MadalinIonel.Patrascu@mdc-berlin.de wrote 3 years ago
(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
1a5699df937b4f44a0d5676a832487e9@mdc-berlin.de
Add r-xnastring (bioconductor) and r-formattable (cran)
- Done
Details
- 3 participants
- MadalinIonel.Patrascu@mdc-berlin.de
- Mădălin Ionel Patrașcu
- Ricardo Wurmus
- Owner
- unassigned
- Submitted by
- MadalinIonel.Patrascu@mdc-berlin.de
- Severity
- normal
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 1/2] gnu: Add r-formattable.
(address . 51464@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)
20211028182609.1880-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/cran.scm (r-formattable): New variable.
---
gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
Toggle diff (42 lines)
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
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 2/2] gnu: Add r-xnastring.
(address . 51464@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)
20211028182609.1880-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-xnastring): New variable.
---
gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
Toggle diff (57 lines)
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
Ricardo Wurmus wrote 3 years ago
Add r-xnastring (bioconductor) and r-formattable (cran)
(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 51464@debbugs.gnu.org)
87mtmqwane.fsf@elephly.net
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
Ricardo Wurmus wrote 3 years ago
(address . 51464-done@debbugs.gnu.org)
871r31pcrk.fsf@elephly.net
The r-xnastring package includes source code of ViennaRNA, which
is not free software. See also:
I don’t think we can add r-xnastring, so I’m closing this.
--
Ricardo
Closed
?