From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id 4P/sAGKCjV9DXgAA0tVLHw (envelope-from ) for ; Mon, 19 Oct 2020 12:11:14 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id cKpNOGGCjV8BZgAAbx9fmQ (envelope-from ) for ; Mon, 19 Oct 2020 12:11:13 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id E42E39400D3 for ; Mon, 19 Oct 2020 12:11:12 +0000 (UTC) Received: from localhost ([::1]:47610 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kUU0M-0004jE-I9 for larch@yhetil.org; Mon, 19 Oct 2020 08:11:10 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:54740) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kUU0E-0004iu-0d for guix-patches@gnu.org; Mon, 19 Oct 2020 08:11:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:56878) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kUU0D-00048m-O4 for guix-patches@gnu.org; Mon, 19 Oct 2020 08:11:01 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kUU0D-0003IZ-Ie for guix-patches@gnu.org; Mon, 19 Oct 2020 08:11:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#44033] [PATCH 1/3] gnu: Add r-decon. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 19 Oct 2020 12:11:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 44033 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Aniket Patil Cc: 44033@debbugs.gnu.org Received: via spool by 44033-submit@debbugs.gnu.org id=B44033.160310941312613 (code B ref 44033); Mon, 19 Oct 2020 12:11:01 +0000 Received: (at 44033) by debbugs.gnu.org; 19 Oct 2020 12:10:13 +0000 Received: from localhost ([127.0.0.1]:40191 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kUTzQ-0003HN-Id for submit@debbugs.gnu.org; Mon, 19 Oct 2020 08:10:12 -0400 Received: from mail-wr1-f67.google.com ([209.85.221.67]:36783) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kUTzO-0003H3-82 for 44033@debbugs.gnu.org; Mon, 19 Oct 2020 08:10:11 -0400 Received: by mail-wr1-f67.google.com with SMTP id x7so11165638wrl.3 for <44033@debbugs.gnu.org>; Mon, 19 Oct 2020 05:10:10 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:references:date:in-reply-to:message-id :user-agent:mime-version:content-transfer-encoding; bh=EnSZetWlguX7EyjbN7XFRBfYAp22t4rNxvpWE6SPwIw=; b=a06+VcEDkur8y3PTBUATIo9ozaov0paIl0yOPhh/RTS3g6KM//DklG/vb/dotkuFry XOqnsbBOM+lQgEBT+rJaHoUWzTMMTRegqrmCMcGDXZBl9J825BI6GLw5Tqg3IeUw3oFQ QYM1gHZeMvzoCokHGxiBNQGu0cafDB6jZgaIoj1k37WWTNzWW0Zp0yvhpNg9vxCL+909 f2y6y1WkC5lnNL0QLtSBIhfF0gUVw7dy08EXN564eIDQXTTQ35WDyGMb6Sm8P5/CNkTY MqkBvuKGvgy4Aefjk/pHkPrVoMIoWG2d48whzIDVRAQl0k9mocWffm22fJJOw9K+txqU EuHw== 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:references:date:in-reply-to :message-id:user-agent:mime-version:content-transfer-encoding; bh=EnSZetWlguX7EyjbN7XFRBfYAp22t4rNxvpWE6SPwIw=; b=SfIBYINlhoY6D6QfbBwFV9sImrTIM6VsP0MebOsvgeHUCGy+R6lTBv9CQoQhKxvDKs eh8ffmWbBsrV+lyriGEU8IchLiuL3AAG9bcaqn2w7uvdo2laII61vSI3MWQ5Ta8ujhZz 1DC5KeIWM8sjFCV2axTOI4Um5V0nFCmPLaue60Rs3OczzCKSlhemXlQH26Uz9CS9tYbv /BAdjXWqIeHye3S1lr/vkkyU5bji5ygJ8To/K1rict3WFIDxU11Q8fwMTpyP+mfMGEnb KQSH4xoS2zvqtZq32oOn4aUkvAcdO6azcWgwXCj3yIeRJ4oRy4gOBnhKRg8n7g+rXq80 qXhA== X-Gm-Message-State: AOAM530aWEQ6xH7O5+QjzVdYHYe28O3Uu2vc3OmBqW1l9f/JWLOw2/Jx B7gvuiHVThVUHHK3kp43XmKzk46mfO4= X-Google-Smtp-Source: ABdhPJy1vdXBMaL79JvgPseGoPR6mNV2EvmFVUhfkhfDUfA6jZkbvfqm0Wf7wTSyL9xV2qe6wk6B2w== X-Received: by 2002:a5d:6a51:: with SMTP id t17mr19426572wrw.80.1603109403650; Mon, 19 Oct 2020 05:10:03 -0700 (PDT) Received: from pfiuh02 ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id a7sm15873939wmh.6.2020.10.19.05.10.01 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 19 Oct 2020 05:10:01 -0700 (PDT) From: zimoun References: <20201016131338.62737-1-aniket112.patil@gmail.com> Date: Mon, 19 Oct 2020 14:09:55 +0200 In-Reply-To: <20201016131338.62737-1-aniket112.patil@gmail.com> (Aniket Patil's message of "Fri, 16 Oct 2020 18:43:36 +0530") Message-ID: <87wnzm76y4.