GNU bug report logs - #44033
[PATCH 1/3] gnu: Add r-decon.

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From: Aniket Patil <aniket112.patil <at> gmail.com>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 44033 <at> debbugs.gnu.org
Subject: [bug#44033] [PATCH 1/3] gnu: Add r-decon.
Date: Mon, 19 Oct 2020 17:57:52 +0530

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Sure, I will do that.

On Mon, 19 Oct 2020 at 5:40 PM, zimoun <zimon.toutoune <at> 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.  Could you rebase on the top?  Please.
>
> (Note that using “git format-patch --base=<hash>” 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 <aniket112.patil <at> gmail.com>
> 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 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.")
> > +    (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
>

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