, I=E2=80=99ve pushed them all. --=20 Ricardo ------------=_1615847642-12689-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 15 Mar 2021 18:07:36 +0000 Received: from localhost ([127.0.0.1]:36928 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrcu-0004ib-6w for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:07:36 -0400 Received: from lists.gnu.org ([209.51.188.17]:43084) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrct-0004iV-8M for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:07:35 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:36884) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrct-0005Mu-1R for guix-patches@gnu.org; Mon, 15 Mar 2021 14:07:35 -0400 Received: from mail-wr1-x432.google.com ([2a00:1450:4864:20::432]:40323) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrco-0002QG-JM for guix-patches@gnu.org; Mon, 15 Mar 2021 14:07:34 -0400 Received: by mail-wr1-x432.google.com with SMTP id l11so9164941wrp.7 for ; Mon, 15 Mar 2021 11:07:30 -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=6HrJQngxNuiMpqot/4zbKQYcw7bvMh1MyWYT0eo9frE=; b=iuFHAUJwcLLMyxBK5d2TKjo1RXNpd7On8H41AC4MMPgcrgYXug7LwT+Tf3o2g3qh+s wIxngVFGplHIorDrT71t1BhUxVTidXXzRk6GDQCTfgu1tDfE44nE/oAIfmipLwwAfKGr 2GUEDN5WRcL+p2H1GAosK2aofu85nSHuqO7Q6jyTY5pabcfHzxoUHyWT19Hq28FVUh6+ oDwGb/Bs4odii0NYroewECnDfV6yADUK6JkPDgDOPCSk/mkgazsf1DiqSOYbus1SHQo0 m6zf6WiF1uvKYEiYLgnPB98/ljLx1F1rPCjwyHzC3qPFCSit+A8Il3i9wMNyWQCAo9kq gL3A== 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=6HrJQngxNuiMpqot/4zbKQYcw7bvMh1MyWYT0eo9frE=; b=MG0usJXq0vo9hNH0PP4Q5S4RITEBK6KMKSvHdjOUlC1TwhTXnBMX/7xaTxPnyrIdvD 33UKe/5+GBUQMR1+WKo/85yqsRracuKG77GpQKzd8CaFC4REvuyyuS1LMLD6sb99l+u1 ezT37pDGAWRuKj5sJyjOq3mWaniBKmdpOnEg4WpaXluCF/rYec6IKyE0+wzHQTPrhXhe FToKON7j5X0JnV527rKslVYkFmL5EwOJLXeu3M29Jx1UuHWCty57T9l+fm65d0LiRWBw 42jLuxfdrB45qa0AP9QHttutlxuLx2J3B2a91/k28ZRodOmwoj2RjNh1NItdE5TRJLuF ++9g== X-Gm-Message-State: AOAM530vX6+u8nOBpilLYzzqMxCau7yCYL9NoQu0P+rciBRKjIc6EAUy tKbVVvbeDawbehzrQbcztpAioSGBDJk= X-Google-Smtp-Source: ABdhPJySxu56C2Aani1aNPRG4vS/LRzkgMhjtpc/Tq4RNxXA4uxqtzdgE+3GQtCI1RgKidjT2W5X+g== X-Received: by 2002:a5d:538d:: with SMTP id d13mr915295wrv.92.1615831649059; Mon, 15 Mar 2021 11:07:29 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id p17sm336613wmq.47.2021.03.15.11.07.27 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:07:27 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Date: Mon, 15 Mar 2021 19:07:14 +0100 Message-Id: <20210315180714.8233-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 X-Debbugs-Cc: Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::432; envelope-from=zimon.toutoune@gmail.com; helo=mail-wr1-x432.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) Hi, Janitor [1] patch set. It moves Bioconductor packages from (gnu packages bioinformatics) to (gnu packages bioconductor). Far to be complete; still 4 pacth set like this one are coming... 1: To transfer the Copyright, I use: git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r- Then, after the move, I run: ./pre-inst-env guix build r- --no-grafts ./pre-inst-env guix build r- --no-grafts --check and at the end of the series, I run: make as-derivation to check that "guix pull" is not broken; just in case. Last, I have not carefully checked the imported modules, so it could be possible to perhaps remove couple of #:use-module (gnu packages ) in gnu/packages/bioinformatics.scm. All the best, simon zimoun (10): gnu: r-limma: Move to (gnu packages bioconductor). gnu: r-xvector: Move to (gnu packages bioconductor). gnu: r-genomicranges: Move to (gnu packages bioconductor). gnu: r-biobase: Move to (gnu packages bioconductor). gnu: r-annotationdbi: Move to (gnu packages bioconductor). gnu: r-biomart: Move to (gnu packages bioconductor). gnu: r-biocparallel: Move to (gnu packages bioconductor). gnu: r-biostrings: Move to (gnu packages bioconductor). gnu: r-rsamtools: Move to (gnu packages bioconductor). gnu: r-delayedarray: Move to (gnu packages bioconductor). gnu/packages/bioconductor.scm | 305 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 305 -------------------------------- 2 files changed, 305 insertions(+), 305 deletions(-) base-commit: 266d55dc3080475544bf45e72359c9b9bbcecd53 -- 2.30.1 ------------=_1615847642-12689-1-- From unknown Mon Aug 18 11:25:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Resent-From: Leo Famulari Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 23:57:02 +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, rekado@elephly.net, zimon.toutoune@gmail.com Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.161585259020914 (code B ref 47171); Mon, 15 Mar 2021 23:57:02 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 23:56:30 +0000 Received: from localhost ([127.0.0.1]:37554 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLx4X-0005RF-Hc for submit@debbugs.gnu.org; Mon, 15 Mar 2021 19:56:29 -0400 Received: from wout3-smtp.messagingengine.com ([64.147.123.19]:51167) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLx4V-0005R3-Ey for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 19:56:28 -0400 Received: from compute2.internal (compute2.nyi.internal [10.202.2.42]) by mailout.west.internal (Postfix) with ESMTP id 4AB5B27E3; Mon, 15 Mar 2021 19:56:21 -0400 (EDT) Received: from mailfrontend1 ([10.202.2.162]) by compute2.internal (MEProxy); Mon, 15 Mar 2021 19:56:21 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=famulari.name; h=date:from:to:subject:message-id:references:mime-version :content-type:content-transfer-encoding:in-reply-to; s=mesmtp; bh=RBurfWDgW+KQN+8ZHaDjL9ltK5dnyq7xVsJjQdc+ReI=; b=n6DNfNvDtILT TuMkGndwRFMKntnLGfaPP3ZYN7QauAcWLt6tuJub50J9hd8giEsZeNLnduYJJ/D1 MdLm165yDNLOePpIaC8LBmCM8gXD1Fs2znz5Gp8M/LeSSNVkHO9LYfJkuuCBj15a 1zhWNPpfav+n5vfF8CQ7giEkzeX5ZQM= DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=content-transfer-encoding:content-type :date:from:in-reply-to:message-id:mime-version:references :subject:to:x-me-proxy:x-me-proxy:x-me-sender:x-me-sender :x-sasl-enc; s=fm2; bh=RBurfWDgW+KQN+8ZHaDjL9ltK5dnyq7xVsJjQdc+R eI=; b=XmP4wwBbf0mF4ajCzMfTWLd+bJQSbIN0niMBtSEEvwsAOlrmVfd94qk+3 8mFHYDa7u9Ck9WrD5jBeh3uQ8hArbEcZMk30wzRBYgisX5TzoCBgN/5EXoXCtStO 5Ky1eDmTPnnmDG0+0KHNFq1k+/fwrHUPktXZIXewj4ymFMnlYhGLr93CRtZBYYC7 jlLoRd7Rasxbktfjl76VzwVWhlSajTkU15W1vNCZcyx/wtWN+oxvdyFoR1JzAQeP 4hgpS/DGxVAyY+DuRdvnGT/c0sxpq6WEu32N188e8hi+agglLDKlwqYCEH2gR8Xm Mm1ETAyz0xqjoIETA1ke8heJgUsAA== X-ME-Sender: X-ME-Proxy-Cause: gggruggvucftvghtrhhoucdtuddrgeduledrudefuddgudegucetufdoteggodetrfdotf fvucfrrhhofhhilhgvmecuhfgrshhtofgrihhlpdfqfgfvpdfurfetoffkrfgpnffqhgen uceurghilhhouhhtmecufedttdenucenucfjughrpeffhffvuffkfhggtggugfgjsehtke ertddttdejnecuhfhrohhmpefnvghoucfhrghmuhhlrghrihcuoehlvghosehfrghmuhhl rghrihdrnhgrmhgvqeenucggtffrrghtthgvrhhnpefgudffteettdekkeduhffgfefgie efgeeuieetudejffelieduueeifffgudfgudenucffohhmrghinhepghhnuhdrohhrghen ucfkphepuddttddruddurdduieelrdduudeknecuvehluhhsthgvrhfuihiivgeptdenuc frrghrrghmpehmrghilhhfrhhomheplhgvohesfhgrmhhulhgrrhhirdhnrghmvg X-ME-Proxy: Received: from localhost (pool-100-11-169-118.phlapa.fios.verizon.net [100.11.169.118]) by mail.messagingengine.com (Postfix) with ESMTPA id A462A24005A; Mon, 15 Mar 2021 19:56:20 -0400 (EDT) Date: Mon, 15 Mar 2021 19:56:18 -0400 From: Leo Famulari Message-ID: References: <20210315180714.8233-1-zimon.toutoune@gmail.com> <87pn00m4ig.