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -1.0 (-) X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=fail (rsa verify failed) header.d=gmail.com header.s=20161025 header.b=a06+VcED; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Spam-Score: 0.09 X-TUID: 6vmb/g7wfK7g Dear, Thank you for this contribution. The file gnu/packages/cran.scm has changed between so your patches do not apply anymore. Could you rebase on the top? Please. (Note that using =E2=80=9Cgit format-patch --base=3D=E2=80=9D where <= hash> is the hash on which your patch is applying simplifies the process. IMHO.) On Fri, 16 Oct 2020 at 18:43, Aniket Patil wrot= e: > * gnu/packages/cran.scm (r-decon): New variable. > --- > gnu/packages/cran.scm | 23 +++++++++++++++++++++++ > 1 file changed, 23 insertions(+) > > diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm > index 59a409f8e9..0370cdd993 100644 > --- a/gnu/packages/cran.scm > +++ b/gnu/packages/cran.scm > @@ -24596,3 +24596,26 @@ enrichment analysis (GSEA) calculation with or w= ithout the absolute filtering. > Without filtering, users can perform (original) two-tailed or one-tail= ed > absolute GSEA.") > (license license:gpl2))) > + > +(define-public r-decon > + (package > + (name "r-decon") > + (version "1.2-4") > + (source > + (origin > + (method url-fetch) > + (uri (cran-uri "decon" version)) > + (sha256 > + (base32 > + "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s")))) The indentation does not seem correct. It should be: (sha256 (base32 "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s")))) > + (properties `((upstream-name . "decon"))) > + (build-system r-build-system) > + (native-inputs `(("gfortran" ,gfortran))) Usually, we use: (native-inputs `(("gfortran" ,gfortran))) instead on the in-line. > + (home-page > + "https://cran.r-project.org/web/packages/decon") > + (synopsis > + "Deconvolution Estimation in Measurement Error Models") Usually, the synopsis is on the same line: (synopsis "Deconvolution Estimation in Measurement Error Models") > + (description > + "This package contains a collection of functions to deal with nonp= arametric measurement error problems using deconvolution kernel methods. W= e focus two measurement error models in the package: (1) an additive measur= ement error model, where the goal is to estimate the density or distributio= n function from contaminated data; (2) nonparametric regression model with = errors-in-variables. The R functions allow the measurement errors to be ei= ther homoscedastic or heteroscedastic. To make the deconvolution estimator= s computationally more efficient in R, we adapt the \"Fast Fourier Transfor= m\" (FFT) algorithm for density estimation with error-free data to the deco= nvolution kernel estimation. Several methods for the selection of the data= -driven smoothing parameter are also provided in the package. See details = in: Wang, X.F. and Wang, B. (2011). Deconvolution estimation in measureme= nt error models: The R package decon. Journal of Statistical Software, 39(= 10), 1-24.") > + (license license:gpl3+))) > + The lines should not be longer than 80 characters. Something like. (description "This package contains a collection of functions to deal with nonparametric measurement error problems using deconvolution kernel methods. We focus two measurement error models in the package: (1) an additive measurement error model, where the goal is to estimate the density or distribution function from contaminated data; (2) nonparametric regression model with errors-in-variables. The R functions allow the measurement errors to be either homoscedastic or heteroscedastic. To make the deconvolution estimators computationally more efficient in R, we adapt the \"Fast Fourier Transform\" (FFT) algorithm for density estimation with error-free data to the deconvolution kernel estimation. Several methods for the selection of the data-driven smoothing parameter are also provided in the package. See details in: Wang, X.F. and Wang, B. (2011). Deconvolution estimation in measurement error models: The R package decon. Journal of Statistical Software, 39(10), 1-24.") To help you to spot, you can apply the linter with: ./pre-inst-env guix lint r-deconv and then address the warnings, if any. Could you send a v2? All the best, simon