Error running topologygsa: is.DAG(gr) throwing "Input must be a matrix or a dgCMatrix"

[ChangqingW]

When running topologygsa with kegg hsa, I got the following error:

kegg.gs <- getGenesets(org = "hsa", db = "kegg")
hsa.grn <- compileGRN(org = "hsa", db = "kegg")
(I) r$> x <- nbea(method="topologygsa", se=se, gs=kegg.gs, grn=hsa.grn)
hsa00010_Glycolysis_/_Gluconeogenesis
hsa00020_Citrate_cycle_(TCA_cycle)
hsa00030_Pentose_phosphate_pathway
hsa00051_Fructose_and_mannose_metabolism
hsa00052_Galactose_metabolism
hsa00053_Ascorbate_and_aldarate_metabolism
hsa00061_Fatty_acid_biosynthesis
hsa00071_Fatty_acid_degradation
hsa00190_Oxidative_phosphorylation
hsa00230_Purine_metabolism
hsa00270_Cysteine_and_methionine_metabolism
hsa00280_Valine,_leucine_and_isoleucine_degradation
hsa00310_Lysine_degradation
hsa00330_Arginine_and_proline_metabolism
hsa00340_Histidine_metabolism
hsa00380_Tryptophan_metabolism
hsa00410_beta-Alanine_metabolism
hsa00480_Glutathione_metabolism
hsa00500_Starch_and_sucrose_metabolism
hsa00520_Amino_sugar_and_nucleotide_sugar_metabolism
hsa00561_Glycerolipid_metabolism
hsa00562_Inositol_phosphate_metabolism
Error in .check.is.matrix(object) : Input must be a matrix or a dgCMatrix
(I) r$> traceback()
10: stop("Input must be a matrix or a dgCMatrix\n")
9: .check.is.matrix(object)
8: is_dag.default(gr)
7: is.DAG(gr)
6: FUN(X[[i]], ...)
5: lapply(X = X, FUN = FUN, ...)
4: sapply(names(gs), function(s) {
       message(s)
       gs.grn <- .queryGRN(gs[[s]], grn, index = FALSE)
       if (nrow(gs.grn) < configEBrowser("GS.MIN.SIZE"))
           return(NA)
       am <- .grn2adjm(gs.grn)
       gr <- graphAM(am, "directed")
       gr <- as(gr, "graphNEL")
       if (!is.DAG(gr)) {
           gr2 <- graph_from_graphnel(gr)
           gr2 <- mst(gr2)
           gr <- as(gr2, "graphNEL")
       }
       r <- try(pathQ(assay(se), grp, gr, perm, alpha), silent = TRUE)
       if (is(r, "try-error"))
           return(NA)
       else return(r$alphaMean)
   })
3: .clipper(se, gs, grn, alpha, perm)
2: .topogsa(se, gs, grn, alpha, perm, ...)
1: nbea(method = "topologygsa", se = se, gs = kegg.gs, grn = hsa.grn)

It seems to be caused by the is_DAG call in .clipper, the object passed to it is a graphNEL object instead of a matrix, causing .check.is.matrix to throw the error.

(I) Browse[2]> object
A graphNEL graph with directed edges
Number of Nodes = 5
Number of Edges = 6
(I) Browse[2]> class(object)
[1] "graphNEL"
attr(,"package")
[1] "graph"

(I) r$> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /stornext/System/data/tools/openBLAS/openBLAS-0.3.23-gcc-11.3.0/lib/libopenblas_haswellp-r0.3.23.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8     LC_MONETARY=en_AU.UTF-8
 [6] LC_MESSAGES=en_AU.UTF-8    LC_PAPER=en_AU.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

time zone: Australia/Melbourne
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] igraph_1.6.0                gRbase_2.0.1                clipper_1.42.0              Matrix_1.6-5
 [5] targets_1.4.1               EnrichmentBrowser_2.32.0    graph_1.80.0                SummarizedExperiment_1.32.0
 [9] Biobase_2.62.0              GenomicRanges_1.54.1        GenomeInfoDb_1.38.6         IRanges_2.36.0
[13] S4Vectors_0.40.2            BiocGenerics_0.48.1         MatrixGenerics_1.14.0       matrixStats_1.2.0

loaded via a namespace (and not attached):
 [1] DBI_1.2.2                bitops_1.0-7             GSEABase_1.64.0          biomaRt_2.58.2           rlang_1.1.3
 [6] magrittr_2.0.3           compiler_4.3.1           RSQLite_2.3.5            GenomicFeatures_1.54.3   png_0.1-8
[11] callr_3.7.5              vctrs_0.6.5              stringr_1.5.1            pkgconfig_2.0.3          crayon_1.5.2
[16] fastmap_1.1.1            backports_1.4.1          dbplyr_2.4.0             XVector_0.42.0           utf8_1.2.4
[21] Rsamtools_2.18.0         ps_1.7.6                 qpgraph_2.36.0           KEGGgraph_1.62.0         bit_4.0.5
[26] xfun_0.42                zlibbioc_1.48.0          cachem_1.0.8             progress_1.2.3           blob_1.2.4
[31] DelayedArray_0.28.0      BiocParallel_1.36.0      parallel_4.3.1           prettyunits_1.2.0        R6_2.5.1
[36] qtl_1.66                 stringi_1.8.3            qs_0.25.7                rtracklayer_1.62.0       Rcpp_1.0.12
[41] knitr_1.45               tidyselect_1.2.0         abind_1.4-5              yaml_2.3.8               stringfish_0.16.0
[46] codetools_0.2-19         curl_5.2.0               processx_3.8.3           lattice_0.22-5           tibble_3.2.1
[51] withr_3.0.0              KEGGREST_1.42.0          RcppParallel_5.1.7       BiocFileCache_2.10.1     xml2_1.3.6
[56] Biostrings_2.70.2        pillar_1.9.0             filelock_1.0.3           generics_0.1.3           RCurl_1.98-1.14
[61] hms_1.1.3                RApiSerialize_0.1.2      xtable_1.8-4             base64url_1.4            glue_1.7.0
[66] tools_4.3.1              BiocIO_1.12.0            data.table_1.15.0        GenomicAlignments_1.38.2 annotate_1.80.0
[71] mvtnorm_1.2-4            XML_3.99-0.16.1          grid_4.3.1               AnnotationDbi_1.64.1     GenomeInfoDbData_1.2.11
[76] restfulr_0.0.15          cli_3.6.2                rappdirs_0.3.3           fansi_1.0.6              S4Arrays_1.2.0
[81] dplyr_1.1.4              corpcor_1.6.10           Rgraphviz_2.46.0         digest_0.6.34            SparseArray_1.2.4
[86] rjson_0.2.21             memoise_2.0.1            lifecycle_1.0.4          httr_1.4.7               bit64_4.0.5