From c9551eced5ef0cac80394c528176842adc5518e7 Mon Sep 17 00:00:00 2001 From: Jitao David Zhang Date: Fri, 12 Jun 2026 17:27:35 +0200 Subject: [PATCH 1/6] exclude macOS-latest due to checking issues --- .github/workflows/standard-ci-workflow.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/standard-ci-workflow.yml b/.github/workflows/standard-ci-workflow.yml index 408ebf6..db4fc3b 100644 --- a/.github/workflows/standard-ci-workflow.yml +++ b/.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'} From b19693e5cac156cacdba5c50c7b3a42fc5a9cd1b Mon Sep 17 00:00:00 2001 From: Jitao David Zhang Date: Fri, 12 Jun 2026 17:28:44 +0200 Subject: [PATCH 2/6] use new naming conventions of gmt files --- DESCRIPTION | 4 ++-- R/gmt.R | 20 ++++++-------------- R/post-processing.R | 3 +-- 3 files changed, 9 insertions(+), 18 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f827194..25a1c5c 100644 --- a/DESCRIPTION +++ b/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", diff --git a/R/gmt.R b/R/gmt.R index a8f11e4..124aa4d 100644 --- a/R/gmt.R +++ b/R/gmt.R @@ -66,14 +66,13 @@ 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")) @@ -81,18 +80,13 @@ readDefaultGenesets <- function(path, 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.ProcessesNetwork.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, @@ -107,9 +101,7 @@ 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) } diff --git a/R/post-processing.R b/R/post-processing.R index c025f2c..c0264e9 100644 --- a/R/post-processing.R +++ b/R/post-processing.R @@ -197,8 +197,7 @@ readSigCameraResults <- function(file, minAbsEffectSize=0.5, minNGenes=5, maxNGenes=200, - excludeNamespace=c("goslim", "immunespace", - "immunomics", "mbdisease", + excludeNamespace=c("mbdisease", "mbpathology", "mbtoxicity", "msigdbC7", "msigdbC2", "MolecularPhenotyping")) { From f1b9853674ca817e1af22bcd2d747d8c3ee27a69 Mon Sep 17 00:00:00 2001 From: Jitao David Zhang Date: Fri, 12 Jun 2026 20:02:10 +0200 Subject: [PATCH 3/6] local test passed --- DESCRIPTION | 3 +-- R/gmt.R | 2 -- R/post-processing.R | 3 +-- R/ribiosGSEA-package.R | 3 +-- man/GeMS_BASE_URL.Rd | 5 ----- man/GeMS_GENESETS_URL.Rd | 5 ----- man/GeMS_INSERT_URL.Rd | 5 ----- man/GeMS_REMOVE_URL.Rd | 5 ----- man/GeMS_TEST_GENESETS_URL.Rd | 5 ----- man/GeMS_TEST_URL.Rd | 5 ----- man/readDefaultGenesets.Rd | 1 - man/readSigCameraResults.Rd | 4 ++-- man/reexports.Rd | 8 ++++---- man/ribiosGSEA-package.Rd | 5 +++++ 14 files changed, 14 insertions(+), 45 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 25a1c5c..7226ac0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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 diff --git a/R/gmt.R b/R/gmt.R index 124aa4d..68bda34 100644 --- a/R/gmt.R +++ b/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. #' @@ -92,7 +91,6 @@ readDefaultGenesets <- function(path, gscs <- BioQC::readGmt(MolecularPhenotyping=mps.pathway, upstream=upstream.file, ronet=ronet.file, - goslim=goslim.file, mbdisease=mbdisease.file, mbmetabolic=mbmetabolic.file, mbpath=mbpath.file, diff --git a/R/post-processing.R b/R/post-processing.R index c0264e9..c0c462d 100644 --- a/R/post-processing.R +++ b/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 diff --git a/R/ribiosGSEA-package.R b/R/ribiosGSEA-package.R index fbdd15c..3475251 100644 --- a/R/ribiosGSEA-package.R +++ b/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 diff --git a/man/GeMS_BASE_URL.Rd b/man/GeMS_BASE_URL.Rd index 38ce80f..1dca208 100644 --- a/man/GeMS_BASE_URL.Rd +++ b/man/GeMS_BASE_URL.Rd @@ -1,14 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/GeMS.R -\docType{data} \name{GeMS_BASE_URL} \alias{GeMS_BASE_URL} \title{GeMS base URL To set GeMS base URL in your environment, use `GeMS_BASE_URL=value` in your "~/.Renviron" file} -\format{ -An object of class \code{character} of length 1. -} \usage{ GeMS_BASE_URL } @@ -17,4 +13,3 @@ GeMS base URL To set GeMS base URL in your environment, use `GeMS_BASE_URL=value` in your "~/.Renviron" file } -\keyword{datasets} diff --git a/man/GeMS_GENESETS_URL.Rd b/man/GeMS_GENESETS_URL.Rd index 69a88f1..95907f6 100644 --- a/man/GeMS_GENESETS_URL.Rd +++ b/man/GeMS_GENESETS_URL.Rd @@ -1,16 +1,11 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/GeMS.R -\docType{data} \name{GeMS_GENESETS_URL} \alias{GeMS_GENESETS_URL} \title{GeMS genesets retrieval URL} -\format{ -An object of class \code{character} of length 1. -} \usage{ GeMS_GENESETS_URL } \description{ GeMS genesets retrieval URL } -\keyword{datasets} diff --git a/man/GeMS_INSERT_URL.Rd b/man/GeMS_INSERT_URL.Rd index 898cc71..7a206f3 100644 --- a/man/GeMS_INSERT_URL.Rd +++ b/man/GeMS_INSERT_URL.Rd @@ -1,16 +1,11 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/GeMS.R -\docType{data} \name{GeMS_INSERT_URL} \alias{GeMS_INSERT_URL} \title{GeMS insert URL} -\format{ -An object of class \code{character} of length 1. -} \usage{ GeMS_INSERT_URL } \description{ GeMS insert URL } -\keyword{datasets} diff --git a/man/GeMS_REMOVE_URL.Rd b/man/GeMS_REMOVE_URL.Rd index 42782bd..2f4829a 100644 --- a/man/GeMS_REMOVE_URL.Rd +++ b/man/GeMS_REMOVE_URL.Rd @@ -1,16 +1,11 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/GeMS.R -\docType{data} \name{GeMS_REMOVE_URL} \alias{GeMS_REMOVE_URL} \title{GeMS remove URL} -\format{ -An object of class \code{character} of length 1. -} \usage{ GeMS_REMOVE_URL } \description{ GeMS remove URL } -\keyword{datasets} diff --git a/man/GeMS_TEST_GENESETS_URL.Rd b/man/GeMS_TEST_GENESETS_URL.Rd index ce97636..9053896 100644 --- a/man/GeMS_TEST_GENESETS_URL.Rd +++ b/man/GeMS_TEST_GENESETS_URL.Rd @@ -1,16 +1,11 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/GeMS.R -\docType{data} \name{GeMS_TEST_GENESETS_URL} \alias{GeMS_TEST_GENESETS_URL} \title{GeMS geneset retrieval URL for testing} -\format{ -An object of class \code{character} of length 1. -} \usage{ GeMS_TEST_GENESETS_URL } \description{ GeMS geneset retrieval URL for testing } -\keyword{datasets} diff --git a/man/GeMS_TEST_URL.Rd b/man/GeMS_TEST_URL.Rd index f1467d6..67f58cc 100644 --- a/man/GeMS_TEST_URL.Rd +++ b/man/GeMS_TEST_URL.Rd @@ -1,16 +1,11 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/GeMS.R -\docType{data} \name{GeMS_TEST_URL} \alias{GeMS_TEST_URL} \title{GeMS URL for testing} -\format{ -An object of class \code{character} of length 1. -} \usage{ GeMS_TEST_URL } \description{ GeMS URL for testing } -\keyword{datasets} diff --git a/man/readDefaultGenesets.Rd b/man/readDefaultGenesets.Rd index f369c04..5f9bcd8 100644 --- a/man/readDefaultGenesets.Rd +++ b/man/readDefaultGenesets.Rd @@ -24,7 +24,6 @@ Publicly available genesets include \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} } } \examples{ diff --git a/man/readSigCameraResults.Rd b/man/readSigCameraResults.Rd index 9b43299..821b541 100644 --- a/man/readSigCameraResults.Rd +++ b/man/readSigCameraResults.Rd @@ -11,8 +11,8 @@ readSigCameraResults( minAbsEffectSize = 0.5, minNGenes = 5, maxNGenes = 200, - excludeNamespace = c("goslim", "immunespace", "immunomics", "mbdisease", "mbpathology", - "mbtoxicity", "msigdbC7", "msigdbC2", "MolecularPhenotyping") + excludeNamespace = c("mbdisease", "mbpathology", "mbtoxicity", "msigdbC7", "msigdbC2", + "MolecularPhenotyping") ) } \arguments{ diff --git a/man/reexports.Rd b/man/reexports.Rd index e9abcec..bbb5540 100644 --- a/man/reexports.Rd +++ b/man/reexports.Rd @@ -15,12 +15,12 @@ These objects are imported from other packages. Follow the links below to see their documentation. \describe{ - \item{edgeR}{\code{\link[edgeR]{DGEList}}} + \item{edgeR}{\code{\link[edgeR:DGEList]{DGEList()}}} - \item{limma}{\code{\link[limma]{camera}}} + \item{limma}{\code{\link[limma:camera]{camera()}}} - \item{ribiosExpression}{\code{\link[ribiosExpression]{DesignContrast}}, \code{\link[ribiosExpression]{designMatrix}}} + \item{ribiosExpression}{\code{\link[ribiosExpression:DesignContrast]{DesignContrast()}}, \code{\link[ribiosExpression:designMatrix]{designMatrix()}}} - \item{ribiosNGS}{\code{\link[ribiosNGS]{EdgeObject}}} + \item{ribiosNGS}{\code{\link[ribiosNGS:EdgeObject]{EdgeObject()}}} }} diff --git a/man/ribiosGSEA-package.Rd b/man/ribiosGSEA-package.Rd index 422c817..09313ad 100644 --- a/man/ribiosGSEA-package.Rd +++ b/man/ribiosGSEA-package.Rd @@ -19,6 +19,11 @@ Useful links: \author{ \strong{Maintainer}: Jitao David Zhang \email{jitao_david.zhang@roche.com} (\href{https://orcid.org/0000-0002-3085-0909}{ORCID}) +Authors: +\itemize{ + \item Jitao David Zhang \email{jitao_david.zhang@roche.com} (\href{https://orcid.org/0000-0002-3085-0909}{ORCID}) +} + Other contributors: \itemize{ \item Balasz Banfai [contributor] From d0df234df0e32943f0c06f2c8d5e870d83842971 Mon Sep 17 00:00:00 2001 From: Jitao David Zhang Date: Sun, 14 Jun 2026 17:52:34 +0200 Subject: [PATCH 4/6] with explicing giving -I and Rcpp path,I could build the package and install it. --- src/Makevars | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Makevars b/src/Makevars index 49b8f3c..c00716c 100644 --- a/src/Makevars +++ b/src/Makevars @@ -1,2 +1,2 @@ PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) -PKG_CXXFLAGS = -I../inst/include $(SHLIB_OPENMP_CXXFLAGS) +PKG_CXXFLAGS = -I../inst/include -I/apps/rocs/pRED/groups/bioinfo/R/4.5.0-foss/Rcpp/include $(SHLIB_OPENMP_CXXFLAGS) From ff9efa80bb1af4343316fed9d319f72f40d5ee4f Mon Sep 17 00:00:00 2001 From: Jitao David Zhang Date: Sun, 14 Jun 2026 18:02:52 +0200 Subject: [PATCH 5/6] ProcessNetwork --- R/gmt.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/gmt.R b/R/gmt.R index 68bda34..9cadebd 100644 --- a/R/gmt.R +++ b/R/gmt.R @@ -79,7 +79,7 @@ readDefaultGenesets <- function(path, 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.ProcessesNetwork.gmt")) + assertFile(mbprocess.file <- file.path(path, "MetaBase.ProcessNetwork.gmt")) if(mps) { mpsGSCs <- readMPSGmt(mps.pathway) From 5af31b3d832e57a40343931e36c7f757396fcaa8 Mon Sep 17 00:00:00 2001 From: Jitao David Zhang Date: Sun, 14 Jun 2026 18:05:32 +0200 Subject: [PATCH 6/6] no need to specify -I: it seems that the problem was caused by devtools::build. The devtools is outdated --- src/Makevars | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Makevars b/src/Makevars index c00716c..49b8f3c 100644 --- a/src/Makevars +++ b/src/Makevars @@ -1,2 +1,2 @@ PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) -PKG_CXXFLAGS = -I../inst/include -I/apps/rocs/pRED/groups/bioinfo/R/4.5.0-foss/Rcpp/include $(SHLIB_OPENMP_CXXFLAGS) +PKG_CXXFLAGS = -I../inst/include $(SHLIB_OPENMP_CXXFLAGS)