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When I run gsva function, the error occured as follows:
Code should be placed in three backticks as shown below
> gsvascore <- gsva(data, geneset, method="gsva", parallel.sz = 2)
Setting parallel calculations through a MulticoreParam back-end
with workers=2 and tasks=100.
Estimating GSVA scores for 186 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating ECDFs in parallel
iteration: Error in serialize(data, node$con, xdr = FALSE) :
error writing to connection
In addition: Warning messages:
1: In .filterFeatures(expr, method) :
3068 genes with constant expression values throuhgout the samples.
2: In .filterFeatures(expr, method) :
Since argument method!="ssgsea", genes with constant expression values are discarded.
Error in serialize(data, node$con, xdr = FALSE) :
error writing to connection
> sessionInfo( )
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS/LAPACK: /usr/local/lib/libopenblas.so.0
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=en_US.UTF-8
[9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] future_1.21.0 BiocParallel_1.24.1 stringr_1.4.0 msigdbr_7.4.1 limma_3.46.0 GSVA_1.38.2
[7] dplyr_1.0.6 SeuratObject_4.0.1 Seurat_4.0.1
loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_2.0-1 deldir_0.2-10 ellipsis_0.3.2
[5] ggridges_0.5.3 XVector_0.30.0 GenomicRanges_1.42.0 rstudioapi_0.13
[9] spatstat.data_2.1-0 leiden_0.3.7 listenv_0.8.0 ggrepel_0.9.1
[13] bit64_4.0.5 AnnotationDbi_1.52.0 fansi_0.4.2 codetools_0.2-18
[17] splines_4.0.4 cachem_1.0.4 polyclip_1.10-0 jsonlite_1.7.2
[21] rJava_1.0-4 annotate_1.68.0 ica_1.0-2 cluster_2.1.2
[25] png_0.1-7 graph_1.68.0 uwot_0.1.10 shiny_1.6.0
[29] sctransform_0.3.2 spatstat.sparse_2.0-0 compiler_4.0.4 httr_1.4.2
[33] Matrix_1.3-3 fastmap_1.1.0 lazyeval_0.2.2 cli_2.5.0
[37] later_1.2.0 htmltools_0.5.1.1 tools_4.0.4 igraph_1.2.6
[41] GenomeInfoDbData_1.2.4 gtable_0.3.0 glue_1.4.2 RANN_2.6.1
[45] reshape2_1.4.4 Rcpp_1.0.6 scattermore_0.7 Biobase_2.50.0
[49] vctrs_0.3.8 babelgene_21.4 nlme_3.1-152 lmtest_0.9-38
[53] globals_0.14.0 xlsxjars_0.6.1 mime_0.10 miniUI_0.1.1.1
[57] lifecycle_1.0.0 irlba_2.3.3 XML_3.99-0.6 xlsx_0.6.5
[61] goftest_1.2-2 zlibbioc_1.36.0 MASS_7.3-54 zoo_1.8-9
[65] scales_1.1.1 spatstat.core_2.1-2 MatrixGenerics_1.2.1 promises_1.2.0.1
[69] spatstat.utils_2.1-0 SummarizedExperiment_1.20.0 parallel_4.0.4 RColorBrewer_1.1-2
[73] memoise_2.0.0 reticulate_1.20 pbapply_1.4-3 gridExtra_2.3
[77] ggplot2_3.3.3 rpart_4.1-15 stringi_1.6.1 RSQLite_2.2.7
[81] S4Vectors_0.28.1 BiocGenerics_0.36.1 GenomeInfoDb_1.26.7 bitops_1.0-7
[85] rlang_0.4.11 pkgconfig_2.0.3 matrixStats_0.58.0 lattice_0.20-44
[89] ROCR_1.0-11 purrr_0.3.4 tensor_1.5 patchwork_1.1.1
[93] htmlwidgets_1.5.3 bit_4.0.4 cowplot_1.1.1 tidyselect_1.1.1
[97] GSEABase_1.52.1 parallelly_1.25.0 RcppAnnoy_0.0.18 plyr_1.8.6
[101] magrittr_2.0.1 R6_2.5.0 IRanges_2.24.1 generics_0.1.0
[105] DelayedArray_0.16.3 DBI_1.1.1 pillar_1.6.0 mgcv_1.8-35
[109] fitdistrplus_1.1-3 RCurl_1.98-1.3 survival_3.2-11 abind_1.4-5
[113] tibble_3.1.1 future.apply_1.7.0 crayon_1.4.1 KernSmooth_2.23-20
[117] utf8_1.2.1 spatstat.geom_2.1-0 plotly_4.9.3 grid_4.0.4
[121] data.table_1.14.0 blob_1.2.1 digest_0.6.27 xtable_1.8-4
[125] tidyr_1.1.3 httpuv_1.6.1 stats4_4.0.4 munsell_0.5.0
[129] viridisLite_0.4.0