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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 17 Mar 2021 20:15:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47171 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47171@debbugs.gnu.org Cc: rekado@elephly.net, zimoun Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.16160120761686 (code B ref 47171); Wed, 17 Mar 2021 20:15:02 +0000 Received: (at 47171) by debbugs.gnu.org; 17 Mar 2021 20:14:36 +0000 Received: from localhost ([127.0.0.1]:44029 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMcYu-0000R7-7S for submit@debbugs.gnu.org; Wed, 17 Mar 2021 16:14:36 -0400 Received: from mail-wr1-f45.google.com ([209.85.221.45]:38546) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMcYo-0000QX-Df for 47171@debbugs.gnu.org; Wed, 17 Mar 2021 16:14:33 -0400 Received: by mail-wr1-f45.google.com with SMTP id z2so3131558wrl.5 for <47171@debbugs.gnu.org>; Wed, 17 Mar 2021 13:14:30 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=/pBMFD5KuZJMFrFI1oilyVUXnxa0ikrUADOAoc4vZoI=; b=WcrK2YhMKCFrO82OiqOfAkEjhKL1pT7z7kwLs3j6itKnei1Y9rR0dkuLG93WaKVZ+g 356W4EQ1SeTkA/czE92SH/Sc3LM5HfOxPcVH2CAO40NWX9OUlEY06r217mDjM6GbgZ07 Cg/HMRACYHrjaRff0mqZe0bxREX5CVTwrkZytP0FTg5VvbO3P3YWCaHqb+1YMYxQyUMr 7PA3Y+dB8R9tq0kUH3oPjB7Gj6GArlHROP5S2+iQ9b3pStLueI9aRMxsiz5dbQ+6zVYb 8NAaLdF+JJ5DO2cYhhUmIsHiwE5mC3awMBRZAvhPC9OBnMQstlTEGb0vYskdcY4a5M8K YJSw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=/pBMFD5KuZJMFrFI1oilyVUXnxa0ikrUADOAoc4vZoI=; b=RJl9d94xomvMpwsV1/Gb6rRc1iPs1mnYgRs+v8CQ6NqzHJrR3GKJ2MYcIzoJQ5Sw81 r5WSY2yqebl7lWOtsrFUn9vChE32zPx9sZBtnDmXB2ZuHe7UxO08SIzwZMVyez004BWO HsaUc5OvcrspcyT5m9A1aKAN0UAkIwWKDCxipXMBirlrfF2ST0UguLNSQyDagVoEIMK7 i9aoBcBSHFbsyUo5k0W9t4AkV4B2MzyVRFIzSK4ICwWnQU31TQAYBpLKsiMbWhCJ2jAT yACPLIwFFxEtOQ8Z0qITZJlkG+WeCGTSKdqgYKWqsqTt+TsOYdxxPDB6R5S/Owe41SNH P7OA== X-Gm-Message-State: AOAM530kRV38Levpk7faNz0uVpI672ZLFXkOXwyr+lB4eF5egKpmspcB j86xyzkKXdHodSbyQsqXBgO3PM7CAso= X-Google-Smtp-Source: ABdhPJyRtL190/DEWscQgFGRhfFiYdLA0AH46i+DSDEtdefF2f9bLL0DKZbQbJxmGPijYGhe/YUXwg== X-Received: by 2002:a5d:42d2:: with SMTP id t18mr6075685wrr.258.1616012064907; Wed, 17 Mar 2021 13:14:24 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id o2sm3424007wmc.23.2021.03.17.13.14.24 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 17 Mar 2021 13:14:24 -0700 (PDT) From: zimoun Date: Wed, 17 Mar 2021 21:14:13 +0100 Message-Id: <20210317201414.10811-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210317201414.10811-1-zimon.toutoune@gmail.com> References: <20210317201414.10811-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/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")