Devel - updated version that passes checks

.github/workflows/standard-ci-workflow.yml

@@ -22,7 +22,6 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: macOS-latest, r: 'devel'}
           - {os: ubuntu-latest, r: 'release'}
           - {os: ubuntu-latest, r: 'oldrel-1'}
 

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ribiosGSEA
 Type: Package
 Title: Gene-Set Enrichment Analysis Tools in 'ribios'
-Version: 1.6.7
-Date: 2026-03-28
+Version: 1.6.8
+Date: 2026-06-12
 Authors@R:
   c(person(given = "Jitao David",
          family = "Zhang",
@@ -73,7 +73,6 @@ Collate:
 LinkingTo: Rcpp
 VignetteBuilder: knitr
 Encoding: UTF-8
-RoxygenNote: 7.3.3
 Additional_repositories: https://bedapub.r-universe.dev
 URL: https://github.com/bedapub/ribiosGSEA
 BugReports: https://github.com/bedapub/ribiosGSEA/issues
@@ -82,4 +81,4 @@ Remotes:
     github::bedapub/ribiosPlot,
     github::bedapub/ribiosExpression,
     github::bedapub/ribiosNGS
-
+Config/roxygen2/version: 8.0.0

R/gmt.R

@@ -52,7 +52,6 @@ readMPSGmt <- function(file) {
 #' \itemize{
 #'  \item{MSigDB: collections C2, C7 and Hallmark}
 #'  \item{RONET: which is a collection of publicly available pathway databases including REACTOME and NCI-Nature}
-#'  \item{goslim}
 #' }
 #' @return A \code{GmtList} object containing the default gene-set collections.
 #'
@@ -66,39 +65,32 @@ readMPSGmt <- function(file) {
 #' @export
 readDefaultGenesets <- function(path,
                                 mps=FALSE) {
-  assertFile(msigdb.c2.file <- file.path(path, "msigdb.c2.all.symbols.gmt"))
-  assertFile(msigdb.c7.file <- file.path(path, "msigdb.c7.all.symbols.gmt"))
-  assertFile(msigdb.hallmark.file <- file.path(path, "msigdb.hallmark.all.symbols.gmt"))
+  assertFile(msigdb.c2.file <- file.path(path, "msigdb.c2.gmt"))
+  assertFile(msigdb.c7.file <- file.path(path, "msigdb.c7.gmt"))
+  assertFile(msigdb.hallmark.file <- file.path(path, "msigdb.hallmark.gmt"))
 
   assertFile(mps.pathway <- file.path(path, "MolecularPhenotyping-genesets.gmt"))
 
   assertFile(ronet.file <- file.path(path, "path.ronet.roche.symbols.gmt"))
-  assertFile(goslim.file <- file.path(path, "go_slim.bp.roche.symbols.gmt"))
 
   assertFile(upstream.file <- file.path(path, "MetaBase.downstream.expression.gmt"))  
   assertFile(mbdisease.file <- file.path(path, "MetaBase.DiseaseBiomarker.gmt"))
   assertFile(mbmetabolic.file <- file.path(path, "MetaBase.Metabolic.gmt"))
   assertFile(mbpath.file <- file.path(path, "MetaBase.PathwayMap.gmt"))
   assertFile(mbtoxicity.file <- file.path(path, "MetaBase.Toxicity.gmt"))
   assertFile(mbpathology.file <- file.path(path, "MetaBase.ToxicPathology.gmt"))
-  assertFile(mbprocess.file <- file.path(path, "MetaBase.TRprocesses.gmt"))
-
-  assertFile(immunomics.file <- file.path(path, "exp.immune.roche.symbols.gmt"))
-  assertFile(immunespace.file <- file.path(path, "immunespace.gmt"))
+  assertFile(mbprocess.file <- file.path(path, "MetaBase.ProcessNetwork.gmt"))
 
   if(mps) {
     mpsGSCs <- readMPSGmt(mps.pathway)
     gscs <- BioQC::readGmt(msigdbC2=msigdb.c2.file,
                     msigdbC7=msigdb.c7.file,
-                    msigdbHallmark = msigdb.hallmark.file,
-                    immunomics = immunomics.file,
-                    immunespace = immunespace.file)
+                    msigdbHallmark = msigdb.hallmark.file)
     gscs <- appendGmtList(mpsGSCs, gscs)
   } else {
     gscs <- BioQC::readGmt(MolecularPhenotyping=mps.pathway,
                     upstream=upstream.file,
                     ronet=ronet.file,
-                    goslim=goslim.file,
                     mbdisease=mbdisease.file,
                     mbmetabolic=mbmetabolic.file,
                     mbpath=mbpath.file,
@@ -107,9 +99,7 @@ readDefaultGenesets <- function(path,
                     mbpathology=mbpathology.file,
                     msigdbC2=msigdb.c2.file,
                     msigdbC7=msigdb.c7.file,
-                    msigdbHallmark = msigdb.hallmark.file,
-                    immunomics = immunomics.file,
-                    immunespace = immunespace.file)
+                    msigdbHallmark = msigdb.hallmark.file)
   }
   return(gscs)
 }

R/post-processing.R

@@ -117,8 +117,7 @@ expandCameraTableGenes <- function(tbl) {
 #' @return A list with two elements: \code{graph} (an igraph object) and
 #' \code{resTbl} (a data.frame with columns Namespace, GeneSet, Score).
 #'
-#' @importFrom igraph make_empty_graph graph_from_adjacency_matrix
-#'     layout_in_circle V
+#' @importFrom igraph make_empty_graph graph_from_adjacency_matrix layout_in_circle V
 #' @importFrom ribiosUtils pairwiseJaccardIndex matchColumn boundNorm
 #' @importFrom ribiosPlot royalbluegrayred
 #' @export
@@ -197,8 +196,7 @@ readSigCameraResults <- function(file,
                                  minAbsEffectSize=0.5,
                                  minNGenes=5, 
                                  maxNGenes=200,
-                                 excludeNamespace=c("goslim", "immunespace", 
-                                                    "immunomics", "mbdisease",
+                                 excludeNamespace=c("mbdisease",
                                                     "mbpathology", "mbtoxicity",
                                                     "msigdbC7", "msigdbC2",
                                                     "MolecularPhenotyping")) {

R/ribiosGSEA-package.R

@@ -8,8 +8,7 @@
 #' @importFrom edgeR DGEList
 #' @importFrom utils read.table write.table
 #' @importFrom methods as callGeneric is new
-#' @importFrom stats ave cor fisher.test kmeans median p.adjust
-#'             pchisq pt qt sd var model.matrix
+#' @importFrom stats ave cor fisher.test kmeans median p.adjust pchisq pt qt sd var model.matrix
 NULL
 
 ## following lines make it not necessary to document