renames a couple of files to try and avoid

long file path warnings

.Rbuildignore

@@ -24,3 +24,5 @@ test_combine_filter.rda
 ^annotations\.json$
 ^test_cytoscape\.rda$
 ^cc2_results_grouped\.txt$
+^doc$
+^Meta$

.gitignore

@@ -3,3 +3,5 @@
 .RData
 executable_related/
 inst/doc
+/doc/
+/Meta/

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: categoryCompare2
-Version: 0.100.19
+Version: 0.100.20
 Title: Meta-Analysis of High-Throughput Experiments Using Feature
         Annotations
 Author: Robert M. Flight <[email protected]>

vignettes/command_line_interface.Rmd

@@ -11,16 +11,18 @@ vignette: >
 ---
 
 ```{r, include = FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>"
-)
-
 if (grepl("mingw", R.version$os)) {
   run_chunks = FALSE
 } else {
   run_chunks = TRUE
 }
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  eval = run_chunks
+)
+
+
 ```
 
 ```{r setup}
@@ -42,7 +44,6 @@ remotes::install("moseleybioinformaticslab/categorycompare2")
 
 ```{r}
 #| label: add-to-path
-#| eval: run_chunks
 cli_location = system.file("exec", package = "categoryCompare2")
 cli_location
 dir(cli_location)
@@ -64,7 +65,6 @@ Assuming that we've saved the path in a shell variable, `CLI_LOCATION`, we can a
 
 ```{sh}
 #| label: add-path-check
-#| eval: run_chunks
 export PATH="$PATH:$CLI_LOCATION"
 chmod 0750 $CLI_LOCATION/*.R 
 ```
@@ -102,7 +102,6 @@ Sys.setenv(TESTLOC = test_loc)
 
 ```{bash}
 #| label: run-everything
-#| eval: run_chunks
 export CURR_DIR=$(pwd)
 export WORKING=$CURR_DIR/cc2_1234
 mkdir -p $WORKING

vignettes/categoryCompare_vignette_v2_visnetwork.Rmd → vignettes/v2_visnetwork_guide.Rmd

@@ -1,12 +1,12 @@
 ---
-title: "categoryCompare2: Alternative Visualization"
+title: "categoryCompare2: visNetwork"
 output: html_document
 editor_options: 
   chunk_output_type: console
 ---
 <!--
 % \VignetteEngine{knitr}
-% \VignetteIndexEntry{categoryCompare2: Alternative Visualization}
+% \VignetteIndexEntry{categoryCompare2: visNetwork}
 % \VignetteDepends{categoryCompare2, GO.db, affy, hgu95av2.db, genefilter, estrogen, limma, DiagrammeR, visNetwork, Cairo}
 % \VignetteKeyword{categoryCompare, meta-analysis, gene ontology, kegg}
 % \VignettePackage{categoryCompare2}