'ssgseaParam' is not an exported object from 'namespace:GSVA'

[FLY-Fiancee]

I used an annotated single-cell data from seurat, but the following problems occurred when using scgsva:
'ssgseaParam' is not an exported object from 'namespace:GSVA'
my codes：`set.seed(123)
library(scGSVA)

anno <- buildAnnot(species="human", keytype="SYMBOL", anntype="KEGG")
res <- scgsva(seurat_object.filt.filt, anno,cores = 60)
`

[guokai8]

Hi @FLY-Fiancee ,
Which version of GSVA do you have? You may need to install the newest GSVA package. Or you can go with the previous scGSVA package.
K

[zhoujiaqi704]

Hi! I meet the same error when I run the example data: Error: 'ssgseaParam' is not an exported object from 'namespace:GSVA'.
The package version is "0.0.22".

[guokai8]

Hi @zhoujiaqi704,
Please go with the newest version of GSVA package
K

[honghh2018]

I get the same error,
version was latest 0.0.22
but still get error

How to fix this issue?
Any advice would be appreciated

[guokai8]

@honghh2018,
Please try below:

BiocManager::install("GSVA", version = "devel")

[curtishongbio-blip]

R version 4.2.3 can not use BiocManager::install("GSVA", version = "devel") to install scGSVA
the gsva package was 0.0.23

@guokai8 Thanks the reply, i download the git repo,and then use the R CMD build the directory, but it still get the error lying below:
Warning message:
distinct_() was deprecated in dplyr 0.7.0.
ℹ Please use distinct() instead.
ℹ See vignette('programming') for more help
ℹ The deprecated feature was likely used in the scGSVA package.
Please report the issue to the authors.
Warning: The following arguments are not used: layer
Error: 'ssgseaParam' is not an exported object from 'namespace:GSVA'
In addition: Warning message:
In asMethod(object) :
sparse->dense coercion: allocating vector of size 1.1 GiB
Execution halted

sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /public/syssoft/R-4.2.3/lib64/R/lib/libRblas.so
LAPACK: /public/syssoft/R-4.2.3/lib64/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] remotes_2.4.2.1 SeuratObject_4.1.3 scGSVA_0.0.23

