[bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran)

[bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran)

[MadalinIonel.Patrascu]

[-- Attachment #1: Type: text/plain, Size: 2 bytes --]



[-- Attachment #2: Type: text/html, Size: 368 bytes --]

[bug#51464] [PATCH 1/2] gnu: Add r-formattable.

[Mădălin Ionel Patrașcu]

* 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

[bug#51464] [PATCH 2/2] gnu: Add r-xnastring.

[Mădălin Ionel Patrașcu]

* 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

[bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran)

[Ricardo Wurmus]

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

bug#51464: Add r-xnastring (bioconductor) and r-formattable (cran)

[Ricardo Wurmus]

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