GNU bug report logs - #51464
Add r-xnastring (bioconductor) and r-formattable (cran)

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Package: guix-patches;

Reported by: "MadalinIonel.Patrascu <at> mdc-berlin.de" <MadalinIonel.Patrascu <at> mdc-berlin.de>

Date: Thu, 28 Oct 2021 18:25:01 UTC

Severity: normal

Done: Ricardo Wurmus <rekado <at> elephly.net>

Bug is archived. No further changes may be made.

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Report forwarded to guix-patches <at> gnu.org:
bug#51464; Package guix-patches. (Thu, 28 Oct 2021 18:25:02 GMT) Full text and rfc822 format available.

Acknowledgement sent to "MadalinIonel.Patrascu <at> mdc-berlin.de" <MadalinIonel.Patrascu <at> mdc-berlin.de>:
New bug report received and forwarded. Copy sent to guix-patches <at> gnu.org. (Thu, 28 Oct 2021 18:25:02 GMT) Full text and rfc822 format available.

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

From: "MadalinIonel.Patrascu <at> mdc-berlin.de"
 <MadalinIonel.Patrascu <at> mdc-berlin.de>
To: "guix-patches <at> gnu.org" <guix-patches <at> gnu.org>
Subject: Add r-xnastring (bioconductor) and r-formattable (cran)
Date: Thu, 28 Oct 2021 18:24:18 +0000
[Message part 1 (text/plain, inline)]

[Message part 2 (text/html, inline)]

Information forwarded to guix-patches <at> gnu.org:
bug#51464; Package guix-patches. (Thu, 28 Oct 2021 18:27:01 GMT) Full text and rfc822 format available.

Message #8 received at 51464 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <51464 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 1/2] gnu: Add r-formattable.
Date: Thu, 28 Oct 2021 20:26:08 +0200
* gnu/packages/cran.scm (r-formattable): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 792ea2a75b..03a1b3206a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -23669,6 +23669,35 @@ (define-public r-forecast
 space models and automatic ARIMA modelling.")
     (license license:gpl3)))
 
+(define-public r-formattable
+  (package
+    (name "r-formattable")
+    (version "0.2.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "formattable" version))
+        (sha256
+          (base32 "1vdxi0xmg019qyzjrp8bkjxciz245jcxsrkhfzd44ynqcwi4s3ag"))))
+    (properties `((upstream-name . "formattable")))
+    (build-system r-build-system)
+    (propagated-inputs
+    `(("r-htmltools" ,r-htmltools)
+      ("r-htmlwidgets" ,r-htmlwidgets)
+      ("r-lifecycle" ,r-lifecycle)
+      ("r-rmarkdown" ,r-rmarkdown)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/renkun-ken/formattable")
+    (synopsis "Printing vectors and data frames with text fromatting")
+    (description
+      "This R package @code{r-formattable} provides functions to create
+formattable vectors and data frames.  @emph{Formattable} vectors are printed
+with text formatting, and formattable data frames are printed with multiple
+types of formatting in HTML to improve the readability of data presented in
+tabular form rendered in web pages.")
+    (license license:expat)))
+
 (define-public r-xmisc
   (package
     (name "r-xmisc")
-- 
2.33.0





Information forwarded to guix-patches <at> gnu.org:
bug#51464; Package guix-patches. (Thu, 28 Oct 2021 18:27:02 GMT) Full text and rfc822 format available.

Message #11 received at 51464 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <51464 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 2/2] gnu: Add r-xnastring.
Date: Thu, 28 Oct 2021 20:26:09 +0200
* gnu/packages/bioconductor.scm (r-xnastring): New variable.
---
 gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 90a0e1f288..abb5b7065d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4627,6 +4627,50 @@ (define-public r-vsn
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
+(define-public r-xnastring
+  (package
+    (name "r-xnastring")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "XNAString" version))
+       (sha256
+        (base32 "1rpcvn54a6s3iwmdg96rshilr1mqcb1nlbvzbyp5xi55km7iwm8i"))))
+    (properties `((upstream-name . "XNAString")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-data-table" ,r-data-table)
+       ("r-formattable" ,r-formattable)
+       ("r-future-apply" ,r-future-apply)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-htmltools" ,r-htmltools)
+       ("r-htmlwidgets" ,r-htmlwidgets)
+       ("r-iranges" ,r-iranges)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-stringi" ,r-stringi)
+       ("r-stringr" ,r-stringr)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://git.bioconductor.org/packages/XNAString")
+    (synopsis "Manipulation of modified oligonucleotide sequences")
+    (description
+     "The R @code{XNAString} package allows for description of base sequences
+and associated chemical modifications in a single object.  XNAString is able to
+capture single stranded, as well as double stranded molecules.  Chemical
+modifications are represented as independent strings associated with different
+features of the molecules (base sequence, sugar sequence, backbone sequence,
+modifications) and can be read or written to a @dfn{Hierarchical Editing
+Language for Macromolecules} (HELM) notation.  It also enables secondary
+structure prediction using RNAfold from ViennaRNA.  XNAString is designed to be
+efficient representation of nucleic-acid based therapeutics, therefore it
+stores information about target sequences and provides interface for matching
+and alignment functions from Biostrings package.")
+    (license license:gpl2)))
+
 (define-public r-xvector
   (package
     (name "r-xvector")
-- 
2.33.0





Information forwarded to guix-patches <at> gnu.org:
bug#51464; Package guix-patches. (Sat, 30 Oct 2021 19:56:02 GMT) Full text and rfc822 format available.

Message #14 received at 51464 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 51464 <at> debbugs.gnu.org
Subject: Add r-xnastring (bioconductor) and r-formattable (cran)
Date: Sat, 30 Oct 2021 19:52:37 +0000
Hi,

thanks for the patches!

I was just about to apply them (with minor changes to indentation 
and description) when I noticed this sentence:

   It also enables secondary structure prediction using RNAfold 
   from ViennaRNA

ViennaRNA is known to be non-free software.  Could you please 
check the source code once again to be absolutely sure that the 
GPLv2 does in fact apply to the full source code?

I’ll apply r-formattable first.

-- 
Ricardo




Reply sent to Ricardo Wurmus <rekado <at> elephly.net>:
You have taken responsibility. (Sat, 27 Nov 2021 20:26:01 GMT) Full text and rfc822 format available.

Notification sent to "MadalinIonel.Patrascu <at> mdc-berlin.de" <MadalinIonel.Patrascu <at> mdc-berlin.de>:
bug acknowledged by developer. (Sat, 27 Nov 2021 20:26:01 GMT) Full text and rfc822 format available.

Message #19 received at 51464-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 51464-done <at> debbugs.gnu.org
Subject: Add r-xnastring (bioconductor) and r-formattable (cran)
Date: Sat, 27 Nov 2021 21:23:42 +0100
The r-xnastring package includes source code of ViennaRNA, which 
is not free software.  See also: 
https://github.com/ViennaRNA/ViennaRNA/issues/97

I don’t think we can add r-xnastring, so I’m closing this.

-- 
Ricardo




bug archived. Request was from Debbugs Internal Request <help-debbugs <at> gnu.org> to internal_control <at> debbugs.gnu.org. (Sun, 26 Dec 2021 12:24:07 GMT) Full text and rfc822 format available.

This bug report was last modified 2 years and 83 days ago.

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