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: 8bit In-Reply-To: <87pn00m4ig.fsf@elephly.net> X-Spam-Score: -0.7 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) On Mon, Mar 15, 2021 at 11:33:11PM +0100, Ricardo Wurmus wrote: > Hi, > > > zimoun (10): > > gnu: r-limma: Move to (gnu packages bioconductor). > > gnu: r-xvector: Move to (gnu packages bioconductor). > > gnu: r-genomicranges: Move to (gnu packages bioconductor). > > gnu: r-biobase: Move to (gnu packages bioconductor). > > gnu: r-annotationdbi: Move to (gnu packages bioconductor). > > gnu: r-biomart: Move to (gnu packages bioconductor). > > gnu: r-biocparallel: Move to (gnu packages bioconductor). > > gnu: r-biostrings: Move to (gnu packages bioconductor). > > gnu: r-rsamtools: Move to (gnu packages bioconductor). > > gnu: r-delayedarray: Move to (gnu packages bioconductor). > > Thanks, I’ve pushed them all. These commits caused `guix pull` to fail, as described here: https://git.savannah.gnu.org/cgit/guix.git/commit/?id=8ec0ca8faff62f19426f22aeb1bd59a8950ca05a I think we just needed to import the bioconductor module in the cran module, but I wasn't sure so I reverted them in order to fix the problem quickly. From unknown Mon Aug 18 11:25:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 16 Mar 2021 12:28:34 +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: Leo Famulari Cc: Ricardo Wurmus , 47171@debbugs.gnu.org Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.161589768615972 (code B ref 47171); Tue, 16 Mar 2021 12:28:34 +0000 Received: (at 47171) by debbugs.gnu.org; 16 Mar 2021 12:28:06 +0000 Received: from localhost ([127.0.0.1]:38401 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lM8na-00047g-GH for submit@debbugs.gnu.org; Tue, 16 Mar 2021 08:27:55 -0400 Received: from mail-qk1-f182.google.com ([209.85.222.182]:35905) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lM8n8-00042u-12 for 47171@debbugs.gnu.org; Tue, 16 Mar 2021 08:27:40 -0400 Received: by mail-qk1-f182.google.com with SMTP id n79so34936546qke.3 for <47171@debbugs.gnu.org>; Tue, 16 Mar 2021 05:27:18 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc:content-transfer-encoding; bh=Kgiq94fgC1A/rCZSPOmoTQ4jr4ZzyGHagGdoOa/GxHk=; b=IOdAGKhGk1XTlEp8r99ZAxecJmlpreHiv5wJ1NGvgu2wbV2Bi8aGfyLjgxV+bkl8n7 Yak2Nzk1A2yQMMHXld3f6LWrk5g0+2a2h/dH6sNbq6CYaeE4QFscamxpDNTqGk5SZ8S3 kY4iMXoiPUZ/2TtknflaPxqJc8KA8niZs4WCQEhDcyPtu1QNYeEQ6YRdJZ2qqVbr79Uq yH15mjuItzp/opJwS6hE2ZEt9d+MjKRGpI00hwtVRCfrITnqOhSq+0t74sxIXEA9Ir6c l/WFh0A+NExC/LII0RRR8b0AwkabaYEN1OcrIo+9z26jeeHvNXrQILNZptZ3Lz8r5jxD dPIg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc:content-transfer-encoding; bh=Kgiq94fgC1A/rCZSPOmoTQ4jr4ZzyGHagGdoOa/GxHk=; b=qUIDEgQ2UpViCv25n4V/QQIAs2A+iaOwzz2vgp+1ZzZE3dXJ21p66OMwt6Lun1fhD/ YSzpO7kBIiPszPY8GrtUkf7AgARSoDOOv4KOdClRfH6HSMQMNHi/BlMbpUCxtTfNUiqY 7hV2+zYJLYZOsxkPJU9JSB2Tc532mvMNdcrf+L9hB9UdlIVjsq1xPO5lcRpvrb0+G7/W XijGik4jbV0T3B3gipuFKDl3mrvOp+AQTBMV2JiG7szCsPrsO8smErxJf4d9s94KyYzY 8kzmOH5euorwijxp61CzcB9hVQf90fhtrKFGnkprRDB0mo2sOZLHPZpf6/e26kAM6X53 8YGw== X-Gm-Message-State: AOAM530M3iFPNl1+LdQD+W+qZSoMr0CjvGearW/w2/AYrDuhyJ0OkIdS LGV9YXdTK1ce5F5SPhovCwo2toMZDaiBurmEaRv+xIavtWY= X-Google-Smtp-Source: ABdhPJy8+RUh8hH/EQyUp+5qdJRtLupCTc3tSJPs1Z2AXX+5p0KpjD+kVpH4bT750FKIi+3e2hqVvYoHXZ3uK5gFs0g= X-Received: by 2002:a05:620a:91b:: with SMTP id v27mr30592397qkv.201.1615897632334; Tue, 16 Mar 2021 05:27:12 -0700 (PDT) MIME-Version: 1.0 References: <20210315180714.8233-1-zimon.toutoune@gmail.com> <87pn00m4ig.fsf@elephly.net> In-Reply-To: From: zimoun Date: Tue, 16 Mar 2021 13:27:01 +0100 Message-ID: Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi Leo, On Tue, 16 Mar 2021 at 00:56, Leo Famulari wrote: > On Mon, Mar 15, 2021 at 11:33:11PM +0100, Ricardo Wurmus wrote: > > > zimoun (10): > > > gnu: r-limma: Move to (gnu packages bioconductor). > > > gnu: r-xvector: Move to (gnu packages bioconductor). > > > gnu: r-genomicranges: Move to (gnu packages bioconductor). > > > gnu: r-biobase: Move to (gnu packages bioconductor). > > > gnu: r-annotationdbi: Move to (gnu packages bioconductor). > > > gnu: r-biomart: Move to (gnu packages bioconductor). > > > gnu: r-biocparallel: Move to (gnu packages bioconductor). > > > gnu: r-biostrings: Move to (gnu packages bioconductor). > > > gnu: r-rsamtools: Move to (gnu packages bioconductor). > > > gnu: r-delayedarray: Move to (gnu packages bioconductor). > > > > Thanks, I=E2=80=99ve pushed them all. > > These commits caused `guix pull` to fail, as described here: > > https://git.savannah.gnu.org/cgit/guix.git/commit/?id=3D8ec0ca8faff62f194= 26f22aeb1bd59a8950ca05a > > I think we just needed to import the bioconductor module in the cran > module, but I wasn't sure so I reverted them in order to fix the problem > quickly. Sorry for the annoyance. I did "make as-derivation" and it reports nothing. But indeed, "./pre-inst-env guix pull -p /tmp/new --url=3D$(pwd) --disable-authentication --branch=3Dtest" breaks. I do not know if I do something wrong (run make in a worktree for the branc= h). Well, thanks for the report and I confirm that adding the bioconductor import in cran fixes "guix pull". But in my memories, this import was adding circular dependency. Ricardo, WDYT? Cheers, simon From unknown Mon Aug 18 11:25:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 16 Mar 2021 13:21:02 +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: zimoun Cc: 47171@debbugs.gnu.org, Leo Famulari Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.161590083424615 (code B ref 47171); Tue, 16 Mar 2021 13:21:02 +0000 Received: (at 47171) by debbugs.gnu.org; 16 Mar 2021 13:20:34 +0000 Received: from localhost ([127.0.0.1]:38506 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lM9cg-0006Ox-25 for submit@debbugs.gnu.org; Tue, 16 Mar 2021 09:20:34 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21182) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lM9cd-0006On-LW for 47171@debbugs.gnu.org; Tue, 16 Mar 2021 09:20:32 