Merge pull request #54 from MoTrPAC/update-vignette

Update dependencies
MoTrPAC · Nov 10, 2023 · 0f38357 · 0f38357
2 parents 2ae5313 + c59598d
commit 0f38357
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Showing 6 changed files with 18 additions and 6 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -11,3 +11,4 @@ devnotes.md
 ^workshops$
 ^\.github$
 ^reports$
+CODEOWNERS
diff --git a/CODEOWNERS b/CODEOWNERS
@@ -0,0 +1 @@
+* @nicolerg
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Type: Package
 Package: MotrpacRatTraining6mo
 Title: Analysis of the MoTrPAC endurance exercise training data in
     6-month-old rats
-Version: 1.6.4
+Version: 1.6.5
 Authors@R: c(
     person("Nicole", "Gay", , "nicole.r.gay@gmail.com", role = c("cre", "aut")),
     person("David", "Amar", , "ddam.am@gmail.com", role = "aut"),
@@ -66,7 +66,8 @@ Suggests:
     MotrpacBicQC (>= 0.6.9),
     multcomp,
     parallel,
-    RCy3,
+    plotrix,
+    RCy3 (>= 2.23.2),
     repfdr,
     RMariaDB,
     rmarkdown,
@@ -89,12 +90,14 @@ Remotes:
     MoTrPAC/MotrpacRatTraining6moData,
     MoTrPAC/MotrpacBicQC,
     YuLab-SMU/ggtree,
-    nicolerg/ssGSEA2
+    nicolerg/ssGSEA2,
+    cytoscape/RCy3,
+    plotrix/plotrix
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Depends: 
-    MotrpacRatTraining6moData (>= 1.8.0),
+    MotrpacRatTraining6moData (>= 2.0.0),
     R (>= 2.10)
 LazyData: true
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# MotrpacRatTraining6mo 1.6.5 (2023-11-08)
+
+* Point to development version of `RCy3` from GitHub to avoid `R-CMD check` error `RCy3: Can't install dependency uchardet`. 
+* Install `plotrix` from GitHub instead of CRAN to avoid `R-CMD check` warning `Requires (indirectly) orphaned package: ‘plotrix’`. 
+  CRAN has marked `plotrix` as orphaned. `plotrix` is a dependency for `mutoss`, which is a dependency for `metap`.
+* Increment required `MotrpacRatTraining6moData` version.
+
 # MotrpacRatTraining6mo 1.6.4 (2023-06-02)
 
 * Bug fix in `transcript_timewise_da()` to run with limited contrasts when `tissue="VENACV"`.

diff --git a/vignettes/MotrpacRatTraining6mo.Rmd b/vignettes/MotrpacRatTraining6mo.Rmd
@@ -64,7 +64,7 @@ div.yellow {
 
 <div class = "yellow">
 
-This vignette is under construction. If something is unclear or obviously missing, 
+If you run into problems,
 please submit an issue [here](https://github.com/MoTrPAC/MotrpacRatTraining6mo/issues). 
 
 </div>

diff --git a/vignettes/key_metabolites.Rmd b/vignettes/key_metabolites.Rmd
@@ -11,7 +11,7 @@ output:
     highlight: tango
 
 vignette: >
-  %\VignetteIndexEntry{Tutorial for MotrpacRatTraining6mo R package}
+  %\VignetteIndexEntry{Key metabolites}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
   %\usepackage[utf8]{inputenc}