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lianos / multiGSEA

NOTE: This package has been renamed to sparrow and will be submitted to Bioconductor 3.14. Please use that package instead. This is kept here for posterity.
https://lianos.github.io/multiGSEA/
MIT License
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getPantherGeneSetDb error #9

Open tomsing1 opened 6 years ago

tomsing1 commented 6 years ago

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