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1615900827; cv=none; d=zohomail.com; s=zohoarc; b=E9SPcC2e9GnEswrYifa0FZSRgRq4+kI9xP/IlyOAvgm0I7+uaLNMv7oH4oAMQPu3puoCyluB7bvP1REwkJ8df9LhubfdH9I/4GiAZiF3VfR5guGj4GgPUt5ivOdk8F/9wRJlcgzSygooxXuYxUXBLo0Y6kDEgH3Zxf4zy4i9nJg= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1615900827; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=Ji4SHYxXg1pq5J/1BhrUdRPwMzidg1HH/0SDGZca/cs=; b=EwLdy+NyZxiS4G7CHyxU5Kvv2irnVIU1nr6evixbHMVCPIwNR3D8Kogr5M/gBAPi3mNZ6jgmCGCZlrpkZMLsz02Fhy2jFnC3myG1yMZDpZd0553Ccv7lZiJ7kEH2r+Grsha2YriYcKuT8RQwKN3mqp2HU/7x+yrcD88bpbCEYug= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1615900827; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=Ji4SHYxXg1pq5J/1BhrUdRPwMzidg1HH/0SDGZca/cs=; b=CeVSpd+kj6A/RZIwNcNZ8KMNJYc3utOuG9QGLinZhmVanQ9duDIYh7uv149n4Yes eovNiIoTK8RsK9JLBgrC5Q3DgL10pV1o5S5KAMMGzs+9GF3srAoRivf8lITc2lgmdnH 1CdEn98xBwgPpYB3Xvgr7rS0ZhCorhNH59hUJ9gY= Received: from localhost (p54ad4b49.dip0.t-ipconnect.de [84.173.75.73]) by mx.zohomail.com with SMTPS id 1615900823512470.34923203468657; Tue, 16 Mar 2021 06:20:23 -0700 (PDT) References: <20210315180714.8233-1-zimon.toutoune@gmail.com> <87pn00m4ig.fsf@elephly.net> User-agent: mu4e 1.4.14; emacs 27.1 From: Ricardo Wurmus In-reply-to: X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 16 Mar 2021 14:20:19 +0100 Message-ID: <87h7lbme0c.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) zimoun writes: > Well, thanks for the report and I confirm that adding the bioconductor > import in cran fixes "guix pull". But in my memories, this import > was adding circular dependency. Ricardo, WDYT? The point of having (gnu packages cran) and (gnu packages bioconductor) be separate modules is to separate independent packages. I=E2=80=99d like to keep it that way and not let (gnu packages cran) depend= on (gnu packages bioconductor). --=20 Ricardo From unknown Mon Aug 18 11:25:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 16 Mar 2021 13:32:01 +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: Ricardo Wurmus Cc: 47171@debbugs.gnu.org, Leo Famulari Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.161590147325662 (code B ref 47171); Tue, 16 Mar 2021 13:32:01 +0000 Received: (at 47171) by debbugs.gnu.org; 16 Mar 2021 13:31:13 +0000 Received: from localhost ([127.0.0.1]:38541 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lM9mz-0006fp-5H for submit@debbugs.gnu.org; Tue, 16 Mar 2021 09:31:13 -0400 Received: from mail-qt1-f174.google.com ([209.85.160.174]:41556) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lM9mx-0006fd-Na for 47171@debbugs.gnu.org; Tue, 16 Mar 2021 09:31:12 -0400 Received: by mail-qt1-f174.google.com with SMTP id x9so11590586qto.8 for <47171@debbugs.gnu.org>; Tue, 16 Mar 2021 06:31:11 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc:content-transfer-encoding; bh=5fZcVihvS91FNp4ryld1PVSXl37xOvsUNcowaZzxcXs=; b=E27W73XQcXN/bvguEzJ9n9vBCHmsKSera3OwfCxAxdYPUStER1w/Hv/oMw/wUdAnz0 7XxW0MjNdbMsE86K5mWuWpbwGscXOhi2KCLQCFUVmSfVWNNkZF+saPjmqg/09HCF3rF6 6vlrakQEoYTx98Csgt9hCD39ctg/wuJQdeEHeoGwlT1wh0JTLE+k4yZl1YfZ3/pSZqm4 36XCvPvJAUZjZZTXWtyKw8wX+LY2r+PgZPiSdnbeYsjksGVBj8hrpv+uctUtOzmvk+mL oOQ58tGgjVyUTi5xD9GYsFNKIQAD/6WCT582TxfBieUEgfqAUim4Q985TRsPMdeOPL86 7Ozg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc:content-transfer-encoding; bh=5fZcVihvS91FNp4ryld1PVSXl37xOvsUNcowaZzxcXs=; b=QsiCJy8HLlFLp7XV53d2wLzPBh923TAv1AQUMj3qtanQ7TMRAsXLCQ/4MJfgjtnem9 tBKpsFBWVHOVJvGYxwEbLc01ibjfQ2xafcedobkMCGAdpRwx9JP9y8PIln3G3B3Yl4TV dYq251LCx4+x9DxMaDdZ3jJ0QnWFB4sIDKp+m4NG7mdhr3FNVQwxkOt7gwjDWfJs72jD jyc/v4lYqb73yRUheKTenghD2C+ZB1YUwIVSyMfr7HI00R9arCgbeOYEWDZXzPfULfzF x2N7ulsxBvL5HYK7AumR9nowT65WJkOXmPpizflpj58/6nFxwjalPETCvukGZMdOjnc9 UTyA== X-Gm-Message-State: AOAM531hSGBiWQMSaF3Wwl0hZDBBY1A6/peJsQai+wymK7PZmiRIZoqm 5YEezvpzVqGC8wQPKmnCRF+qmIujm4PKRjz4ekj060CF8pQ= X-Google-Smtp-Source: ABdhPJxSZhHssLs2mhvTPq4QLvLS3pgdAM0J+/pRK1YHV6yYpwhSN6z3g5Hd1QY4LhiosAIn/9jAI6nNUES0Ms1YyDM= X-Received: by 2002:ac8:7241:: with SMTP id l1mr17203546qtp.217.1615901464753; Tue, 16 Mar 2021 06:31:04 -0700 (PDT) MIME-Version: 1.0 References: <20210315180714.8233-1-zimon.toutoune@gmail.com> <87pn00m4ig.fsf@elephly.net> <87h7lbme0c.fsf@elephly.net> In-Reply-To: <87h7lbme0c.fsf@elephly.net> From: zimoun Date: Tue, 16 Mar 2021 14:30:53 +0100 Message-ID: Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi, On Tue, 16 Mar 2021 at 14:20, Ricardo Wurmus wrote: > zimoun writes: > > > Well, thanks for the report and I confirm that adding the bioconductor > > import in cran fixes "guix pull". But in my memories, this import > > was adding circular dependency. Ricardo, WDYT? > > The point of having (gnu packages cran) and (gnu packages bioconductor) > be separate modules is to separate independent packages. > > I=E2=80=99d like to keep it that way and not let (gnu packages cran) depe= nd on > (gnu packages bioconductor). Therefore, the fix is to move the CRAN r-bisquerna and r-absfiltergsea packages from (gnu packages cran) to (gnu packages bioconductor) because they depend on the Bioconductor package r-biobase (and r-limma). Right? How do I proceed? Submit a patch moving these 2 packages and then another patch reverting the revert? Thanks, simon From unknown Mon Aug 18 11:25:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 16 Mar 2021 16:09:02 +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: zimoun Cc: 47171@debbugs.gnu.org, Leo Famulari Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.161591091710522 (code B ref 47171); Tue, 16 Mar 2021 16:09:02 +0000 Received: (at 47171) by debbugs.gnu.org; 16 Mar 2021 16:08:37 +0000 Received: from localhost ([127.0.0.1]:40848 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMCFJ-0002je-9J for submit@debbugs.gnu.org; Tue, 16 Mar 2021 12:08:37 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21151) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMCFH-0002jW-MM for 47171@debbugs.gnu.org; Tue, 16 Mar 2021 12:08:36 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1615910911; cv=none; d=zohomail.com; s=zohoarc; b=V2Pe4ZqIEgkpiBV5COF8o9fzQiwSVFT3wtMfjXi1ZYlYAPi1dINVcEHMQ0VxKvD5Gmh8Yu164ZOnvGZrg91erZxjaF24gFtwdhZtgCXQPjAPolfnIP8yJb/iVUFUt6iYgy1HoSva2zcQ5xLbAn2NeSevTU81R/mihK59FbE6RiY= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1615910911; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=0hahom0/bdBXGkNweN/2iaUKZ//DJfk5rZzQBRIjajc=; b=Uo5proEIXXpaOLmJPBVB6s9MIQejiMA2fVYuKw7FXb6KnmZZjPVM+iNaqSqQWZOB9sBbO88ihXx7QAsrKjWG4g6o93kcZL/Ixz9jnorDbG6DpZnElbMEQhj4pUNIgcgHVXpp7islBjPEUDbuJo97ZAzMeosh+myleBs9zXvBOPk= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1615910911; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=0hahom0/bdBXGkNweN/2iaUKZ//DJfk5rZzQBRIjajc=; b=J5XLAyQis57P4tH3ZYlfHVzh841Qq5WjRSH0G7pU13MiH7RCnZdRHUmkwHDNRZdz avxm3XV8SIF7L8+GgOrkspZjeKwD4e30g+/IwUWWi433WiAKeWiYMTxGuH/6CMMvvFO 6kCGjTDOV/DySogD4JIKj0xN+AeeRZLo/gEWPXFA= Received: from localhost (p54ad4b49.dip0.t-ipconnect.de [84.173.75.73]) by mx.zohomail.com with SMTPS id 1615910905431876.9106914571731; Tue, 16 Mar 2021 09:08:25 -0700 (PDT) References: <20210315180714.8233-1-zimon.toutoune@gmail.com> <87pn00m4ig.fsf@elephly.net> <87h7lbme0c.fsf@elephly.net> User-agent: mu4e 1.4.14; emacs 27.1 From: Ricardo Wurmus In-reply-to: X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 16 Mar 2021 17:08:22 +0100 Message-ID: <87eegfm689.