loaded via a namespace (and not attached):
[1] backports_1.4.1 plyr_1.8.8
[3] igraph_2.0.3 lazyeval_0.2.2
[5] sp_2.0-0 GSEABase_1.60.0
[7] splines_4.2.3 BiocParallel_1.32.6
[9] listenv_0.9.0 scattermore_1.2
[11] GenomeInfoDb_1.34.9 ggplot2_3.4.4
[13] digest_0.6.33 htmltools_0.5.5
[15] viridis_0.6.4 fansi_1.0.4
[17] magrittr_2.0.3 memoise_2.0.1
[19] ScaledMatrix_1.6.0 tensor_1.5
[21] cluster_2.1.4 ROCR_1.0-11
[23] limma_3.54.2 globals_0.16.2
[25] Biostrings_2.66.0 annotate_1.76.0
[27] matrixStats_1.0.0 spatstat.sparse_3.0-2
[29] prettyunits_1.1.1 colorspace_2.1-0
[31] blob_1.2.4 ggrepel_0.9.6
[33] dplyr_1.1.4 callr_3.7.3
[35] crayon_1.5.2 RCurl_1.98-1.12
[37] jsonlite_1.8.7 graph_1.76.0
[39] progressr_0.13.0 spatstat.data_3.0-1
[41] survival_3.5-3 zoo_1.8-12
[43] glue_1.8.0 polyclip_1.10-4
[45] gtable_0.3.3 zlibbioc_1.44.0
[47] XVector_0.38.0 leiden_0.4.3
[49] DelayedArray_0.24.0 pkgbuild_1.4.2
[51] car_3.1-2 BiocSingular_1.14.0
[53] Rhdf5lib_1.20.0 future.apply_1.11.0
[55] SingleCellExperiment_1.20.1 BiocGenerics_0.44.0
[57] HDF5Array_1.26.0 msigdbr_7.5.1
[59] abind_1.4-5 scales_1.3.0
[61] pheatmap_1.0.12 DBI_1.1.3
[63] rstatix_0.7.2 spatstat.random_3.1-5
[65] miniUI_0.1.1.1 Rcpp_1.0.11
[67] viridisLite_0.4.2 xtable_1.8-4
[69] reticulate_1.30 bit_4.0.5
[71] rsvd_1.0.5 stats4_4.2.3
[73] GSVA_1.46.0 htmlwidgets_1.6.2
[75] httr_1.4.6 RColorBrewer_1.1-3
[77] ellipsis_0.3.2 Seurat_4.3.0.1
[79] ica_1.0-3 pkgconfig_2.0.3
[81] XML_3.99-0.14 farver_2.1.1
[83] uwot_0.1.16 deldir_1.0-9
[85] utf8_1.2.3 tidyselect_1.2.1
[87] rlang_1.1.5 reshape2_1.4.4
[89] later_1.4.1 AnnotationDbi_1.60.2
[91] munsell_0.5.0 tools_4.2.3
[93] cachem_1.0.8 cli_3.6.5
[95] generics_0.1.3 RSQLite_2.3.1
[97] broom_1.0.5 ggridges_0.5.4
[99] stringr_1.5.0 fastmap_1.1.1
[101] goftest_1.2-3 processx_3.8.2
[103] babelgene_22.9 bit64_4.0.5
[105] fitdistrplus_1.1-11 purrr_1.0.4
[107] RANN_2.6.1 KEGGREST_1.38.0
[109] nlme_3.1-162 pbapply_1.7-2
[111] future_1.33.0 sparseMatrixStats_1.10.0
[113] mime_0.12 compiler_4.2.3
[115] curl_6.2.0 plotly_4.10.2
[117] png_0.1-8 spatstat.utils_3.0-5
[119] tibble_3.2.1 stringi_1.7.12
[121] ps_1.7.5 desc_1.4.2
[123] lattice_0.20-45 Matrix_1.6-1
[125] vctrs_0.6.5 pillar_1.9.0
[127] lifecycle_1.0.4 rhdf5filters_1.10.1
[129] BiocManager_1.30.21.1 spatstat.geom_3.2-4
[131] lmtest_0.9-40 RcppAnnoy_0.0.21
[133] data.table_1.14.8 cowplot_1.1.1
[135] bitops_1.0-7 irlba_2.3.5.1
[137] httpuv_1.6.11 patchwork_1.3.0
[139] GenomicRanges_1.50.2 R6_2.5.1
[141] promises_1.3.2 KernSmooth_2.23-20
[143] gridExtra_2.3 IRanges_2.32.0
[145] parallelly_1.36.0 codetools_0.2-19
[147] MASS_7.3-58.2 rhdf5_2.42.1
[149] SummarizedExperiment_1.28.0 rprojroot_2.0.3
[151] sctransform_0.3.5 S4Vectors_0.36.2
[153] GenomeInfoDbData_1.2.9 parallel_4.2.3
[155] grid_4.2.3 beachmat_2.14.2
[157] tidyr_1.3.0 DelayedMatrixStats_1.20.0
[159] carData_3.0-5 MatrixGenerics_1.10.0
[161] Rtsne_0.16 spatstat.explore_3.2-1
[163] Biobase_2.54.0 shiny_1.7.4.1

Any advice would be appreciate
Best
hanhuihong

[curtishongbio-blip]

R version 4.2.3 can not use BiocManager::install("GSVA", version = "devel") to install scGSVA
the gsva package was 0.0.23

@guokai8 Thanks the reply, i download the git repo,and then use the R CMD build the directory, but it still get the error lying below:
Warning message:
distinct_() was deprecated in dplyr 0.7.0.
ℹ Please use distinct() instead.
ℹ See vignette('programming') for more help
ℹ The deprecated feature was likely used in the scGSVA package.
Please report the issue to the authors.
Warning: The following arguments are not used: layer
Error: 'ssgseaParam' is not an exported object from 'namespace:GSVA'
In addition: Warning message:
In asMethod(object) :
sparse->dense coercion: allocating vector of size 1.1 GiB
Execution halted

sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /public/syssoft/R-4.2.3/lib64/R/lib/libRblas.so
LAPACK: /public/syssoft/R-4.2.3/lib64/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] remotes_2.4.2.1 SeuratObject_4.1.3 scGSVA_0.0.23

