added Error documentation section to rnaseq-rmd.rst and hyperlnked to it in helpers.R error message

docs/rnaseq-rmd.rst

@@ -544,6 +544,28 @@ enrichment RMarkdown document.
 
 The output of sessionInfo records the versions of packages used in the analysis.
 
+Errors
+------
+
+This section addresses errors encountered during the RNA-Seq downstream analysis.
+
+Error: "Found duplicate names after removing pattern ^contr_[^_]+_"
+
+   Cause:
+       - If no duplicate contrast names exist in your ``results_##`` chunks,
+         the error can arise from changes to previously cached chunks.
+         Even if the change is undone and the environment is cleared,
+         the error may persist. For example, changing ``contr_01``
+         in ``results_01`` to ``contr_05`` and then reknitting the file
+         will cause the R environment to contain both ``contr_01`` and
+         ``contr_05`` patterns after that chunk is loaded, leading to
+         this error.
+
+   Solution:
+      - Clear all cache and R environment objects.
+        Quit R without saving the workspace, delete the .RData file,
+        remove the ``rnaseq_cache`` directory, open rnaseq.Rmd and re-knit.
+
 Glossary
 --------
 .. glossary::

lib/lcdbwf/R/helpers.R

@@ -81,7 +81,7 @@ collect_objects <- function(pattern, fixed=FALSE){
   # If there was a wildcard in the pattern there is a risk that the modified
   # names are no longer unique
   if (length(unique(modified_names)) != length(var_names)){
-    stop(paste("Found duplicate names after removing pattern", pattern))
+    stop(paste("Found duplicate names after removing pattern", pattern, "see https://lcdb.github.io/lcdb-wf/rnaseq-rmd.html#Errors for details"))
   }
   names(obj_list) <- modified_names
   return(obj_list)