multiGSEA
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getPantherGeneSetDb error
The getPantherGeneSetDb
function throws an error when I try to reproduce the example provided in the vignette. No object is returned:
library(multiGSEA)
goslimdb <- getPantherGeneSetDb('goslim', 'human')
Warning in getPantherGOSLIM(p.db, org.db) :
172957 GOSLIM terms were not found in GO.db
Error in `[<-.data.table`(x, j = name, value = value) :
RHS of assignment is not NULL, not an an atomic vector (see ?is.atomic) and not a list column.
sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] GO.db_3.6.0 AnnotationDbi_1.42.1 IRanges_2.14.10 S4Vectors_0.18.3 Biobase_2.40.0 BiocGenerics_0.26.0 multiGSEA_0.11.1
[8] edgeR_3.22.3 limma_3.36.2 BiocInstaller_1.30.0 devtools_1.13.6
loaded via a namespace (and not attached):
[1] viridis_0.5.1 httr_1.3.1 tidyr_0.8.1 bit64_0.9-7 jsonlite_1.5 viridisLite_0.3.0 shiny_1.1.0
[8] assertthat_0.2.0 blob_1.1.1 yaml_2.2.0 pillar_1.3.0 RSQLite_2.1.1 lattice_0.20-35 glue_1.3.0
[15] digest_0.6.15 promises_1.0.1 RColorBrewer_1.1-2 colorspace_1.3-2 Matrix_1.2-14 htmltools_0.3.6 httpuv_1.4.5
[22] plyr_1.8.4 GSEABase_1.42.0 XML_3.98-1.16 pkgconfig_2.0.2 GetoptLong_0.1.7 purrr_0.2.5 xtable_1.8-2
[29] scales_1.0.0 later_0.7.3 BiocParallel_1.14.2 tibble_1.4.2 GSVA_1.28.0 annotate_1.58.0 ggplot2_3.0.0.9000
[36] withr_2.1.2 lazyeval_0.2.1 mime_0.5 magrittr_1.5 crayon_1.3.4 memoise_1.1.0 graph_1.58.0
[43] tools_3.5.0 data.table_1.11.4 GlobalOptions_0.1.0 matrixStats_0.54.0 ComplexHeatmap_1.18.1 stringr_1.3.1 plotly_4.8.0
[50] munsell_0.5.0 locfit_1.5-9.1 bindrcpp_0.2.2 compiler_3.5.0 rlang_0.2.2 grid_3.5.0 RCurl_1.95-4.11
[57] rstudioapi_0.7 rjson_0.2.20 htmlwidgets_1.2 circlize_0.4.4 bitops_1.0-6 gtable_0.2.0 DBI_1.0.0
[64] reshape2_1.4.3 R6_2.2.2 gridExtra_2.3 dplyr_0.7.6 bit_1.1-14 shinythemes_1.1.1 bindr_0.1.1
[71] shape_1.4.4 stringi_1.2.4 Rcpp_0.12.18 geneplotter_1.58.0 tidyselect_0.2.4