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) zimoun writes: > Hi, > > On Tue, 16 Mar 2021 at 14:20, Ricardo Wurmus wrote: >> zimoun writes: >> >> > Well, thanks for the report and I confirm that adding the bioconductor >> > import in cran fixes "guix pull". But in my memories, this import >> > was adding circular dependency. Ricardo, WDYT? >> >> The point of having (gnu packages cran) and (gnu packages bioconductor) >> be separate modules is to separate independent packages. >> >> I=E2=80=99d like to keep it that way and not let (gnu packages cran) dep= end on >> (gnu packages bioconductor). > > Therefore, the fix is to move the CRAN r-bisquerna and r-absfiltergsea > packages from (gnu packages cran) to (gnu packages bioconductor) > because they depend on the Bioconductor package r-biobase (and > r-limma). Right? Correct. We don=E2=80=99t want any CRAN packages to depend on Bioconductor things. When this is unavoidable, though, we move them to (gnu packages bioconductor) with a comment. > How do I proceed? Submit a patch moving these 2 packages and then > another patch reverting the revert? Sounds good. (You could do this all in the same issue.) --=20 Ricardo From unknown Mon Aug 18 11:25:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 16 Mar 2021 16:37:02 +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: Ricardo Wurmus Cc: 47171@debbugs.gnu.org, Leo Famulari Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.161591258413111 (code B ref 47171); Tue, 16 Mar 2021 16:37:02 +0000 Received: (at 47171) by debbugs.gnu.org; 16 Mar 2021 16:36:24 +0000 Received: from localhost ([127.0.0.1]:40879 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMCgB-0003PP-Oo for submit@debbugs.gnu.org; Tue, 16 Mar 2021 12:36:24 -0400 Received: from mail-qk1-f180.google.com ([209.85.222.180]:46086) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMCg9-0003P9-MH for 47171@debbugs.gnu.org; Tue, 16 Mar 2021 12:36:23 -0400 Received: by mail-qk1-f180.google.com with SMTP id a9so35815027qkn.13 for <47171@debbugs.gnu.org>; Tue, 16 Mar 2021 09:36:21 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc:content-transfer-encoding; bh=x4RKLPdIbTVZdJ4RVS9EmPNDts0VGFcZoi7jIZKvLgE=; b=Yi27XlV6Mes+EACclz5wtzzHNgtI4mdu763j3Xl5mlUxTdsUy10Od4VBE7ecY84CTa lp0VD3SI6QR5kwD4xsAP+eD30j/XQ492QwTvMFXmDPeXWwC+Rb5vg+oPgWUPnEyB7Yni rJAvciczw15lDYssZLsGoQ0cwp3KteMAxROKY+uhrB+5TdDI4qFrIdnvzFAbrEoPYElI j5NhRLpozTWGQINHYl3N9Zf8DNqwGBd3SJdd/4nhD/Yc6Zd3243ZGWFla99ZhllLIFiF M6GBi7M9gUk/K8ZB7pytSm3NCP8wmImJpw9ZVA4dGDvFwuCYugJBZ5T5dbltit1OgqeJ Uv3g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc:content-transfer-encoding; bh=x4RKLPdIbTVZdJ4RVS9EmPNDts0VGFcZoi7jIZKvLgE=; b=LDcqX07o5bi+LAY7BVUEmlXMR3xUrUQtsyVOdRuuyTEXdfsR4KfFxbmvbAoqWwAbfH LO6laDjrfCfeQ5qmugd78trhL3YIMP5gq0MSdcnxSWzhYKOCjfyoxuni5SyxkmyyUk1t taKZ7hZWKIdl4myqVG9S50GMCaick/K4slV41LlNdmFsd5VMqkMmse4SztpD34/S+m++ c6puJaw0jgeUtud6Cxd3FOOOxXl82mnWLCIRjXug3WEYbNX5rRQvnhDZHNPapJGmuLPS BlZ7RYs9CW3SfcMS4E+EmEJpz/f2QgbSMoDAAPnVbcvFAh3wUdVdCjzP/qJr2+nh6nck jZtg== X-Gm-Message-State: AOAM5335D2wcKIHOFcXH2JFjRhrHRn6KDA8DMsOtANjB3gEa1nyfxh9a FXqNngizM71v7f4EeTr40XLR0GjeVwqiiHLKLvWq2qfe X-Google-Smtp-Source: ABdhPJxt/aJBvTLYYEJW+BNDN3TCTzKXj6y9Yu0dogwbVFEDnUvpqJ3Vke5GdRmYBDW/GM0N2Em64t+N/MVpwgqLL0E= X-Received: by 2002:a37:b807:: with SMTP id i7mr478496qkf.126.1615912576094; Tue, 16 Mar 2021 09:36:16 -0700 (PDT) MIME-Version: 1.0 References: <20210315180714.8233-1-zimon.toutoune@gmail.com> <87pn00m4ig.fsf@elephly.net> <87h7lbme0c.fsf@elephly.net> <87eegfm689.fsf@elephly.net> In-Reply-To: <87eegfm689.fsf@elephly.net> From: zimoun Date: Tue, 16 Mar 2021 17:36:04 +0100 Message-ID: Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) On Tue, 16 Mar 2021 at 17:08, Ricardo Wurmus wrote: > > Therefore, the fix is to move the CRAN r-bisquerna and r-absfiltergsea > > packages from (gnu packages cran) to (gnu packages bioconductor) > > because they depend on the Bioconductor package r-biobase (and > > r-limma). Right? > > Correct. We don=E2=80=99t want any CRAN packages to depend on Bioconduct= or > things. When this is unavoidable, though, we move them to (gnu packages > bioconductor) with a comment. Ok. > > How do I proceed? Submit a patch moving these 2 packages and then > > another patch reverting the revert? > > Sounds good. (You could do this all in the same issue.) By the same issue, do you mean the same guix-patches number? Or the same commit? Cheers, simon From unknown Mon Aug 18 11:25:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 16 Mar 2021 22:05:01 +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: zimoun Cc: 47171@debbugs.gnu.org, Leo Famulari Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.161593228319666 (code B ref 47171); Tue, 16 Mar 2021 22:05:01 +0000 Received: (at 47171) by debbugs.gnu.org; 16 Mar 2021 22:04:43 +0000 Received: from localhost ([127.0.0.1]:41396 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMHnu-000578-Un for submit@debbugs.gnu.org; Tue, 16 Mar 2021 18:04:43 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21121) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMHnr-00056y-9V for 47171@debbugs.gnu.org; Tue, 16 Mar 2021 18:04:41 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1615932276; cv=none; d=zohomail.com; s=zohoarc; b=PxoOLn/3Mv8ntJXjQwfY5QrEQdsWFjYzdu38UPLJbzirrEM0lmBSTSNNQolMQvHHh86ofnigSIqqZe8AviwXCoI8/mzOvVS/b+l+Mr5a7SKUMj+NT0GGSWU+bA+rdlAavxVhJcQNh79+C82WBPag14w2qTyo4mEN9b1vzaZVlJQ= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1615932276; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=9Vs+MuRrsB3gOWftelWT7/4HEEbDlQqF2VSY7ncW8rM=; b=Jljoz6vBnzKD3ZByyUpMP7JLECCo5rmotFbSy2KyaKApxaIGhljtMxrRtVpkhIeKiS1j7Qcl7hGIahiuaNY5Iiv7bs1XbjX2CeGs0hV0OoijT9g9PwWsykANYcv+X4AGnXwElJxKPmehMl4F7Me6sY5tDg6/mPkasU8Yn2ZvbOs= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1615932276; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type; bh=9Vs+MuRrsB3gOWftelWT7/4HEEbDlQqF2VSY7ncW8rM=; b=hDb3IplDfFX8b2jb1BHMnODaqo6QQoL41On0MA2fNIK+47s03HDpFykQvV3AinPe ylWL+tqAj9J3CU+wi1FTi/F71cQi8c+y6iYNKNtp5GohWgCShdd+eclB6P8syVAEZfw PN/K/IlbrJkjyYSWEMjMK0S366LVOhOK7bMQRAgo= Received: from localhost (p54ad4b49.dip0.t-ipconnect.de [84.173.75.73]) by mx.zohomail.com with SMTPS id 1615932274253241.22781729035182; Tue, 16 Mar 2021 15:04:34 -0700 (PDT) References: <20210315180714.8233-1-zimon.toutoune@gmail.com> <87pn00m4ig.fsf@elephly.net> <87h7lbme0c.fsf@elephly.net> <87eegfm689.fsf@elephly.net> User-agent: mu4e 1.4.14; emacs 27.1 From: Ricardo Wurmus In-reply-to: X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 16 Mar 2021 23:04:31 +0100 Message-ID: <871rcen4b4.