loaded via a namespace (and not attached):
[1] backports_1.4.1 plyr_1.8.8
[3] igraph_2.0.3 lazyeval_0.2.2
[5] sp_2.0-0 GSEABase_1.60.0
[7] splines_4.2.3 BiocParallel_1.32.6
[9] listenv_0.9.0 scattermore_1.2
[11] GenomeInfoDb_1.34.9 ggplot2_3.4.4
[13] digest_0.6.33 htmltools_0.5.5
[15] viridis_0.6.4 fansi_1.0.4
[17] magrittr_2.0.3 memoise_2.0.1
[19] ScaledMatrix_1.6.0 tensor_1.5
[21] cluster_2.1.4 ROCR_1.0-11
[23] limma_3.54.2 globals_0.16.2
[25] Biostrings_2.66.0 annotate_1.76.0
[27] matrixStats_1.0.0 spatstat.sparse_3.0-2
[29] prettyunits_1.1.1 colorspace_2.1-0
[31] blob_1.2.4 ggrepel_0.9.6
[33] dplyr_1.1.4 callr_3.7.3
[35] crayon_1.5.2 RCurl_1.98-1.12
[37] jsonlite_1.8.7 graph_1.76.0
[39] progressr_0.13.0 spatstat.data_3.0-1
[41] survival_3.5-3 zoo_1.8-12
[43] glue_1.8.0 polyclip_1.10-4
[45] gtable_0.3.3 zlibbioc_1.44.0
[47] XVector_0.38.0 leiden_0.4.3
[49] DelayedArray_0.24.0 pkgbuild_1.4.2
[51] car_3.1-2 BiocSingular_1.14.0
[53] Rhdf5lib_1.20.0 future.apply_1.11.0
[55] SingleCellExperiment_1.20.1 BiocGenerics_0.44.0
[57] HDF5Array_1.26.0 msigdbr_7.5.1
[59] abind_1.4-5 scales_1.3.0
[61] pheatmap_1.0.12 DBI_1.1.3
[63] rstatix_0.7.2 spatstat.random_3.1-5
[65] miniUI_0.1.1.1 Rcpp_1.0.11
[67] viridisLite_0.4.2 xtable_1.8-4
[69] reticulate_1.30 bit_4.0.5
[71] rsvd_1.0.5 stats4_4.2.3
[73] GSVA_1.46.0 htmlwidgets_1.6.2
[75] httr_1.4.6 RColorBrewer_1.1-3
[77] ellipsis_0.3.2 Seurat_4.3.0.1
[79] ica_1.0-3 pkgconfig_2.0.3
[81] XML_3.99-0.14 farver_2.1.1
[83] uwot_0.1.16 deldir_1.0-9
[85] utf8_1.2.3 tidyselect_1.2.1
[87] rlang_1.1.5 reshape2_1.4.4
[89] later_1.4.1 AnnotationDbi_1.60.2
[91] munsell_0.5.0 tools_4.2.3
[93] cachem_1.0.8 cli_3.6.5
[95] generics_0.1.3 RSQLite_2.3.1
[97] broom_1.0.5 ggridges_0.5.4
[99] stringr_1.5.0 fastmap_1.1.1
[101] goftest_1.2-3 processx_3.8.2
[103] babelgene_22.9 bit64_4.0.5
[105] fitdistrplus_1.1-11 purrr_1.0.4
[107] RANN_2.6.1 KEGGREST_1.38.0
[109] nlme_3.1-162 pbapply_1.7-2
[111] future_1.33.0 sparseMatrixStats_1.10.0
[113] mime_0.12 compiler_4.2.3
[115] curl_6.2.0 plotly_4.10.2
[117] png_0.1-8 spatstat.utils_3.0-5
[119] tibble_3.2.1 stringi_1.7.12
[121] ps_1.7.5 desc_1.4.2
[123] lattice_0.20-45 Matrix_1.6-1
[125] vctrs_0.6.5 pillar_1.9.0
[127] lifecycle_1.0.4 rhdf5filters_1.10.1
[129] BiocManager_1.30.21.1 spatstat.geom_3.2-4
[131] lmtest_0.9-40 RcppAnnoy_0.0.21
[133] data.table_1.14.8 cowplot_1.1.1
[135] bitops_1.0-7 irlba_2.3.5.1
[137] httpuv_1.6.11 patchwork_1.3.0
[139] GenomicRanges_1.50.2 R6_2.5.1
[141] promises_1.3.2 KernSmooth_2.23-20
[143] gridExtra_2.3 IRanges_2.32.0
[145] parallelly_1.36.0 codetools_0.2-19
[147] MASS_7.3-58.2 rhdf5_2.42.1
[149] SummarizedExperiment_1.28.0 rprojroot_2.0.3
[151] sctransform_0.3.5 S4Vectors_0.36.2
[153] GenomeInfoDbData_1.2.9 parallel_4.2.3
[155] grid_4.2.3 beachmat_2.14.2
[157] tidyr_1.3.0 DelayedMatrixStats_1.20.0
[159] carData_3.0-5 MatrixGenerics_1.10.0
[161] Rtsne_0.16 spatstat.explore_3.2-1
[163] Biobase_2.54.0 shiny_1.7.4.1

Any advice would be appreciate
Best
hanhuihong