From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp2 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id EO/2CcmKjV8WFwAA0tVLHw (envelope-from ) for ; Mon, 19 Oct 2020 12:47:05 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp2 with LMTPS id GIzEBcmKjV+obwAAB5/wlQ (envelope-from ) for ; Mon, 19 Oct 2020 12:47:05 +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 831729404D7 for ; Mon, 19 Oct 2020 12:47:04 +0000 (UTC) Received: from localhost ([::1]:59048 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kUUZ5-0006sc-4y for larch@yhetil.org; Mon, 19 Oct 2020 08:47:03 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:33108) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kUUVC-0003wM-OB for guix-patches@gnu.org; Mon, 19 Oct 2020 08:43:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:56901) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kUUVC-0007xm-EE for guix-patches@gnu.org; Mon, 19 Oct 2020 08:43:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kUUVC-00049f-Bu for guix-patches@gnu.org; Mon, 19 Oct 2020 08:43:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#44033] [PATCH 1/3] gnu: Add r-decon. Resent-From: Aniket Patil Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 19 Oct 2020 12:43:02 +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: zimoun Cc: 44033@debbugs.gnu.org Received: via spool by 44033-submit@debbugs.gnu.org id=B44033.160311137115950 (code B ref 44033); Mon, 19 Oct 2020 12:43:02 +0000 Received: (at 44033) by debbugs.gnu.org; 19 Oct 2020 12:42:51 +0000 Received: from localhost ([127.0.0.1]:40214 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kUUUz-00049A-PE for submit@debbugs.gnu.org; Mon, 19 Oct 2020 08:42:51 -0400 Received: from mail-oi1-f169.google.com ([209.85.167.169]:42974) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kUUGo-0003kM-Cz for 44033@debbugs.gnu.org; Mon, 19 Oct 2020 08:28:11 -0400 Received: by mail-oi1-f169.google.com with SMTP id 16so12142156oix.9 for <44033@debbugs.gnu.org>; Mon, 19 Oct 2020 05:28:10 -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; bh=fFfnA/0ZGGuMK38qQ0PCovNyCve97awgRVr7gd1hdgE=; b=GjUh2BN3k3mxMf8Q/odNUHZnmDO++PQXl9i9WI7aO6yBfIM3B4PtJW2DFZtx6m5glI BgdemflsuMCUVtyzRa3mazJFp2u/cwZ+MOjw/8nOfXauLAEamA/fAEhola/r4QWEdLdC FCEmt/tzhVs6r4vzL7np6kYvBriamyPKIwFozxbJI5cExiQo12ZpuqJKnzCiaNEx5lZ9 w6bq3QGfn8w5o1iaUIwyUzvy/2jPVPrfcpmVqMF5bnmEqBq53UWRBViHWvRBRbWG7jnY KHfmth70hlQdbzIT+0jXk+jF4yvInt4NMkyjRO5VOUbMYtCi9Yr6pEay6hWVa7a2bVtp IDnQ== 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; bh=fFfnA/0ZGGuMK38qQ0PCovNyCve97awgRVr7gd1hdgE=; b=NeV7qjjlc7vC4Kd18jUElAyzRhdzuSYb6UFRektk+ZDtt5iG7PyiYrkDgKIFrolkjI 0muGy4gmP3GOxHuWjAXv4BTChjeK2tTrRUvmEvc8kQYFzYDONly1F+uAkJbCb2OZOflj Y0EvzqSKjOYyyGy0SzW19Lt2TZfIcJI6b3ZNG1Q3xDYYVcpZfqcc0f2528IFrOMuTaec iugv+JRKYuFuRFoEGEwWzU/9fg4UlXD8pEUT0rfS278SrtJ5Hkc7NYutWuT1MMP0+ogJ 9Bf2gn07J6YG/1QrR8tgFa3M3IIO0jRv+je7waQK0O2Cpzw2So5TP1Tk3Mim/GAPSyOI fE+w== X-Gm-Message-State: AOAM533YFj9kRUu72fQqqo5JutjK6UVf1Gfypce/oVMaHCizY7j63CFj 9KzRmOF008oydlwPVOm0gq91FutCnVfKtRU77Sc= X-Google-Smtp-Source: ABdhPJxL/jYweU78FvWotCVmnS8fb08j8vUNWgY4aEmvffdUq+/iG12aLK82BcGK9sfl05ZY60LAc3NQmYTLCjC9Dvo= X-Received: by 2002:aca:580a:: with SMTP id m10mr10254476oib.122.1603110484580; Mon, 19 Oct 2020 05:28:04 -0700 (PDT) MIME-Version: 1.0 References: <20201016131338.62737-1-aniket112.patil@gmail.com> <87wnzm76y4.fsf@gmail.com> In-Reply-To: <87wnzm76y4.fsf@gmail.com> From: Aniket Patil Date: Mon, 19 Oct 2020 17:57:52 +0530 Message-ID: Content-Type: multipart/alternative; boundary="000000000000f81dbc05b2053ec8" X-Spam-Score: 0.0 (/) X-Mailman-Approved-At: Mon, 19 Oct 2020 08:42:48 -0400 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=GjUh2BN3; 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: /KpCG2tpoF+0 --000000000000f81dbc05b2053ec8 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Sure, I will do that. On Mon, 19 Oct 2020 at 5:40 PM, zimoun wrote: > 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= is the > hash on which your patch is applying simplifies the process. IMHO.) > > > On Fri, 16 Oct 2020 at 18:43, Aniket Patil > wrote: > > * 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 > without the absolute filtering. > > Without filtering, users can perform (original) two-tailed or > one-tailed > > 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 > 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 densi= ty > 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 mak= e > the deconvolution estimators computationally more efficient in R, we adap= t > the \"Fast Fourier Transform\" (FFT) algorithm for density estimation wit= h > error-free data to the deconvolution kernel estimation. Several methods > for the selection of the data-driven smoothing parameter are also provide= d > 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.") > > + (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 > --000000000000f81dbc05b2053ec8 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Sure, I will do that.