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) zimoun writes: >> > How do I proceed? Submit a patch moving these 2 packages and then >> > another patch reverting the revert? >> >> Sounds good. (You could do this all in the same issue.) > > By the same issue, do you mean the same guix-patches number? Or the > same commit? I meant the same guix-patches issue number; separate commits. -- Ricardo From unknown Mon Aug 18 11:25:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH v2 1/3] gnu: r-bisquerna: 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: Wed, 17 Mar 2021 20:15:02 +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: rekado@elephly.net, zimoun Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.16160120741671 (code B ref 47171); Wed, 17 Mar 2021 20:15:02 +0000 Received: (at 47171) by debbugs.gnu.org; 17 Mar 2021 20:14:34 +0000 Received: from localhost ([127.0.0.1]:44027 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMcYr-0000Qo-LY for submit@debbugs.gnu.org; Wed, 17 Mar 2021 16:14:34 -0400 Received: from mail-wr1-f41.google.com ([209.85.221.41]:35377) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMcYo-0000QW-As for 47171@debbugs.gnu.org; Wed, 17 Mar 2021 16:14:32 -0400 Received: by mail-wr1-f41.google.com with SMTP id j18so3135322wra.2 for <47171@debbugs.gnu.org>; Wed, 17 Mar 2021 13:14:30 -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=qXcXIgCUVWcfSnp+ZfNbzfN7WDA/2Tz+jyugGwYrrpI=; b=QA7jxdXcqk1gfT2BzPwwsxg8VG7hCfiq6RAnnQv646oNyITgEXHgJHw+QjFSd4jQek IH+bUaGA0gSmNf8NPL3QMfg73xd7Vl2n9EcTU63i4NUN1t617plwTJcDKg+HAdd7lwTb 1RYd9IBPP5pX/ixOhH7Zu1Cm+AfMsi1M53wFrN2dUY4LfxaQ1Bn6HvM7tLjdlbw0C8Nt JftEeHyxZ3kcvjUzLmTbarT5PzJcwfSzc6eYOM8iDlJ8ImrtqTWA0w/QKrXSvlZjRsa6 ufzta9fNDgncVX9w7zYdyBo21hSz3RFNfZ85Dxy7fmh/DoL2BgpjB28ldU2yUMZqQvPZ cxDQ== 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=qXcXIgCUVWcfSnp+ZfNbzfN7WDA/2Tz+jyugGwYrrpI=; b=JTZofFFKwXqHm36+jMKnBErMvFrxiD5+QMhEIAXF+3kBJhLL/rhDduH4TZ1QyTwZSv kAYmXc7nsgr8huWuneKTNyh/YiNgF3waMMh5Gq4KBe2poIFdnID4r+z49D36jPM+wmhv EdWb967DDrl72B+mBEwosUH/yPRiEyrjGq2vLedrK/iZ1MNrCmlWVb86mYFgiME1/Ojh DBx/mZWX1+eF5msn4cdJqk4ndhZV28F+aegww4eZ2LMaRhxnV5nBeMNerrqvDJdQdtfj eKXhHyJsF7VJcILQy1RvF9YvB+nK/rspi/+9kzlzMjyKnekiAhOPxueqqeP3cuiOyQ8M +Qpg== X-Gm-Message-State: AOAM5318DSLBzJj78BZ00xe6ZpyBNXHmkmFoLUISMaMxGEDEunIvcD/A qbZUYljpk0u6XjQdQ9PtqUVP60Sh48U= X-Google-Smtp-Source: ABdhPJw917FWLBlX9KH+ZPBqg1l/NQxBn7848mF7hbRncMId0jqPhsIUWjatt5jhmqNlMlj28MY7Aw== X-Received: by 2002:a5d:528f:: with SMTP id c15mr6105856wrv.142.1616012064440; Wed, 17 Mar 2021 13:14:24 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id o2sm3424007wmc.23.2021.03.17.13.14.23 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 17 Mar 2021 13:14:24 -0700 (PDT) From: zimoun Date: Wed, 17 Mar 2021 21:14:12 +0100 Message-Id: <20210317201414.10811-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/cran.scm (r-bisquerna): Move this variable from here... * gnu/packages/bioconductor.scm (r-bisquerna): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/cran.scm | 25 ------------------------- 2 files changed, 26 insertions(+), 25 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d611f3a491..b5ac2750f3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1294,6 +1294,32 @@ 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-biobase from Bioconductor. +(define-public r-bisquerna + (package + (name "r-bisquerna") + (version "1.0.4") + (source (origin + (method url-fetch) + (uri (cran-uri "BisqueRNA" version)) + (sha256 + (base32 + "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2")))) + (properties `((upstream-name . "BisqueRNA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-limsolve" ,r-limsolve))) + (home-page "https://www.biorxiv.org/content/10.1101/669911v1") + (synopsis "Decomposition of bulk expression with single-cell sequencing") + (description "This package provides tools to accurately estimate cell type +abundances from heterogeneous bulk expression. A reference-based method +utilizes single-cell information to generate a signature matrix and +transformation of bulk expression for accurate regression based estimates. +A marker-based method utilizes known cell-specific marker genes to measure +relative abundances across samples.") + (license license:gpl3))) + ;; 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/cran.scm b/gnu/packages/cran.scm index 5617383cbc..93fe44c25c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2838,31 +2838,6 @@ where the bound function accepts additional arguments.") bindings that call a C++ function.") (license license:expat))) -(define-public r-bisquerna - (package - (name "r-bisquerna") - (version "1.0.4") - (source (origin - (method url-fetch) - (uri (cran-uri "BisqueRNA" version)) - (sha256 - (base32 - "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2")))) - (properties `((upstream-name . "BisqueRNA"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limsolve" ,r-limsolve))) - (home-page "https://www.biorxiv.org/content/10.1101/669911v1") - (synopsis "Decomposition of bulk expression with single-cell sequencing") - (description "This package provides tools to accurately estimate cell type -abundances from heterogeneous bulk expression. A reference-based method -utilizes single-cell information to generate a signature matrix and -transformation of bulk expression for accurate regression based estimates. -A marker-based method utilizes known cell-specific marker genes to measure -relative abundances across samples.") - (license license:gpl3))) - (define-public r-auc (package (name "r-auc") base-commit: d79d63e7829d53f6a501d8df7e264ff70033abca -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH v2 2/3] gnu: r-absfiltergsea: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 17 Mar 2021 20:15:02 +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: rekado@elephly.net, zimoun Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.16160120761686 (code B ref 47171); Wed, 17 Mar 2021 20:15:02 +0000 Received: (at 47171) by debbugs.gnu.org; 17 Mar 2021 20:14:36 +0000 Received: from localhost ([127.0.0.1]:44029 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMcYu-0000R7-7S for submit@debbugs.gnu.org; Wed, 17 Mar 2021 16:14:36 -0400 Received: from mail-wr1-f45.google.com ([209.85.221.45]:38546) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMcYo-0000QX-Df for 47171@debbugs.gnu.org; Wed, 17 Mar 2021 16:14:33 -0400 Received: by mail-wr1-f45.google.com with SMTP id z2so3131558wrl.5 for <47171@debbugs.gnu.org>; Wed, 17 Mar 2021 13:14:30 -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=/pBMFD5KuZJMFrFI1oilyVUXnxa0ikrUADOAoc4vZoI=; b=WcrK2YhMKCFrO82OiqOfAkEjhKL1pT7z7kwLs3j6itKnei1Y9rR0dkuLG93WaKVZ+g 356W4EQ1SeTkA/czE92SH/Sc3LM5HfOxPcVH2CAO40NWX9OUlEY06r217mDjM6GbgZ07 Cg/HMRACYHrjaRff0mqZe0bxREX5CVTwrkZytP0FTg5VvbO3P3YWCaHqb+1YMYxQyUMr 7PA3Y+dB8R9tq0kUH3oPjB7Gj6GArlHROP5S2+iQ9b3pStLueI9aRMxsiz5dbQ+6zVYb 8NAaLdF+JJ5DO2cYhhUmIsHiwE5mC3awMBRZAvhPC9OBnMQstlTEGb0vYskdcY4a5M8K YJSw== 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=/pBMFD5KuZJMFrFI1oilyVUXnxa0ikrUADOAoc4vZoI=; b=RJl9d94xomvMpwsV1/Gb6rRc1iPs1mnYgRs+v8CQ6NqzHJrR3GKJ2MYcIzoJQ5Sw81 r5WSY2yqebl7lWOtsrFUn9vChE32zPx9sZBtnDmXB2ZuHe7UxO08SIzwZMVyez004BWO HsaUc5OvcrspcyT5m9A1aKAN0UAkIwWKDCxipXMBirlrfF2ST0UguLNSQyDagVoEIMK7 i9aoBcBSHFbsyUo5k0W9t4AkV4B2MzyVRFIzSK4ICwWnQU31TQAYBpLKsiMbWhCJ2jAT yACPLIwFFxEtOQ8Z0qITZJlkG+WeCGTSKdqgYKWqsqTt+TsOYdxxPDB6R5S/Owe41SNH P7OA== X-Gm-Message-State: AOAM530kRV38Levpk7faNz0uVpI672ZLFXkOXwyr+lB4eF5egKpmspcB j86xyzkKXdHodSbyQsqXBgO3PM7CAso= X-Google-Smtp-Source: ABdhPJyRtL190/DEWscQgFGRhfFiYdLA0AH46i+DSDEtdefF2f9bLL0DKZbQbJxmGPijYGhe/YUXwg== X-Received: by 2002:a5d:42d2:: with SMTP id t18mr6075685wrr.258.1616012064907; Wed, 17 Mar 2021 13:14:24 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id o2sm3424007wmc.23.2021.03.17.13.14.24 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 17 Mar 2021 13:14:24 -0700 (PDT) From: zimoun Date: Wed, 17 Mar 2021 21:14:13 +0100 Message-Id: <20210317201414.10811-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210317201414.10811-1-zimon.toutoune@gmail.com> References: <20210317201414.10811-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/cran.scm (r-absfiltergsea): Move this variable from here... * gnu/packages/bioconductor.scm (r-absfiltergsea): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/cran.scm | 27 --------------------------- 2 files changed, 28 insertions(+), 27 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b5ac2750f3..6530a31fb5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1294,6 +1294,34 @@ 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-biobase and r-limma from Bioconductor. +(define-public r-absfiltergsea + (package + (name "r-absfiltergsea") + (version "1.5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "AbsFilterGSEA" version)) + (sha256 + (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) + (properties `((upstream-name . "AbsFilterGSEA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-deseq" ,r-deseq) + ("r-limma" ,r-limma) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") + (synopsis "Improved false positive control of gene-permuting with absolute filtering") + (description + "This package provides a function that performs gene-permuting of a gene-set +enrichment analysis (GSEA) calculation with or without the absolute filtering. + Without filtering, users can perform (original) two-tailed or one-tailed +absolute GSEA.") + (license license:gpl2))) + ;; This is a CRAN package, but it depends on r-biobase from Bioconductor. (define-public r-bisquerna (package diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 93fe44c25c..54d895e9fe 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26591,33 +26591,6 @@ include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.") (license license:gpl2+))) -(define-public r-absfiltergsea - (package - (name "r-absfiltergsea") - (version "1.5.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "AbsFilterGSEA" version)) - (sha256 - (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) - (properties `((upstream-name . "AbsFilterGSEA"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq" ,r-deseq) - ("r-limma" ,r-limma) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) - (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") - (synopsis "Improved false positive control of gene-permuting with absolute filtering") - (description - "This package provides a function that performs gene-permuting of a gene-set -enrichment analysis (GSEA) calculation with or without the absolute filtering. - Without filtering, users can perform (original) two-tailed or one-tailed -absolute GSEA.") - (license license:gpl2))) - (define-public r-calculus (package (name "r-calculus") -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH v2 3/3] Revert "Revert some commits that caused `guix pull` to fail." Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 17 Mar 2021 20:15:03 +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: rekado@elephly.net, zimoun Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.16160120781695 (code B ref 47171); Wed, 17 Mar 2021 20:15:03 +0000 Received: (at 47171) by debbugs.gnu.org; 17 Mar 2021 20:14:38 +0000 Received: from localhost ([127.0.0.1]:44031 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMcYu-0000R9-It for submit@debbugs.gnu.org; Wed, 17 Mar 2021 16:14:37 -0400 Received: from mail-wm1-f54.google.com ([209.85.128.54]:54124) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMcYp-0000QZ-DU for 47171@debbugs.gnu.org; Wed, 17 Mar 2021 16:14:34 -0400 Received: by mail-wm1-f54.google.com with SMTP id g20so2216360wmk.3 for <47171@debbugs.gnu.org>; Wed, 17 Mar 2021 13:14:31 -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=+W43wBdEv369JLdvXVDoczIWKRyjSve68Ud1660j9eI=; b=trnAkM8WgHoxtZ+iCLL9SLqjnehseu+bgj3esvPhJvq8MAMiTBJYF80FpMe9t+hilZ vEf7KZdi5UfQD6iIFCmp+nosWNGUK8eOO/VIRHPj6fQrqUMA/Os28qTQB/UPuyi/nX/w GB/Egz5AQ6GAAkzG+qGDGYxn3SVQOD8S4HQU+jJinzgFLYch5qHtQhwx4km5gwQlLiGD M+vzxTjb5vzBWdL0EaZiDYLTNStvgAFKlQwoYMKTx7AapupMMYYpVIk/iIrArHZ8sSYu UBUSGbMAHW1UsKNeJ9QXMQgp+I840I1pVAtrNyQ4O/dBShFjuC465hmB20Z9OrbQ6ahp xW6A== 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=+W43wBdEv369JLdvXVDoczIWKRyjSve68Ud1660j9eI=; b=CgfDXgXbJTr+wnCy/cWnN+qKiJZiZXNQlIqz5ZplHG5aeoo/qxovQUzSsXO3lW8XX6 LBR16cygUiMTaNMSHK3xBnjtaywC2tfmlu8fHeHnHLORGu2ssTVKEFO4t/qXW4w6uCI7 gHj1gpCfcnJpaUKZfT7a7a3eNo9CqRktPu/PYhR6nwQ7WpIsAlLomP/hubbODR8Tlwl0 wvmDEBww4f1R2IRlGspjztv2b8NklR6TjFZw9+sg67WELvAonqWYgOCcKARgELWnhzB/ ooUUgzjUordUtQe0K6mRrhNOPpHou/S6tUV7Qqif8/7vo+eR57Yy1fMUWhbdRLMGs4n4 FRUg== X-Gm-Message-State: AOAM531oPBnpdnMX8Ps+VyZksv056JMUSMSWxCi8uf2I4zOzVt0Tp0qt fllrjEXOue4CC/ONG5CLAwIx2llfNFo= X-Google-Smtp-Source: ABdhPJzNaqug6mhleoEWQMCm7BGEDZ1vmp1dkslSjrQkiEbWAs10bP3K02CGWC3oi0XYYrwf37nILA== X-Received: by 2002:a05:600c:210a:: with SMTP id u10mr455086wml.147.1616012065433; Wed, 17 Mar 2021 13:14:25 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id