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Error: object 'upsetplot' not found #31

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TimJCooper opened this issue Feb 18, 2020 · 1 comment
Open

Error: object 'upsetplot' not found #31

TimJCooper opened this issue Feb 18, 2020 · 1 comment

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@TimJCooper
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I'm unable to use 'upsetplot' (either as part of DOSE or clusterProfiler) - why am I receiving this error? DOSE was installed via:

BiocManager::install("DOSE")

[](> library(DOSE)
DOSE v3.12.0  For help: https://guangchuangyu.github.io/software/DOSE

If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

> upsetplot
Error: object 'upsetplot' not found
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 19.10

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

locale:
 [1] LC_CTYPE=en_IL.UTF-8       LC_NUMERIC=C               LC_TIME=en_IL.UTF-8        LC_COLLATE=en_IL.UTF-8     LC_MONETARY=en_IL.UTF-8   
 [6] LC_MESSAGES=en_IL.UTF-8    LC_PAPER=en_IL.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_IL.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] DOSE_3.12.0

loaded via a namespace (and not attached):
 [1] Biobase_2.46.0         viridis_0.5.1          httr_1.4.1             tidyr_1.0.2            tidygraph_1.1.2        bit64_0.9-7           
 [7] jsonlite_1.6.1         viridisLite_0.3.0      splines_3.6.1          ggraph_2.0.1           assertthat_0.2.1       DO.db_2.9             
[13] BiocManager_1.30.10    rvcheck_0.1.7          triebeard_0.3.0        urltools_1.7.3         stats4_3.6.1           blob_1.2.1            
[19] progress_1.2.2         ggrepel_0.8.1          pillar_1.4.3           RSQLite_2.2.0          lattice_0.20-38        glue_1.3.1            
[25] digest_0.6.23          RColorBrewer_1.1-2     polyclip_1.10-0        qvalue_2.18.0          colorspace_1.4-1       cowplot_1.0.0         
[31] Matrix_1.2-17          plyr_1.8.5             pkgconfig_2.0.3        clusterProfiler_3.14.3 purrr_0.3.3            GO.db_3.10.0          
[37] scales_1.1.0           ggplotify_0.0.4        europepmc_0.3          tweenr_1.0.1           enrichplot_1.6.1       BiocParallel_1.20.1   
[43] ggforce_0.3.1          tibble_2.1.3           farver_2.0.3           IRanges_2.20.2         ggplot2_3.2.1          BiocGenerics_0.32.0   
[49] lazyeval_0.2.2         magrittr_1.5           crayon_1.3.4           memoise_1.1.0          MASS_7.3-51.4          xml2_1.2.2            
[55] tools_3.6.1            data.table_1.12.8      prettyunits_1.1.1      hms_0.5.3              lifecycle_0.1.0        stringr_1.4.0         
[61] S4Vectors_0.24.3       munsell_0.5.0          AnnotationDbi_1.48.0   compiler_3.6.1         gridGraphics_0.4-1     rlang_0.4.4           
[67] ggridges_0.5.2         grid_3.6.1             rstudioapi_0.10        igraph_1.2.4.2         gtable_0.3.0           DBI_1.1.0             
[73] reshape2_1.4.3         graphlayouts_0.5.0     R6_2.4.1               gridExtra_2.3          dplyr_0.8.4            bit_1.1-15.1          
[79] fastmatch_1.1-0        fgsea_1.12.0           GOSemSim_2.12.0        stringi_1.4.5          parallel_3.6.1         Rcpp_1.0.3            
[85] vctrs_0.2.2            tidyselect_1.0.0      )
@huerqiang
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huerqiang commented Feb 19, 2020

upsetplot is a function in package enrichplot.

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