GNU bug report logs - #59908
[PATCH] gnu: Add r-rcppde, r-ptw, r-pepsnmr and r-asics.

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 59908 in the body.
You can then email your comments to 59908 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

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: [PATCH] gnu: Add r-rcppde, r-ptw, r-pepsnmr and r-asics.
Date: Thu, 8 Dec 2022 18:41:17 +0000

[Message part 1 (text/plain, inline)]

* gnu/packages/bioconductor.scm (r-pepsnmr, r-asics): New variables.
* gnu/packages/cran.scm (r-rcppde, r-ptw): New variables.

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

Message #8 received at 59908 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <59908 <at> debbugs.gnu.org>
Subject: [PATCH 2/4] gnu: Add r-ptw.
Date: Thu, 8 Dec 2022 20:22:30 +0100

* gnu/packages/cran.scm (r-ptw): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 016eeb4821..4561d50e02 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4858,6 +4858,32 @@ (define-public r-powerlaw
     ;; Any of these GPL versions.
     (license (list license:gpl2 license:gpl3))))
 
+(define-public r-ptw
+  (package
+    (name "r-ptw")
+    (version "1.9-16")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "ptw" version))
+              (sha256
+               (base32
+                "0rma3h9ksc5qigdvk5vappb4ipd4rpk64wckzcxvxspakr5w71vy"))))
+    (properties `((upstream-name . "ptw")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rcppde))
+    (home-page "https://github.com/rwehrens/ptw")
+    (synopsis "Parametric time warping")
+    (description
+     "Parametric time warping aligns patterns.  It aims to put corresponding
+features at the same locations.  The algorithm searches for an optimal polynomial
+describing the warping.  It is possible to align one sample to a reference, several
+samples to the same reference, or several samples to several references.  One can
+choose between calculating individual warpings, or one global warping for a set
+of samples and one reference.  Two optimization criteria are implemented: @acronym{
+RMS, Root Mean Square} error and @acronym{WCC, Weighted Cross Correlation}.  Both
+warping of peak profiles and of peak lists are supported.")
+    (license license:gpl2+)))
+
 (define-public r-compare
   (package
     (name "r-compare")
-- 
2.38.1

Message #11 received at 59908 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <59908 <at> debbugs.gnu.org>
Subject: [PATCH 1/4] gnu: Add r-rcppde.
Date: Thu, 8 Dec 2022 20:22:29 +0100

* gnu/packages/cran.scm (r-rcppde): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5c5258d6e0..016eeb4821 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4569,6 +4569,32 @@ (define-public r-rcpp
 @code{citation(\"Rcpp\")} for details on these last two.")
     (license license:gpl2+)))
 
+(define-public r-rcppde
+  (package
+    (name "r-rcppde")
+    (version "0.1.6")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "RcppDE" version))
+              (sha256
+               (base32
+                "1i9jj595nqpb16y22z2b8fcf0gq1fg0pbiisbd837p1cyw4nff69"))))
+    (properties `((upstream-name . "RcppDE")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-rcpp
+           r-rcpparmadillo))
+    (home-page "https://cran.r-project.org/package=RcppDE")
+    (synopsis "Global optimization by differential evolution in C++")
+    (description
+     "This package provides an iteration of the @code{DEoptim} function.  It
+performs global optimization by differential evolution.  The implementation
+employs the @code{Rcpp} package.  The last one provides tools for integration
+of R objects at the C++ level—and vice versa.  @code{R-rcppde} uses the @code{
+RcppArmadillo} package.  This one provides an interface from R to the Armadillo
+linear algebra package written in C++.")
+    (license license:gpl2+)))
+
 (define-public r-rcppml
   (package
     (name "r-rcppml")

base-commit: 81191e3410cc00c6438f532599dd0b96d521982f
-- 
2.38.1

Message #14 received at 59908 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <59908 <at> debbugs.gnu.org>
Subject: [PATCH 3/4] gnu: Add r-pepsnmr.
Date: Thu, 8 Dec 2022 20:22:31 +0100

* gnu/packages/bioconductor.scm (r-pepsnmr): New variable.
---
 gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c62c5970b8..740ec4b84b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8323,6 +8323,35 @@ (define-public r-perfmeas
 a given recall, F-score for single and multiple classes are available.")
     (license license:gpl2+)))
 
+(define-public r-pepsnmr
+  (package
+    (name "r-pepsnmr")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "PepsNMR" version))
+              (sha256
+               (base32
+                "02i29jinawssqlb33wvj0h9w6cfcvamlyfxdynd38jmwx23l15l5"))))
+    (properties `((upstream-name . "PepsNMR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ggplot2
+           r-gridextra
+           r-matrix
+           r-matrixstats
+           r-ptw
+           r-reshape2))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/ManonMartin/PepsNMR")
+    (synopsis "Pre-process 1H-NMR FID signals")
+    (description
+     "This package provides R functions for common pre-processing steps that are
+applied on @acronym{1H-NMR, proton nuclear magnetic resonance} data.  It also
+provides a function to read the @acronym{FID, free induction decay} signals
+directly in the Bruker format.")
+    (license license:gpl2)))
+
 ;; This is a CRAN package, but it depends on a Bioconductor package.
 (define-public r-codedepends
   (package
-- 
2.38.1

Message #17 received at 59908 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <59908 <at> debbugs.gnu.org>
Subject: [PATCH 4/4] gnu: Add r-asics.
Date: Thu, 8 Dec 2022 20:22:32 +0100

* gnu/packages/bioconductor.scm (r-asics): New variable.
---
 gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 740ec4b84b..64dbea97d0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2720,6 +2720,40 @@ (define-public r-asgsca
 model as latent variables.")
     (license license:gpl3)))
 
+(define-public r-asics
+  (package
+    (name "r-asics")
+    (version "2.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ASICS" version))
+              (sha256
+               (base32
+                "0c2b3gdza58vqhharhw8967p2w2knnrm5s2svvnnjbf67qbg45b7"))))
+    (properties `((upstream-name . "ASICS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-ggplot2
+           r-glmnet
+           r-gridextra
+           r-matrix
+           r-mvtnorm
+           r-pepsnmr
+           r-plyr
+           r-quadprog
+           r-ropls
+           r-summarizedexperiment
+           r-zoo))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/ASICS")
+    (synopsis "Automatic statistical identification in complex spectra")
+    (description
+     "@code{ASICS} quantifies concentration of metabolites in a complex spectrum.
+The identification of metabolites is performed by fitting a mixture model to the
+spectra of the library with a sparse penalty.")
+    (license license:gpl2+)))
+
 (define-public r-aspli
   (package
     (name "r-aspli")
-- 
2.38.1

Message #22 received at 59908-done <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: 59908-done <at> debbugs.gnu.org
Subject: Re: [bug#59908] [PATCH 1/4] gnu: Add r-rcppde.
Date: Mon, 12 Dec 2022 18:44:34 +0100

Thanks for the patches.  I applied them with negligible formatting
changes.

-- 
Ricardo

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.