From bd12aead95664c7fa52e3fb6aab68232527cef1b Mon Sep 17 00:00:00 2001
From: "Afkhami, Navid" <Navid.Afkhami@mdc-berlin.de>
Date: Fri, 13 Oct 2023 15:57:14 +0000
Subject: [PATCH] gnu: r-tgstat: Update to 2.3.24.

* gnu/packages/statistics.scm (r-tgstat): Delete variable.
* gnu/packages/cran.scm (r-tgstat): Add updated variable here.
[native-inputs]: Add r-knitr.
[propagated-inputs]: Remove r-rcpp.
[arguments]: Remove fix-isnan phase.
---
 gnu/packages/cran.scm       | 23 +++++++++++++++++++++++
 gnu/packages/statistics.scm | 35 -----------------------------------
 2 files changed, 23 insertions(+), 35 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1c37635ea5..de31f44dbd 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3257,6 +3257,29 @@ (define-public r-tgp
 noisy black-box functions.")
     (license license:lgpl2.0+)))
 
+(define-public r-tgstat
+  (package
+    (name "r-tgstat")
+    (version "2.3.24")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tgstat" version))
+       (sha256
+        (base32 "0czd3j7z30jgb03813s0jc0701ypnwpkkq7var6n6f6cj7sdvc0l"))))
+    (properties `((upstream-name . "tgstat")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "https://cran.r-project.org/package=tgstat")
+    (synopsis "Amos Tanay's Group High Performance Statistical Utilities")
+    (description
+     "This package provides a collection of high-performance utilities.
+It can be used to compute distances, correlations, autocorrelations,
+clustering, and other tasks.  It also contains a graph clustering
+algorithm described in MetaCell analysis of single-cell RNA-seq
+data using K-nn graph partitions.")
+    (license license:gpl2)))
+
 (define-public r-tidyft
   (package
     (name "r-tidyft")
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 64ed73d16a..2ee41bd8e5 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -6527,41 +6527,6 @@ (define-public r-forcats
 manually \"recoding\").")
     (license license:gpl3)))
 
-(define-public r-tgstat
-  (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
-        (revision "1"))
-    (package
-      (name "r-tgstat")
-      (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
-      (source
-       (origin
-         (method hg-fetch)
-         (uri (hg-reference
-               (url "https://bitbucket.org/tanaylab/tgstat")
-               (changeset changeset)))
-         (file-name (string-append name "-" version "-checkout"))
-         (sha256
-          (base32
-           "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
-      (build-system r-build-system)
-      (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'fix-isnan
-             (lambda _
-               (substitute* "src/tgstat.h"
-                 (("#define isnan ::isnan")
-                  "#define isnan std::isnan"))
-               #t)))))
-      (propagated-inputs
-       (list r-rcpp))
-      (home-page "https://bitbucket.org/tanaylab/tgstat/")
-      (synopsis "Tanay's group statistical utilities")
-      (description
-       "The goal of tgstat is to provide fast and efficient statistical
-tools.")
-      (license license:gpl2))))
-
 (define-public r-tgconfig
   (let ((commit "15cf199436ae0b2ac0006b2ca7f0aeeb5c9d4445")
         (revision "1"))