On Mon, 19 Oct 2020 at 5:40 PM, zimoun <<= a href=3D"mailto:zimon.toutoune@gmail.com">zimon.toutoune@gmail.com>= wrote:
Dear,

Thank you for this contribution.


The file gnu/packages/cran.scm has changed between so your patches do
not apply anymore.=C2=A0 Could you rebase on the top?=C2=A0 Please.

(Note that using =E2=80=9Cgit format-patch --base=3D<hash>=E2=80=9D w= here <hash> is the
hash on which your patch is applying simplifies the process.=C2=A0 IMHO.)

On Fri, 16 Oct 2020 at 18:43, Aniket Patil <aniket112.patil@gmail.com> wrote:=
> * gnu/packages/cran.scm (r-decon): New variable.
> ---
>=C2=A0 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
>=C2=A0 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 o= r without the absolute filtering.
>=C2=A0 =C2=A0 Without filtering, users can perform (original) two-taile= d or one-tailed
>=C2=A0 absolute GSEA.")
>=C2=A0 =C2=A0 =C2=A0 (license license:gpl2)))
> +
> +(define-public r-decon
> +=C2=A0 (package
> +=C2=A0 =C2=A0 (name "r-decon")
> +=C2=A0 =C2=A0 (version "1.2-4")
> +=C2=A0 =C2=A0 (source
> +=C2=A0 =C2=A0 =C2=A0 (origin
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 (method url-fetch)
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 (uri (cran-uri "decon" version)= )
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 (sha256
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (base32
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 "1v4l0xq29rm8mks354g40= g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))

The indentation does not seem correct.=C2=A0 It should be:

=C2=A0 =C2=A0 =C2=A0 =C2=A0 (sha256
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(base32
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 "1v4l0xq29rm8mks354g40g9jxn0didzlxg= 3g7z08m0gvj29zdj7s"))))

> +=C2=A0 =C2=A0 (properties `((upstream-name . "decon")))
> +=C2=A0 =C2=A0 (build-system r-build-system)
> +=C2=A0 =C2=A0 (native-inputs `(("gfortran" ,gfortran)))

Usually, we use:

=C2=A0 =C2=A0 (native-inputs
=C2=A0 =C2=A0 =C2=A0`(("gfortran" ,gfortran)))

instead on the in-line.

