GNU bug report logs - #32587
[PATCH] gnu: Add r-pore.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: pimi <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: pimi <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add r-pore.
Date: Thu, 30 Aug 2018 12:37:03 +0200

gnu/packages/bioinformatics.scm (r-pore): New variable
---
 gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 22a00894c..0605e4564 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13558,3 +13558,30 @@ reference transcripts provided in a annotation file (also in GTF/GFF3 format).
        (list
         license:expat                   ;license for gffcompare
         license:artistic2.0)))))        ;license for gclib
+
+(define-public r-pore
+  (package
+    (name "r-pore")
+    (version "0.24")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://sourceforge.net/projects/rpore/files/"version"/poRe_"version".tar.gz"))
+       (sha256
+        (base32 "0pih9nljbv8g4x8rkk29i7aqq681b782r5s5ynp4nw9yzqnmmksv"))))
+    (properties `((upstream-name . "poRe")))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-rhdf5" ,r-rhdf5)
+       ("r-shiny" ,r-shiny)
+       ("r-svdialogs" ,r-svdialogs)
+       ("r-data-table" ,r-data-table)
+       ("r-bit64" ,r-bit64)))
+    (home-page "https://sourceforge.net/projects/rpore/files/")
+    (synopsis "This R package enable visualisation of nanopore sequencing data")
+    (description
+     "The Oxford Nanopore MinION is a revolutionary sequencer with a unique model of data
+delivery, requiring novel tools for the novice user.  This package enables
+organisation and visualisation of MinION data.")
+    (license license:gpl3)))
-- 
2.17.1

Message #8 received at 32587 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de>
To: <MadalinIonel.Patrascu <at> mdc-berlin.de>
Cc: 32587 <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-pore.
Date: Mon, 3 Sep 2018 17:22:29 +0200

Hi,

thanks for the patch!

> +
> +(define-public r-pore
> +  (package
> +    (name "r-pore")
> +    (version "0.24")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (string-append
> +             "https://sourceforge.net/projects/rpore/files/"version"/poRe_"version".tar.gz"))

Please use mirror://sourceforge/ here.

> +       (sha256
> +        (base32 "0pih9nljbv8g4x8rkk29i7aqq681b782r5s5ynp4nw9yzqnmmksv"))))
> +    (properties `((upstream-name . "poRe")))
> +    (build-system r-build-system)
> +    (native-inputs
> +     `(("r-rhdf5" ,r-rhdf5)
> +       ("r-shiny" ,r-shiny)
> +       ("r-svdialogs" ,r-svdialogs)
> +       ("r-data-table" ,r-data-table)
> +       ("r-bit64" ,r-bit64)))

Are you sure these should be native-inputs?  They probably should be
propagated inputs, because they should be installed together with the
“r-pore” package.

Please also sort these inputs alphabetically.

> +    (home-page "https://sourceforge.net/projects/rpore/files/")

Please use “https://sourceforge.net/projects/rpore”.

> +    (synopsis "This R package enable visualisation of nanopore sequencing data")

Please use “Visualize Nanopore sequencing data”.

> +    (description
> +     "The Oxford Nanopore MinION is a revolutionary sequencer with a unique model of data
> +delivery, requiring novel tools for the novice user.  This package enables
> +organisation and visualisation of MinION data.")

Please try to avoid marketing terms such as “revolutionary”, “unique”,
“novel” etc.  Could you try to come up with a description that better
describes the features of the poRe package?

Here’s a draft:

  This package provides graphical user interfaces to organize and
  visualize Nanopore sequencing data.

> +    (license license:gpl3)))

I don’t think this is correct.  The DESCRIPTION file says “BSD”, but
fails to state the variant.  I have opened an issue about this here:

    https://github.com/mw55309/poRe_docs/issues/10

Could you please send an updated patch?

--
Ricardo

Message #11 received at 32587 <at> debbugs.gnu.org (full text, mbox):

From: pimi <madalinionel.patrascu <at> mdc-berlin.de>
To: <32587 <at> debbugs.gnu.org>
Cc: pimi <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add r-pore.
Date: Tue, 11 Sep 2018 16:54:32 +0200

gnu/packages/bioinformatics.scm (r-pore): New variable.
---
 gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f6410c3ca..49ed19535 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13699,3 +13699,31 @@ are highly customizable.  Currently, it is possible to plot: bigwig, bed (many
 options), bedgraph, links (represented as arcs), and Hi-C matrices.
 pyGenomeTracks can make plots with or without Hi-C data.")
     (license license:gpl3+)))
+
+(define-public r-pore
+  (package
+    (name "r-pore")
+    (version "0.24")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append
+         "mirror://sourceforge/projects/rpore/files/"version"/poRe_"version".tar.gz"))
+       (sha256
+        (base32 "0pih9nljbv8g4x8rkk29i7aqq681b782r5s5ynp4nw9yzqnmmksv"))))
+    (properties `((upstream-name . "poRe")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bit64" ,r-bit64)
+       ("r-data-table" ,r-data-table)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-shiny" ,r-shiny)
+       ("r-svdialogs" ,r-svdialogs)))
+    (home-page "https://sourceforge.net/projects/rpore")
+    (synopsis "Visualize Nanopore sequencing data")
+    (description
+     "This package provides graphical user interfaces to organize and visualize Nanopore
+sequencing data.")
+    ;;license unclear https://github.com/mw55309/poRe_docs/issues/10
+    (license license:bsd-3)))
-- 
2.17.1

Message #18 received at 32587-done <at> debbugs.gnu.org (full text, mbox):

From: ludo <at> gnu.org (Ludovic Courtès)
To: pimi <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 32587-done <at> debbugs.gnu.org
Subject: Re: [bug#32587] [PATCH] gnu: Add r-pore.
Date: Fri, 21 Sep 2018 14:29:08 +0200

Hello,

pimi <madalinionel.patrascu <at> mdc-berlin.de> skribis:

> gnu/packages/bioinformatics.scm (r-pore): New variable.

[...]

> +        (string-append
> +         "mirror://sourceforge/projects/rpore/files/"version"/poRe_"version".tar.gz"))

I fixed the URL, clarified the comment about the license, and committed.

Thanks!

Ludo’.

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