o2sm3424007wmc.23.2021.03.17.13.14.24 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 17 Mar 2021 13:14:25 -0700 (PDT) From: zimoun Date: Wed, 17 Mar 2021 21:14:14 +0100 Message-Id: <20210317201414.10811-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210317201414.10811-1-zimon.toutoune@gmail.com> References: <20210317201414.10811-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) This reverts commit 8ec0ca8faff62f19426f22aeb1bd59a8950ca05a. --- gnu/packages/bioconductor.scm | 333 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 305 ----------------------------- 2 files changed, 333 insertions(+), 305 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6530a31fb5..d9e938db5c 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") @@ -1592,6 +1625,35 @@ 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") @@ -1624,6 +1686,148 @@ 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-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") + (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) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-reproducible + (lambda _ + ;; Remove generated documentation. + (for-each delete-file + '("inst/doc/BiocParallel_BatchtoolsParam.pdf" + "inst/doc/Introduction_To_BiocParallel.pdf" + "inst/doc/Errors_Logs_And_Debugging.pdf" + "inst/doc/BiocParallel_BatchtoolsParam.R" + "inst/doc/Introduction_To_BiocParallel.R" + "inst/doc/Errors_Logs_And_Debugging.R")) + + ;; Remove time-dependent macro + (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw" + "inst/doc/Introduction_To_BiocParallel.Rnw" + "inst/doc/Errors_Logs_And_Debugging.Rnw" + "vignettes/BiocParallel_BatchtoolsParam.Rnw" + "vignettes/Introduction_To_BiocParallel.Rnw" + "vignettes/Errors_Logs_And_Debugging.Rnw") + (("\\today") "later")) + + ;; Initialize the random number generator seed when building. + (substitute* "R/internal_rng_stream.R" + (("\"L'Ecuyer-CMRG\"\\)" m) + (string-append + m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) + (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") + (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") @@ -1824,6 +2028,37 @@ 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") @@ -1904,6 +2139,25 @@ 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") @@ -2008,6 +2262,49 @@ 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") @@ -2143,6 +2440,42 @@ 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 eb466868d1..51301a9603 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7695,311 +7695,6 @@ 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") - (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") - (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") - (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") - (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") - (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") - (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") - (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") - (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") - (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") -- 2.30.1 From unknown Mon Aug 18 11:25:20 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 17 Mar 2021 20:20:01 +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: Ricardo Wurmus Cc: 47171@debbugs.gnu.org, Leo Famulari Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.16160123792196 (code B ref 47171); Wed, 17 Mar 2021 20:20:01 +0000 Received: (at 47171) by debbugs.gnu.org; 17 Mar 2021 20:19:39 +0000 Received: from localhost ([127.0.0.1]:44041 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMcdn-0000ZL-H7 for submit@debbugs.gnu.org; Wed, 17 Mar 2021 16:19:39 -0400 Received: from mail-wr1-f43.google.com ([209.85.221.43]:36669) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMcdl-0000Z6-5u for 47171@debbugs.gnu.org; Wed, 17 Mar 2021 16:19:37 -0400 Received: by mail-wr1-f43.google.com with SMTP id k8so3147274wrc.3 for <47171@debbugs.gnu.org>; Wed, 17 Mar 2021 13:19:37 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:in-reply-to:references:date:message-id :mime-version; bh=ZWCazQs37WebuPokYkhWzePDXYjMykgpDOO9WEPPKdg=; b=vDnFBor641Y1YdKx8HqkzITxYZHW7wF35XxRxCYdTOZRzfIJpZcx6bv1DL2ctsAvKA zHzwn1Dya48Yz3Xnm2CWRMlGbQG/8cNtqR443dUno0myA/Ohj3Nmbfe7n3KWLqD5DORg HsFILAWWNpGh7RZPvZm5YfdKZH+XQ3p8Q+WN/6/dKeNwc9BXMno+9E4GR888EefYqbvP TAs9112jaXgnSQAJMlYvxBEu/wJwfJse03ECQfTX4fM/eyYvdudAdNQTjFSnFsTEnGdN xOalG7rG3hGD9YJiuL5taXbhUcCg4KbV1TZwURuOMZ9Lj09fHmGSTXtDF7JACQeaoL0J Xluw== 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:in-reply-to:references:date :message-id:mime-version; bh=ZWCazQs37WebuPokYkhWzePDXYjMykgpDOO9WEPPKdg=; b=UTOhZQWLwcoVmwzuqVd5QRi4VumtkSgMuTHvACxQzOt+kxxC+FnT+2602XJacXvxiJ kbxfqkI3vtv5Olo+WTRYxqkkdOcN3g+E+OREdwdSZQRW7cZDyF4Cqx6kNF6XjVtYBO+b qWGSShTXNIZlNXyN1+WwrGPMXHNCp+5W5KUTYWYKuipccrhWB619g3/VsAgHdyW7+yLz WPlnMaqOCNI59QQyDxN8x0MoprBcoUT8r+cLVD7irX9XIuLKFPUQTjD0drDVi8ZNxvIt Z0c9nGPuugPjAxjEDYnsF6dmEKJ3zVkx4Y9IXfzued/T4sodeWI5YscYp/vuF4YCUVz2 gH3Q== X-Gm-Message-State: AOAM53247hvvjhnA3TiiaAno6g7PcpJWgXdgC9blbCdhZgs2blqHFNdE vNFYsvxB9DSz3bwFHjG0axpNH65kvsw= X-Google-Smtp-Source: ABdhPJxouCI0oqjrz7HCEP7VHX9pKQOrNAthdC23gqSaGsZ9ZCaOZB4pV7ybYVJgn0JAcjAH9+fAqw== X-Received: by 2002:adf:efc7:: with SMTP id i7mr6139574wrp.182.1616012371465; Wed, 17 Mar 2021 13:19:31 -0700 (PDT) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id z1sm22878wru.95.2021.03.17.13.19.30 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 17 Mar 2021 13:19:31 -0700 (PDT) From: zimoun In-Reply-To: <871rcen4b4.fsf@elephly.net> References: <20210315180714.8233-1-zimon.toutoune@gmail.com> <87pn00m4ig.fsf@elephly.net> <87h7lbme0c.fsf@elephly.net> <87eegfm689.fsf@elephly.net> <871rcen4b4.fsf@elephly.net> Date: Wed, 17 Mar 2021 21:15:14 +0100 Message-ID: <86o8fhv8od.