GNU bug report logs - #70535
[Patch] gnu: Add r-lpsolveapi, r-roi, r-roi-plugin-lpsolve, r-detectseparation and r-metadeconfoundr.

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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-lpsolveapi, r-roi, r-roi-plugin-lpsolve,
 r-detectseparation and r-metadeconfoundr.
Date: Tue, 23 Apr 2024 11:20:14 +0000

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

* gnu/packages/cran.scm (r-lpsolveapi, r-roi, r-roi-plugin-lpsolve, r-detectseparation and r-metadeconfoundr): New variables.

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

Message #8 received at 70535 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70535 <at> debbugs.gnu.org>
Subject: [PATCH 1/5] gnu: Add r-lpsolveapi.
Date: Tue, 23 Apr 2024 13:25:42 +0200

* gnu/packages/cran.scm (r-lpsolveapi): New variable.

Change-Id: I6a93603a5814df0eb43a214b5c2a0f4865901bcd
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ee0aac7f7a..4b6ece1eb1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8191,6 +8191,26 @@ (define-public r-lpsolve
 transportation problems.")
     (license license:lgpl2.0)))
 
+(define-public r-lpsolveapi
+  (package
+    (name "r-lpsolveapi")
+    (version "5.5.2.0-17.11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lpSolveAPI" version))
+       (sha256
+        (base32 "191zjgyap3kcsvh8fygqqyr9p0agbzm160fzynnpaxf19yp6r3dh"))))
+    (properties `((upstream-name . "lpSolveAPI")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/package=lpSolveAPI")
+    (synopsis "Interface to lp_solve")
+    (description
+     "The lpSolveAPI package provides an R interface to lp_solve, a @acronym{MILP,
+Mixed Integer Linear Programming}, solver with support for pure linear, (mixed)
+integer/binary, semi-continuous and @acronym{SOS, special ordered sets} models.")
+    (license license:lgpl2.0)))
+
 (define-public r-limsolve
   (package
     (name "r-limsolve")

base-commit: 2d19e505f6f9f82aebc9ba8c74ba223818acd9bc
-- 
2.41.0

Message #11 received at 70535 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70535 <at> debbugs.gnu.org>
Subject: [PATCH 2/5] gnu: Add r-roi.
Date: Tue, 23 Apr 2024 13:25:43 +0200

* gnu/packages/cran.scm (r-roi): New variable.

Change-Id: I58cbb4be238a5cc9f861ee9dafea03a133f7c0f1
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4b6ece1eb1..53a964e60a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -12211,6 +12211,26 @@ (define-public r-randomizr
 experimental designs and random samples for common sampling designs.")
     (license license:expat)))
 
+(define-public r-roi
+  (package
+    (name "r-roi")
+    (version "1.0-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ROI" version))
+       (sha256
+        (base32 "05hnj9fskfm2klz7zv97lb0r60akjq4a1cay8p62whpi0hri9zyl"))))
+    (properties `((upstream-name . "ROI")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-checkmate r-registry r-slam))
+    (home-page "https://roi.r-forge.r-project.org/")
+    (synopsis "R optimization infrastructure")
+    (description
+     "The @acronym{ROI, R Optimization Infrastructure} is a framework for handling
+optimization problems in R.")
+    (license license:gpl3)))
+
 (define-public r-roptim
   (package
     (name "r-roptim")
-- 
2.41.0

Message #14 received at 70535 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70535 <at> debbugs.gnu.org>
Subject: [PATCH 3/5] gnu: Add r-roi-plugin-lpsolve.
Date: Tue, 23 Apr 2024 13:25:44 +0200

* gnu/packages/cran.scm (r-roi-plugin-lpsolve): New variable.

Change-Id: Ia3f47ba0b414ecd9273c101977ec8d14916fa656
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 53a964e60a..1fdd5eb685 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1680,6 +1680,26 @@ (define-public r-rocit
 metrics.")
     (license license:gpl3)))
 
+(define-public r-roi-plugin-lpsolve
+  (package
+    (name "r-roi-plugin-lpsolve")
+    (version "1.0-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ROI.plugin.lpsolve" version))
+       (sha256
+        (base32 "0xgg1fzq5sba3yvvrci3iw97p31walpnhv4zwnd39gw8v5z6f9dj"))))
+    (properties `((upstream-name . "ROI.plugin.lpsolve")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-lpsolveapi r-roi))
+    (home-page "https://roigrp.gitlab.io")
+    (synopsis "Plugin of lp_solve for the R optimization infrastructure")
+    (description
+     "This package enhances the @acronym{ROI, R Optimization Infrastructure} with
+the lp_solve solver.")
+    (license license:gpl3)))
+
 (define-public r-rorcid
   (package
     (name "r-rorcid")
-- 
2.41.0

Message #17 received at 70535 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70535 <at> debbugs.gnu.org>
Subject: [PATCH 4/5] gnu: Add r-detectseparation.
Date: Tue, 23 Apr 2024 13:25:45 +0200

* gnu/packages/cran.scm (r-detectseparation): New variable.

