first remote error: 'ssgseaParam' is not an exported object from 'namespace:GSVA' #168
Description
Hello, I am running into this issue when running escape.matrix. Could you please help me, I did install GSVA but I am getting this error. Please see the attached session info.
Thank you so much!
new_gene_set<- c("GOBP_NEGATIVE_REGULATION_OF_CELL_CELL_ADHESION_MEDIATED_BY_CADHERIN",
"GOBP_CELL_CELL_ADHESION",
"GOBP_CELL_CELL_ADHESION_MEDIATED_BY_CADHERIN",
"GOBP_CELL_CELL_ADHESION_MEDIATED_BY_INTEGRIN",
"GOBP_CELL_CELL_ADHESION_VIA_PLASMA_MEMBRANE_ADHESION_MOLECULES",
"GOBP_SPINDLE_ELONGATION", "GOBP_EPITHELIAL_CELL_CELL_ADHESION",
"GOBP_NEGATIVE_REGULATION_OF_CELL_ADHESION",
"GOBP_NEGATIVE_REGULATION_OF_CELL_ADHESION_MEDIATED_BY_INTEGRIN", "GOBP_NEGATIVE_REGULATION_OF_CELL_CELL_ADHESION_MEDIATED_BY_CADHERIN")
gene.sets_2<- getGeneSets(library= c("C5"), gene.sets = new_gene_set, species= "Mus musculus")
> enrichment.scores <- escape.matrix(seurat_obj,
+ gene.sets = gene.sets_2,
+ groups = 1000,
+ min.size = 5)
escape.matrix(): processing 9 chunk(s)...
Error: BiocParallel errors
1 remote errors, element index: 1
8 unevaluated and other errors
first remote error: 'ssgseaParam' is not an exported object from 'namespace:GSVA'
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GSVA_1.42.0 escape_2.5.4 dplyr_1.1.4 ggplot2_3.5.2 SeuratObject_4.1.3 Seurat_4.3.0.1
[7] Signac_1.10.0
loaded via a namespace (and not attached):
[1] spatstat.explore_3.4-3 reticulate_1.42.0 tidyselect_1.2.1 RSQLite_2.4.1
[5] AnnotationDbi_1.56.2 htmlwidgets_1.6.4 grid_4.1.0 BiocParallel_1.28.3
[9] Rtsne_0.17 ScaledMatrix_1.2.0 codetools_0.2-18 ica_1.0-3
[13] future_1.58.0 miniUI_0.1.2 withr_3.0.2 spatstat.random_3.4-1
[17] colorspace_2.1-1 progressr_0.15.1 Biobase_2.54.0 rstudioapi_0.17.1
[21] stats4_4.1.0 SingleCellExperiment_1.16.0 ROCR_1.0-11 ggsignif_0.6.4
[25] tensor_1.5.1 listenv_0.9.1 MatrixGenerics_1.6.0 GenomeInfoDbData_1.2.7
[29] polyclip_1.10-7 bit64_4.6.0-1 farver_2.1.2 rhdf5_2.38.1
[33] parallelly_1.45.0 vctrs_0.6.5 generics_0.1.4 R6_2.6.1
[37] GenomeInfoDb_1.30.1 rsvd_1.0.5 spatstat.univar_3.1-3 bitops_1.0-9
[41] rhdf5filters_1.6.0 spatstat.utils_3.1-4 cachem_1.1.0 DelayedArray_0.20.0
[45] promises_1.3.3 scales_1.4.0 gtable_0.3.6 beachmat_2.10.0
[49] globals_0.18.0 goftest_1.2-3 rlang_1.1.6 RcppRoll_0.3.1
[53] splines_4.1.0 rstatix_0.7.2 lazyeval_0.2.2 dichromat_2.0-0.1
[57] spatstat.geom_3.4-1 broom_1.0.8 BiocManager_1.30.26 reshape2_1.4.4
[61] abind_1.4-8 backports_1.5.0 httpuv_1.6.16 tools_4.1.0
[65] RColorBrewer_1.1-3 BiocGenerics_0.40.0 ggridges_0.5.6 Rcpp_1.0.14
[69] plyr_1.8.9 sparseMatrixStats_1.6.0 zlibbioc_1.40.0 purrr_1.0.4
[73] RCurl_1.98-1.17 ggpubr_0.6.0 deldir_2.0-4 pbapply_1.7-2
[77] cowplot_1.1.3 S4Vectors_0.32.4 zoo_1.8-14 SummarizedExperiment_1.24.0
[81] ggrepel_0.9.6 cluster_2.1.8.1 magrittr_2.0.3 data.table_1.17.6
[85] scattermore_1.2 ggdist_3.3.3 lmtest_0.9-40 RANN_2.6.2
[89] fitdistrplus_1.2-2 matrixStats_1.5.0 patchwork_1.3.1 mime_0.13
[93] xtable_1.8-4 XML_3.99-0.18 IRanges_2.28.0 gridExtra_2.3
[97] compiler_4.1.0 tibble_3.3.0 KernSmooth_2.23-20 crayon_1.5.3
[101] htmltools_0.5.8.1 later_1.4.2 Formula_1.2-5 tidyr_1.3.1
[105] DBI_1.2.3 MASS_7.3-60 Matrix_1.6-1 car_3.1-3
[109] cli_3.6.5 parallel_4.1.0 igraph_2.1.4 GenomicRanges_1.46.1
[113] pkgconfig_2.0.3 sp_2.2-0 plotly_4.11.0 spatstat.sparse_3.1-0
[117] annotate_1.72.0 XVector_0.34.0 stringr_1.5.1 distributional_0.5.0
[121] digest_0.6.37 sctransform_0.4.2 RcppAnnoy_0.0.22 graph_1.72.0
[125] spatstat.data_3.1-6 Biostrings_2.62.0 leiden_0.4.3.1 fastmatch_1.1-6
[129] uwot_0.2.3 DelayedMatrixStats_1.16.0 GSEABase_1.56.0 shiny_1.11.0
[133] Rsamtools_2.10.0 lifecycle_1.0.4 nlme_3.1-168 jsonlite_2.0.0
[137] Rhdf5lib_1.16.0 carData_3.0-5 viridisLite_0.4.2 pillar_1.10.2
[141] lattice_0.22-7 KEGGREST_1.34.0 fastmap_1.2.0 httr_1.4.7
[145] survival_3.8-3 glue_1.8.0 png_0.1-8 bit_4.6.0
[149] stringi_1.8.7 HDF5Array_1.22.1 blob_1.2.4 BiocSingular_1.10.0
[153] memoise_2.0.1 irlba_2.3.5.1 future.apply_1.20.0
`