Revert epigenomics vignette to eval=FALSE: remote bigwig access too fragile for CI

These chunks download large bigwig files from UCSC and fail intermittently
on GHA runners. Keep as reference code blocks with explanatory notes.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: bschilder

vignettes/cell_type_specific_epigenomics.Rmd

@@ -13,12 +13,6 @@ vignette: >
 ```{r setup, echo=FALSE, include=FALSE}
 pkg <- read.dcf("../DESCRIPTION", fields = "Package")[1]
 library(pkg, character.only = TRUE)
-has_internet <- tryCatch(
-    !is.null(curl::nslookup("github.com", error = FALSE)),
-    error = function(e) FALSE
-)
-## Epigenomic data functions require remote bigwig access (not available on Windows)
-can_run <- has_internet && .Platform$OS.type != "windows"
 ```
 
 ```R
@@ -34,7 +28,10 @@ library(`r pkg`)
 
 ### Import data
 
-```{r nott2019_import, eval=can_run}
+*Note:* These functions download remote bigwig files from UCSC, which
+requires network access and may take several minutes.
+
+```{r nott2019_import, eval=FALSE}
 superenhancers <- echoannot::get_NOTT2019_superenhancer_interactome()
 enhancers_promoters <- echoannot::NOTT2019_get_promoter_interactome_data()
 peaks <- echoannot::NOTT2019_get_epigenomic_peaks()
@@ -43,15 +40,15 @@ peaks <- echoannot::NOTT2019_get_epigenomic_peaks()
 
 ### Plot
 
-```{r nott2019_plot, eval=can_run}
+```{r nott2019_plot, eval=FALSE}
 dat <- echodata::BST1
 histo_out <- echoannot::NOTT2019_epigenomic_histograms(dat = dat)
 ```
 
 In addition to the plot object,
 tables of both raw read ranges and called peaks are included in the output list.
 
-```{r nott2019_tables, eval=can_run}
+```{r nott2019_tables, eval=FALSE}
 knitr::kable(head(histo_out$data$raw))
 knitr::kable(head(histo_out$data$peaks))
 ```
@@ -60,13 +57,13 @@ knitr::kable(head(histo_out$data$peaks))
 ## Corces2020
 
 `echoannot` also includes data generated by
-["Corces2019"](https://doi.org/10.1038/s41588-020-00721-x):
+["Corces2020"](https://doi.org/10.1038/s41588-020-00721-x):
 
 > Corces, M.R., Shcherbina, A., Kundu, S. et al. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases. Nat Genet 52, 1158-1168 (2020). https://doi.org/10.1038/s41588-020-00721-x
 
 ### Import data
 
-```{r corces2020_import, eval=can_run}
+```{r corces2020_import, eval=FALSE}
 bulkATACseq_peaks <- echoannot::get_CORCES2020_bulkATACseq_peaks()
 cicero_coaccessibility <- echoannot::get_CORCES2020_cicero_coaccessibility()
 hichip_fithichip_loop_calls <- echoannot::get_CORCES2020_hichip_fithichip_loop_calls()
@@ -76,9 +73,6 @@ scATACseq_peaks <- echoannot::get_CORCES2020_scATACseq_peaks()
 
 ### Plot
 
-*Note:* This chunk is kept as `eval=FALSE` because it depends on
-the `dat` variable from a prior analysis and `ggbio::autoplot`.
-
 ```{r corces2020_plot, eval=FALSE}
 peak_dat <- echoannot::granges_overlap(
     dat1 = dat,