Subject: bug#54903: closed ([PATCH] gnu: r-catalyst: Update to 1.18.1.)

From: [email-masked] (GNU bug Tracking System)
Date: Thu, 14 Apr 2022 09:47:02 +0000

Your bug report

#54903: [PATCH] gnu: r-catalyst: Update to 1.18.1.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to [email-masked].

-- 
54903: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=54903
GNU Bug Tracking System
Contact [email-masked] with problems

Subject: [PATCH] gnu: r-catalyst: Update to 1.18.1.
From: Ricardo Wurmus <[email-masked]>
To: [email-masked]
Date: Thu, 14 Apr 2022 11:44:58 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

Thanks for the patch.

I edited the description a little bit and applied it.  Since I already
made a bulk upgrade of all Bioconductor packages (better to keep them
all in sync) I edited the commit message to only refer to the changes
to the description.

-- 
Ricardo

Subject: [PATCH] gnu: r-catalyst: Update to 1.18.1.
From: Mădălin Ionel Patrașcu<[email-masked]>
To: <[email-masked]>
Date: Wed, 13 Apr 2022 13:21:03 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

* gnu/packages/bioconductor.scm (r-catalyst): Update to 1.18.1.
[description]: Add Texinfo markups and clarify a sentence.
---
 gnu/packages/bioconductor.scm | 31 +++++++++++++++++++------------
 1 file changed, 19 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 803437a033..d57a09f39d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13786,14 +13786,14 @@ (define-public r-msmstests
 (define-public r-catalyst
   (package
     (name "r-catalyst")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "CATALYST" version))
         (sha256
           (base32
-            "15lah45lf16zh1ankbpjvz8zp38lldvq074nmvb99rhhqys2gbgi"))))
+            "0dvcs7nz1yawcrsf9lqiwdcrvjmbs8ajrmvj0ji4qq2a86n3dkg0"))))
     (properties `((upstream-name . "CATALYST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13829,16 +13829,23 @@ (define-public r-catalyst
       "https://github.com/HelenaLC/CATALYST")
     (synopsis "Cytometry data analysis tools")
     (description
-      "This package is Cytometry dATa anALYSis Tools (CATALYST).  Mass
-cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
-reporters to label antibodies, thereby substantially decreasing spectral
-overlap and allowing for examination of over 50 parameters at the single cell
-level.  While spectral overlap is significantly less pronounced in CyTOF than
-flow cytometry, spillover due to detection sensitivity, isotopic impurities,
-and oxide formation can impede data interpretability.  We designed
-CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
-preprocessing of cytometry data, including i) normalization using bead
-standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
+      "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST).  Mass
+cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal
+isotopes rather than fluorescent tags as reporters to label antibodies, thereby
+substantially decreasing spectral overlap and allowing for examination of over
+50 parameters at the single cell level.  While spectral overlap is
+significantly less pronounced in CyTOF than flow cytometry, spillover due to
+detection sensitivity, isotopic impurities, and oxide formation can impede data
+interpretability.  We designed @code{CATALYST} to provide a pipeline for
+preprocessing of cytometry data, including:
+@enumerate
+@item
+normalization using bead standards;
+@item
+single-cell deconvolution;
+@item
+bead-based compensation.
+@end enumerate")
     (license license:gpl2+)))
 
 (define-public r-erma
-- 
2.34.0