prints the os we are running on

.github/workflows/r.yml

@@ -47,6 +47,10 @@ jobs:
       - name: Reinstall preprocessCore
         run: BiocManager::install("preprocessCore", configure.args = c(preprocessCore = "--disable-threading"), force= TRUE, update=TRUE, type = "source")
         shell: Rscript {0}
+
+      - name: check os
+        run: R.version$os
+        shell: Rscript {0}
 
       - uses: r-lib/actions/check-r-package@v2
 

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: categoryCompare2
-Version: 0.100.18
+Version: 0.100.19
 Title: Meta-Analysis of High-Throughput Experiments Using Feature
         Annotations
 Author: Robert M. Flight <[email protected]>

vignettes/categoryCompare_vignette_v2.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "categoryCompare: High-throughput data meta-analysis using feature annotations"
+title: "categoryCompare: High-throughput data meta-analysis using gene annotations, V2"
 author: "Robert M Flight"
 date: "`r Sys.time()`"
 editor_options: 

vignettes/categoryCompare_vignette_v2_visnetwork.Rmd

@@ -1,4 +1,5 @@
 ---
+title: "categoryCompare2: Alternative Visualization"
 output: html_document
 editor_options: 
   chunk_output_type: console
@@ -123,15 +124,15 @@ in the GO DAG. We can generate this list using the `GOALL` column of the `org.Hs
 and then filter to the terms of interest, or use them all.
 
 ```{r create_go_annotation}
-go_all_gene <- select(org.Hs.eg.db, keys = gUniverse, columns = c("GOALL", "ONTOLOGYALL"))
+go_all_gene <- AnnotationDbi::select(org.Hs.eg.db, keys = gUniverse, columns = c("GOALL", "ONTOLOGYALL"))
 go_all_gene <- go_all_gene[go_all_gene$ONTOLOGYALL == "BP", ]
 bp_2_gene <- split(go_all_gene$ENTREZID, go_all_gene$GOALL)
 
 bp_2_gene <- lapply(bp_2_gene, unique)
-bp_desc <- select(GO.db, keys = names(bp_2_gene), columns = "TERM", keytype = "GOID")$TERM
+bp_desc <- AnnotationDbi::select(GO.db, keys = names(bp_2_gene), columns = "TERM", keytype = "GOID")$TERM
 names(bp_desc) <- names(bp_2_gene)
 
-bp_annotation <- annotation(annotation_features = bp_2_gene,
+bp_annotation <- categoryCompare2::annotation(annotation_features = bp_2_gene,
                             description = bp_desc,
                             annotation_type = "GO.BP")
 ```

vignettes/command_line_interface.Rmd

@@ -1,11 +1,11 @@
 ---
-title: "Command Line Interface"
+title: "categoryCompare2: Command Line Interface"
 output: rmarkdown::html_vignette
 date: "`r Sys.time()`"
 editor_options: 
   chunk_output_type: console
 vignette: >
-  %\VignetteIndexEntry{categoryCompare2: Command Line Internet}
+  %\VignetteIndexEntry{categoryCompare2: Command Line Interface}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -15,6 +15,12 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
+
+if (grepl("mingw", R.version$os)) {
+  run_chunks = FALSE
+} else {
+  run_chunks = TRUE
+}
 ```
 
 ```{r setup}
@@ -36,6 +42,7 @@ remotes::install("moseleybioinformaticslab/categorycompare2")
 
 ```{r}
 #| label: add-to-path
+#| eval: run_chunks
 cli_location = system.file("exec", package = "categoryCompare2")
 cli_location
 dir(cli_location)
@@ -57,13 +64,14 @@ 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 
 ```
 
 After we make the scripts executable, we can check that we can actually use it.
 
-```{bash}
+```bash
 categoryCompare2.R --help
 ```
 
@@ -94,7 +102,7 @@ Sys.setenv(TESTLOC = test_loc)
 
 ```{bash}
 #| label: run-everything
-#| eval: false
+#| eval: run_chunks
 export CURR_DIR=$(pwd)
 export WORKING=$CURR_DIR/cc2_1234
 mkdir -p $WORKING