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi Ricardo, On Tue, 16 Mar 2021 at 23:04, Ricardo Wurmus wrote: > I meant the same guix-patches issue number; separate commits. Done in v2. I have double-checked but who knows. :-) Thanks, simon From unknown Mon Aug 18 11:25:20 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#47171: closed (Re: [PATCH v2 1/3] gnu: r-bisquerna: Move to (gnu packages bioconductor).) Message-ID: References: <871rbv3yvm.fsf@elephly.net> <20210315180714.8233-1-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 47171 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 47171@debbugs.gnu.org Date: Wed, 31 Mar 2021 19:30:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1617219002-23323-1" This is a multi-part message in MIME format... ------------=_1617219002-23323-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #47171: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioc= onductor). which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 47171@debbugs.gnu.org. --=20 47171: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D47171 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1617219002-23323-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 47171-done) by debbugs.gnu.org; 31 Mar 2021 19:30:01 +0000 Received: from localhost ([127.0.0.1]:55554 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lRgXR-00063f-9W for submit@debbugs.gnu.org; Wed, 31 Mar 2021 15:30:01 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21193) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lRgXP-00063W-6E for 47171-done@debbugs.gnu.org; Wed, 31 Mar 2021 15:30:00 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1617218996; cv=none; d=zohomail.com; s=zohoarc; b=EajdR7dosXPc7An0uGcKMouPFKhKStFKVYqRxl3fAb+f+idBMKqd2eKv8zBUFDpnMii/MA0xhRTma9nMrBeAGeQ735Eg4rgWSD5FhUTU5bHKPcaLe9ou99X9HqSb3/ylOK7IEAJXDzksaZxPjNScJh4tj0D4Jzt/XYl79ZkRfnA= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1617218996; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=q0WCT0kDJ0WJWFp6LaGCxFRfndBbj5cYyk3iq8Ah6T8=; b=AzZCSdJTd7HYIS85FVFqiJTmdLxWFEscbGtyP2/1D1ChninaZY1qIt+L+FkFbbaCAdY1qC3spvuG/eIz8ADGngqKybM9wPzjmbtCDgHT2g9GDffWm2v5tsfPLJC30MNzwdfxfltEYWZ/rnxafNM4JMouPFjWKyDc0T6V2wU/88Q= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1617218996; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=q0WCT0kDJ0WJWFp6LaGCxFRfndBbj5cYyk3iq8Ah6T8=; b=MBJ74smZfgLHKgcOB1QoqYd1yUilhUa1N6m9CZU25BCD6McTDEDKjYGiX9ND33lH DKJ8D8LSX65EMAgQUW6aVeuqpDBXIcWJQHrQWXdg2X7Me3HDvEJtjc8YClai+2G7qB+ mQN3NSoQfecF8P8hIAyjlFVvxW4kBHmUo327UZao= Received: from localhost (p54ad4ee7.dip0.t-ipconnect.de [84.173.78.231]) by mx.zohomail.com with SMTPS id 1617218992293726.9720894970058; Wed, 31 Mar 2021 12:29:52 -0700 (PDT) References: <20210317201414.10811-1-zimon.toutoune@gmail.com> User-agent: mu4e 1.4.15; emacs 27.2 From: Ricardo Wurmus To: zimoun Subject: Re: [PATCH v2 1/3] gnu: r-bisquerna: Move to (gnu packages bioconductor). In-reply-to: <20210317201414.10811-1-zimon.toutoune@gmail.com> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Wed, 31 Mar 2021 21:29:49 +0200 Message-ID: <871rbv3yvm.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 47171-done Cc: 47171-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Thanks for this new patch set. I applied it and ran =E2=80=9Cmake as-derivation=E2=80=9D without problems. I pushed these three commits to the master branch. --=20 Ricardo ------------=_1617219002-23323-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 15 Mar 2021 18:07:36 +0000 Received: from localhost ([127.0.0.1]:36928 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrcu-0004ib-6w for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:07:36 -0400 Received: from lists.gnu.org ([209.51.188.17]:43084) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrct-0004iV-8M for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:07:35 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:36884) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrct-0005Mu-1R for guix-patches@gnu.org; Mon, 15 Mar 2021 14:07:35 -0400 Received: from mail-wr1-x432.google.com ([2a00:1450:4864:20::432]:40323) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrco-0002QG-JM for guix-patches@gnu.org; Mon, 15 Mar 2021 14:07:34 -0400 Received: by mail-wr1-x432.google.com with SMTP id l11so9164941wrp.7 for ; Mon, 15 Mar 2021 11:07:30 -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=6HrJQngxNuiMpqot/4zbKQYcw7bvMh1MyWYT0eo9frE=; b=iuFHAUJwcLLMyxBK5d2TKjo1RXNpd7On8H41AC4MMPgcrgYXug7LwT+Tf3o2g3qh+s wIxngVFGplHIorDrT71t1BhUxVTidXXzRk6GDQCTfgu1tDfE44nE/oAIfmipLwwAfKGr 2GUEDN5WRcL+p2H1GAosK2aofu85nSHuqO7Q6jyTY5pabcfHzxoUHyWT19Hq28FVUh6+ oDwGb/Bs4odii0NYroewECnDfV6yADUK6JkPDgDOPCSk/mkgazsf1DiqSOYbus1SHQo0 m6zf6WiF1uvKYEiYLgnPB98/ljLx1F1rPCjwyHzC3qPFCSit+A8Il3i9wMNyWQCAo9kq gL3A== 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=6HrJQngxNuiMpqot/4zbKQYcw7bvMh1MyWYT0eo9frE=; b=MG0usJXq0vo9hNH0PP4Q5S4RITEBK6KMKSvHdjOUlC1TwhTXnBMX/7xaTxPnyrIdvD 33UKe/5+GBUQMR1+WKo/85yqsRracuKG77GpQKzd8CaFC4REvuyyuS1LMLD6sb99l+u1 ezT37pDGAWRuKj5sJyjOq3mWaniBKmdpOnEg4WpaXluCF/rYec6IKyE0+wzHQTPrhXhe FToKON7j5X0JnV527rKslVYkFmL5EwOJLXeu3M29Jx1UuHWCty57T9l+fm65d0LiRWBw 42jLuxfdrB45qa0AP9QHttutlxuLx2J3B2a91/k28ZRodOmwoj2RjNh1NItdE5TRJLuF ++9g== X-Gm-Message-State: AOAM530vX6+u8nOBpilLYzzqMxCau7yCYL9NoQu0P+rciBRKjIc6EAUy tKbVVvbeDawbehzrQbcztpAioSGBDJk= X-Google-Smtp-Source: ABdhPJySxu56C2Aani1aNPRG4vS/LRzkgMhjtpc/Tq4RNxXA4uxqtzdgE+3GQtCI1RgKidjT2W5X+g== X-Received: by 2002:a5d:538d:: with SMTP id d13mr915295wrv.92.1615831649059; Mon, 15 Mar 2021 11:07:29 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id p17sm336613wmq.47.2021.03.15.11.07.27 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:07:27 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Date: Mon, 15 Mar 2021 19:07:14 +0100 Message-Id: <20210315180714.8233-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 X-Debbugs-Cc: Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::432; envelope-from=zimon.toutoune@gmail.com; helo=mail-wr1-x432.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) Hi, Janitor [1] patch set. It moves Bioconductor packages from (gnu packages bioinformatics) to (gnu packages bioconductor). Far to be complete; still 4 pacth set like this one are coming... 1: To transfer the Copyright, I use: git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r- Then, after the move, I run: ./pre-inst-env guix build r- --no-grafts ./pre-inst-env guix build r- --no-grafts --check and at the end of the series, I run: make as-derivation to check that "guix pull" is not broken; just in case. Last, I have not carefully checked the imported modules, so it could be possible to perhaps remove couple of #:use-module (gnu packages ) in gnu/packages/bioinformatics.scm. All the best, simon zimoun (10): gnu: r-limma: Move to (gnu packages bioconductor). gnu: r-xvector: Move to (gnu packages bioconductor). gnu: r-genomicranges: Move to (gnu packages bioconductor). gnu: r-biobase: Move to (gnu packages bioconductor). gnu: r-annotationdbi: Move to (gnu packages bioconductor). gnu: r-biomart: Move to (gnu packages bioconductor). gnu: r-biocparallel: Move to (gnu packages bioconductor). gnu: r-biostrings: Move to (gnu packages bioconductor). gnu: r-rsamtools: Move to (gnu packages bioconductor). gnu: r-delayedarray: Move to (gnu packages bioconductor). gnu/packages/bioconductor.scm | 305 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 305 -------------------------------- 2 files changed, 305 insertions(+), 305 deletions(-) base-commit: 266d55dc3080475544bf45e72359c9b9bbcecd53 -- 2.30.1 ------------=_1617219002-23323-1--