* [bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran) @ 2021-10-28 18:24 MadalinIonel.Patrascu 2021-10-28 18:26 ` [bug#51464] [PATCH 1/2] gnu: Add r-formattable Mădălin Ionel Patrașcu ` (2 more replies) 0 siblings, 3 replies; 5+ messages in thread From: MadalinIonel.Patrascu @ 2021-10-28 18:24 UTC (permalink / raw) To: 51464 [-- Attachment #1: Type: text/plain, Size: 2 bytes --] [-- Attachment #2: Type: text/html, Size: 368 bytes --] ^ permalink raw reply [flat|nested] 5+ messages in thread
* [bug#51464] [PATCH 1/2] gnu: Add r-formattable. 2021-10-28 18:24 [bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran) MadalinIonel.Patrascu @ 2021-10-28 18:26 ` Mădălin Ionel Patrașcu 2021-10-28 18:26 ` [bug#51464] [PATCH 2/2] gnu: Add r-xnastring Mădălin Ionel Patrașcu 2021-10-30 19:52 ` [bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran) Ricardo Wurmus 2021-11-27 20:23 ` bug#51464: " Ricardo Wurmus 2 siblings, 1 reply; 5+ messages in thread From: Mădălin Ionel Patrașcu @ 2021-10-28 18:26 UTC (permalink / raw) To: 51464; +Cc: rekado, 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 ^ permalink raw reply related [flat|nested] 5+ messages in thread
* [bug#51464] [PATCH 2/2] gnu: Add r-xnastring. 2021-10-28 18:26 ` [bug#51464] [PATCH 1/2] gnu: Add r-formattable Mădălin Ionel Patrașcu @ 2021-10-28 18:26 ` Mădălin Ionel Patrașcu 0 siblings, 0 replies; 5+ messages in thread From: Mădălin Ionel Patrașcu @ 2021-10-28 18:26 UTC (permalink / raw) To: 51464; +Cc: rekado, 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 ^ permalink raw reply related [flat|nested] 5+ messages in thread
* [bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran) 2021-10-28 18:24 [bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran) MadalinIonel.Patrascu 2021-10-28 18:26 ` [bug#51464] [PATCH 1/2] gnu: Add r-formattable Mădălin Ionel Patrașcu @ 2021-10-30 19:52 ` Ricardo Wurmus 2021-11-27 20:23 ` bug#51464: " Ricardo Wurmus 2 siblings, 0 replies; 5+ messages in thread From: Ricardo Wurmus @ 2021-10-30 19:52 UTC (permalink / raw) To: Mădălin Ionel Patrașcu; +Cc: 51464 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 ^ permalink raw reply [flat|nested] 5+ messages in thread
* bug#51464: Add r-xnastring (bioconductor) and r-formattable (cran) 2021-10-28 18:24 [bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran) MadalinIonel.Patrascu 2021-10-28 18:26 ` [bug#51464] [PATCH 1/2] gnu: Add r-formattable Mădălin Ionel Patrașcu 2021-10-30 19:52 ` [bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran) Ricardo Wurmus @ 2021-11-27 20:23 ` Ricardo Wurmus 2 siblings, 0 replies; 5+ messages in thread From: Ricardo Wurmus @ 2021-11-27 20:23 UTC (permalink / raw) To: 51464-done 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 ^ permalink raw reply [flat|nested] 5+ messages in thread
end of thread, other threads:[~2021-11-27 20:26 UTC | newest] Thread overview: 5+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2021-10-28 18:24 [bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran) MadalinIonel.Patrascu 2021-10-28 18:26 ` [bug#51464] [PATCH 1/2] gnu: Add r-formattable Mădălin Ionel Patrașcu 2021-10-28 18:26 ` [bug#51464] [PATCH 2/2] gnu: Add r-xnastring Mădălin Ionel Patrașcu 2021-10-30 19:52 ` [bug#51464] Add r-xnastring (bioconductor) and r-formattable (cran) Ricardo Wurmus 2021-11-27 20:23 ` bug#51464: " Ricardo Wurmus
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