From 380e8fc9fe78fe97597a87a9ce97b014f00ff1ab Mon Sep 17 00:00:00 2001
From: rmflight <r.flight79@gmail.com>
Date: Fri, 26 Jul 2024 15:17:45 -0400
Subject: [PATCH] adds fixes for NOTES

- parsing NEWS file
- missing full definition of vignette engine in vignettes
---
 DESCRIPTION                       |  2 +-
 NEWS                              | 49 +++++++++++++++++++++++++++----
 vignettes/v2_guide.Rmd            |  2 +-
 vignettes/v2_visnetwork_guide.Rmd |  2 +-
 4 files changed, 46 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b8526ea..6af55b4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: categoryCompare2
-Version: 0.100.22
+Version: 0.100.23
 Title: Meta-Analysis of High-Throughput Experiments Using Feature
         Annotations
 Author: Robert M. Flight <rflight79@gmail.com>
diff --git a/NEWS b/NEWS
index 05fa7a7..ec3b564 100644
--- a/NEWS
+++ b/NEWS
@@ -1,6 +1,43 @@
-2.0.0 Complete redesign! Comparisons are of first importance, enrichments are added on after.
-1.5.1 Fixed vignette issue with new version of limma
-0.99.0 First review in Bioconductor
-0.7.8 Updated the vignette. Removed long lines, added links to figures, fixed some errors
-0.7.4 changed category in ccCompare to categoryName for GENccEnrichResults-class
-0.7.3 First commit
+# categoryCompare2 0.100.22
+
+- Fixed a bug where if nothing was significant, then all annotations were pulled into the graph.
+
+# categoryCompare2 0.100.21
+
+- Added more output in the binomial testing.
+
+# categoryCompare2 0.100.16
+
+- Fixing bugs around binomial testing.
+
+# categoryCompare2 0.100.9
+
+- Better importing of gocats objects.
+
+# categoryCompare2 0.100.8
+
+- Made it possible to do iterative filtering and grouping of the graph in the CLI.
+
+# categoryCompare2 0.100.7
+
+- Fixes to the CLI.
+
+# categoryCompare2 0.100.1
+
+- P-value adjustment is done by default.
+
+# categoryCompare2 0.99.161
+
+- Binomial enrichment.
+
+# categoryCompare2 0.99.160
+
+- Document finding communities in the vignettes.
+
+# categoryCompare2 0.99.159
+
+- CLI executables are available.
+
+# categoryCompare2 0.99.129
+
+- Really became the try inheritor to the original categoryCompare.
diff --git a/vignettes/v2_guide.Rmd b/vignettes/v2_guide.Rmd
index 40913b2..e0f1fbf 100644
--- a/vignettes/v2_guide.Rmd
+++ b/vignettes/v2_guide.Rmd
@@ -8,7 +8,7 @@ editor_options:
 
 
 <!--
-% \VignetteEngine{knitr}
+% \VignetteEngine{knitr::rmarkdown}
 % \VignetteIndexEntry{categoryCompare: High-throughput data meta-analysis using gene annotations, V2}
 % \VignetteDepends{categoryCompare2, GO.db, affy, hgu95av2.db, genefilter, estrogen, limma, Cairo, hgu95av2cdf}
 % \VignetteKeyword{categoryCompare, meta-analysis, gene ontology, kegg}
diff --git a/vignettes/v2_visnetwork_guide.Rmd b/vignettes/v2_visnetwork_guide.Rmd
index 4e61544..3d70c88 100644
--- a/vignettes/v2_visnetwork_guide.Rmd
+++ b/vignettes/v2_visnetwork_guide.Rmd
@@ -5,7 +5,7 @@ editor_options:
   chunk_output_type: console
 ---
 <!--
-% \VignetteEngine{knitr}
+% \VignetteEngine{knitr::rmarkdown}
 % \VignetteIndexEntry{categoryCompare2: visNetwork}
 % \VignetteDepends{categoryCompare2, GO.db, affy, hgu95av2.db, genefilter, estrogen, limma, DiagrammeR, visNetwork, Cairo}
 % \VignetteKeyword{categoryCompare, meta-analysis, gene ontology, kegg}