Change-Id: I6c795719c22a6ff929785e799f749ce053e83fbe
---
 gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1fdd5eb685..57dabc8ec3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4253,6 +4253,38 @@ (define-public r-depmixs4
 mixture models.")
     (license license:gpl2+)))
 
+(define-public r-detectseparation
+  (package
+    (name "r-detectseparation")
+    (version "0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "detectseparation" version))
+       (sha256
+        (base32 "05z3p1z5mhmdj5qdknz1b8f6fwbghzckl88pv79v59cfwpbvgmz8"))))
+    (properties `((upstream-name . "detectseparation")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-lpsolveapi r-pkgload r-roi r-roi-plugin-lpsolve))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/ikosmidis/detectseparation")
+    (synopsis
+     "Detect and check for separation and infinite maximum likelihood estimates")
+    (description
+     "This package provides pre-fit and post-fit methods for detecting separation
+and infinite maximum likelihood estimates in generalized linear models with
+categorical responses.  The pre-fit methods apply on binomial-response generalized
+liner models such as logit, probit and cloglog regression, and can be directly
+supplied as fitting methods to the @code{glm()} function.  The post-fit methods
+apply to models with categorical responses, including binomial-response
+generalized linear models and multinomial-response models, such as baseline
+category logits and adjacent category logits models; for example, the models
+implemented in the brglm2 package.  The post-fit methods successively refit the
+model with increasing number of iteratively reweighted least squares iterations,
+and monitor the ratio of the estimated standard error for each parameter to what
+it has been in the first iteration.")
+    (license license:gpl3)))
+
 (define-public r-readxl
   (package
     (name "r-readxl")
-- 
2.41.0

Message #20 received at 70535 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70535 <at> debbugs.gnu.org>
Subject: [PATCH 5/5] gnu: Add r-metadeconfoundr.
Date: Tue, 23 Apr 2024 13:25:46 +0200

* gnu/packages/cran.scm (r-metadeconfoundr): New variable.

Change-Id: I733fb464d2a3c7fd1335826be9f23e2610e6fd60
---
 gnu/packages/cran.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 57dabc8ec3..46749aa714 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -41612,6 +41612,47 @@ (define-public r-metadat
 analyses.")
     (license license:gpl2+)))
 
+(define-public r-metadeconfoundr
+  ;; There are some consistent updates after the release of version 0.3.0.
+  (let ((commit "90aec0226c5128bfcbbc08903452eff460d21424")
+        (revision "1"))
+    (package
+      (name "r-metadeconfoundr")
+      (version (git-version "0.3.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/TillBirkner/metadeconfoundR")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0zkqar27p5qwq46xbxsw5x1pl50xbkgqiizw5bydlyhwb0ga2f3h"))))
+      (properties `((upstream-name . "metadeconfoundR")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-bigmemory
+                               r-detectseparation
+                               r-doparallel
+                               r-dosnow
+                               r-foreach
+                               r-futile-logger
+                               r-ggplot2
+                               r-lme4
+                               r-lmtest
+                               r-reshape2
+                               r-snow))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/TillBirkner/metadeconfoundR")
+      (synopsis "Check multiple covariates for potenial confounding effects")
+      (description
+       "This package detects naive associations between omics features and
+metadata in cross-sectional data-sets using non-parametric tests.  In a second
+step, confounding effects between metadata associated to the same omics feature
+are detected and labeled using nested post-hoc model comparison tests.  The
+generated output can be graphically summarized using the built-in plotting
+function.")
+      (license license:gpl2))))
+
 (define-public r-mathjaxr
   (package
     (name "r-mathjaxr")
-- 
2.41.0

Message #25 received at 70535-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: 70535-done <at> debbugs.gnu.org
Subject: Re: [bug#70535] [PATCH 1/5] gnu: Add r-lpsolveapi.
Date: Mon, 06 May 2024 11:37:49 +0200

I've applied this series.  Thank you for the patches!
I've moved r-metadeconfoundr to bioconductor.scm because it's not on CRAN.

-- 
Ricardo

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