> +=C2=A0 =C2=A0 (home-page
> +=C2=A0 =C2=A0 =C2=A0 "https://cran.r-project= .org/web/packages/decon")
> +=C2=A0 =C2=A0 (synopsis
> +=C2=A0 =C2=A0 =C2=A0 "Deconvolution Estimation in Measurement Er= ror Models")

Usually, the synopsis is on the same line:

=C2=A0 =C2=A0 (synopsis "Deconvolution Estimation in Measurement Error= Models")


> +=C2=A0 =C2=A0 (description
> +=C2=A0 =C2=A0 =C2=A0 "This package contains a collection of func= tions to deal with nonparametric measurement error problems using deconvolu= tion kernel methods.=C2=A0 We focus two measurement error models in the pac= kage: (1) an additive measurement error model, where the goal is to estimat= e the density or distribution function from contaminated data; (2) nonparam= etric regression model with errors-in-variables.=C2=A0 The R functions allo= w the measurement errors to be either homoscedastic or heteroscedastic.=C2= =A0 To make the deconvolution estimators computationally more efficient in = R, we adapt the \"Fast Fourier Transform\" (FFT) algorithm for de= nsity estimation with error-free data to the deconvolution kernel estimatio= n.=C2=A0 Several methods for the selection of the data-driven smoothing par= ameter are also provided in the package.=C2=A0 See details in: Wang, X.F.= =C2=A0 and Wang, B. (2011).=C2=A0 Deconvolution estimation in measurement e= rror models: The R package decon.=C2=A0 Journal of Statistical Software, 39= (10), 1-24.")
> +=C2=A0 =C2=A0 (license license:gpl3+)))
> +

The lines should not be longer than 80 characters.=C2=A0 Something like.
=C2=A0 =C2=A0 (description
=C2=A0 =C2=A0 =C2=A0"This package contains a collection of functions t= o deal with
=C2=A0 =C2=A0 =C2=A0nonparametric measurement error problems using deconvol= ution
=C2=A0 =C2=A0 =C2=A0kernel methods.=C2=A0 We focus two measurement error mo= dels in the
=C2=A0 =C2=A0 =C2=A0package: (1) an additive measurement error model, where= the goal
=C2=A0 =C2=A0 =C2=A0is to estimate the density or distribution function fro= m
=C2=A0 =C2=A0 =C2=A0contaminated data; (2) nonparametric regression model w= ith
=C2=A0 =C2=A0 =C2=A0errors-in-variables.=C2=A0 The R functions allow the me= asurement errors
=C2=A0 =C2=A0 =C2=A0to be either homoscedastic or heteroscedastic.=C2=A0 To= make the
=C2=A0 =C2=A0 =C2=A0deconvolution estimators computationally more efficient= in R, we
=C2=A0 =C2=A0 =C2=A0adapt the \"Fast Fourier Transform\" (FFT) al= gorithm for density
=C2=A0 =C2=A0 =C2=A0estimation with error-free data to the deconvolution ke= rnel
=C2=A0 =C2=A0 =C2=A0estimation.=C2=A0 Several methods for the selection of = the data-driven
=C2=A0 =C2=A0 =C2=A0smoothing parameter are also provided in the package.= =C2=A0 See details
=C2=A0 =C2=A0 =C2=A0in: Wang, X.F.=C2=A0 and Wang, B. (2011).=C2=A0 Deconvo= lution estimation in
=C2=A0 =C2=A0 =C2=A0measurement error models: The R package decon.=C2=A0 Jo= urnal of
=C2=A0 =C2=A0 =C2=A0Statistical Software, 39(10), 1-24.")


To help you to spot, you can apply the linter with:

=C2=A0 ./pre-inst-env guix lint r-deconv

and then address the warnings, if any.


Could you send a v2?

All the best,
simon
--000000000000f81dbc05b2053ec8--