From debbugs-submit-bounces@debbugs.gnu.org Mon Mar 15 14:07:36 2021 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 From debbugs-submit-bounces@debbugs.gnu.org Mon Mar 15 14:09:25 2021 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 To: 47171@debbugs.gnu.org Subject: [PATCH 01/10] gnu: r-limma: Move to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 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: -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 debbugs-submit-bounces@debbugs.gnu.org Mon Mar 15 14:09:29 2021 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 To: 47171@debbugs.gnu.org Subject: [PATCH 02/10] gnu: r-xvector: Move to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 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: -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 debbugs-submit-bounces@debbugs.gnu.org Mon Mar 15 14:09:30 2021 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 To: 47171@debbugs.gnu.org Subject: [PATCH 03/10] gnu: r-genomicranges: Move to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 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: -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 debbugs-submit-bounces@debbugs.gnu.org Mon Mar 15 14:09:30 2021 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 To: 47171@debbugs.gnu.org Subject: [PATCH 04/10] gnu: r-biobase: Move to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 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: -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 debbugs-submit-bounces@debbugs.gnu.org Mon Mar 15 14:09:31 2021 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 To: 47171@debbugs.gnu.org Subject: [PATCH 05/10] gnu: r-annotationdbi: Move to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 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: -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 debbugs-submit-bounces@debbugs.gnu.org Mon Mar 15 14:09:31 2021 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 To: 47171@debbugs.gnu.org Subject: [PATCH 06/10] gnu: r-biomart: Move to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 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: -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 debbugs-submit-bounces@debbugs.gnu.org Mon Mar 15 14:09:32 2021 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 To: 47171@debbugs.gnu.org Subject: [PATCH 07/10] gnu: r-biocparallel: Move to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 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: -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 debbugs-submit-bounces@debbugs.gnu.org Mon Mar 15 14:09:33 2021 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 To: 47171@debbugs.gnu.org Subject: [PATCH 08/10] gnu: r-biostrings: Move to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 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: -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 debbugs-submit-bounces@debbugs.gnu.org Mon Mar 15 14:09:33 2021 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 To: 47171@debbugs.gnu.org Subject: [PATCH 09/10] gnu: r-rsamtools: Move to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 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: -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 debbugs-submit-bounces@debbugs.gnu.org Mon Mar 15 14:09:34 2021 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 To: 47171@debbugs.gnu.org Subject: [PATCH 10/10] gnu: r-delayedarray: Move to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 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: -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 debbugs-submit-bounces@debbugs.gnu.org Mon Mar 15 18:33:23 2021 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 From debbugs-submit-bounces@debbugs.gnu.org Mon Mar 15 19:56:29 2021 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 To: 47171@debbugs.gnu.org, rekado@elephly.net, zimon.toutoune@gmail.com Subject: Re: bug#47171: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 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 09:00:25 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: Did not alter fixed versions and reopened. Date: Mon, 15 Mar 2021 23:57:02 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # Did not alter fixed versions and reopened. thanks # This fakemail brought to you by your local debbugs # administrator From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 16 08:27:58 2021 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: Subject: Re: bug#47171: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). To: Leo Famulari Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 47171 Cc: Ricardo Wurmus , 47171@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 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 debbugs-submit-bounces@debbugs.gnu.org Tue Mar 16 09:20:34 2021 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 To: zimoun Subject: Re: bug#47171: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 Cc: 47171@debbugs.gnu.org, Leo Famulari 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 debbugs-submit-bounces@debbugs.gnu.org Tue Mar 16 09:31:13 2021 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: Subject: Re: bug#47171: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). To: Ricardo Wurmus Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 47171 Cc: 47171@debbugs.gnu.org, Leo Famulari 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 debbugs-submit-bounces@debbugs.gnu.org Tue Mar 16 12:08:37 2021 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 To: zimoun Subject: Re: bug#47171: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 Cc: 47171@debbugs.gnu.org, Leo Famulari 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 debbugs-submit-bounces@debbugs.gnu.org Tue Mar 16 12:36:24 2021 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: Subject: Re: bug#47171: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). To: Ricardo Wurmus Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 47171 Cc: 47171@debbugs.gnu.org, Leo Famulari 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 debbugs-submit-bounces@debbugs.gnu.org Tue Mar 16 18:04:43 2021 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 To: zimoun Subject: Re: bug#47171: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 Cc: 47171@debbugs.gnu.org, Leo Famulari 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 debbugs-submit-bounces@debbugs.gnu.org Wed Mar 17 16:14:34 2021 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 To: 47171@debbugs.gnu.org Subject: [PATCH v2 1/3] gnu: r-bisquerna: Move to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 Cc: rekado@elephly.net, 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: -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 debbugs-submit-bounces@debbugs.gnu.org Wed Mar 17 16:14:36 2021 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 To: 47171@debbugs.gnu.org Subject: [PATCH v2 2/3] gnu: r-absfiltergsea: Move to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 Cc: rekado@elephly.net, 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: -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 debbugs-submit-bounces@debbugs.gnu.org Wed Mar 17 16:14:37 2021 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 To: 47171@debbugs.gnu.org Subject: [PATCH v2 3/3] Revert "Revert some commits that caused `guix pull` to fail." 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-Debbugs-Envelope-To: 47171 Cc: rekado@elephly.net, 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: -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 debbugs-submit-bounces@debbugs.gnu.org Wed Mar 17 16:19:39 2021 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 To: Ricardo Wurmus Subject: Re: bug#47171: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). 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-Debbugs-Envelope-To: 47171 Cc: 47171@debbugs.gnu.org, Leo Famulari 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 debbugs-submit-bounces@debbugs.gnu.org Wed Mar 31 15:30:01 2021 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 From unknown Mon Aug 18 09:00:25 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Thu, 29 Apr 2021 11:24:07 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator