namespace conflict flowAI and ggCyto
Entering edit mode
Robert Baer ▴ 70
Last seen 17 months ago
United States

Context Trying to load ggcyto library for the autoplot() function.

> search()
 [1] ".GlobalEnv"            "package:shiny"         "package:CytoExploreR"  "package:openCyto"      "package:flowWorkspace"
 [6] "package:flowCore"      "tools:rstudio"         "package:stats"         "package:graphics"      "package:grDevices"    
[11] "package:utils"         "package:datasets"      "package:methods"       "Autoloads"             "package:base"    

> library(ggcyto)
Loading required package: ggplot2
Error in value[[3L]](cond) : 
  Package ‘ggplot2’ version 3.3.0 cannot be unloaded:
 Error in unloadNamespace(package) : namespace ‘ggplot2’ is imported by ‘flowAI’ so cannot be unloaded

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] shiny_1.4.0.2       CytoExploreR_1.0.7  openCyto_2.1.0      flowWorkspace_4.1.2 flowCore_2.1.0     

loaded via a namespace (and not attached):
  [1] Rtsne_0.15          colorspace_1.4-1    ellipsis_0.3.1      mclust_5.4.6        rprojroot_1.3-2     cytolib_2.1.2      
  [7] corpcor_1.6.9       fs_1.4.1            clue_0.3-57         rstudioapi_0.11     hexbin_1.28.1       IDPmisc_1.1.20     
 [13] remotes_2.1.1       RSpectra_0.16-0     fansi_0.4.1         mvtnorm_1.1-0       splines_4.0.0       R.methodsS3_1.8.0  
 [19] mnormt_1.5-7        robustbase_0.93-6   knitr_1.28          shinythemes_1.1.2   pkgload_1.0.2       jsonlite_1.6.1     
 [25] umap_0.2.5.0        cluster_2.1.0       png_0.1-7           R.oo_1.23.0         graph_1.66.0        BiocManager_1.30.10
 [31] rrcov_1.5-2         compiler_4.0.0      backports_1.1.7     fastmap_1.0.1       assertthat_0.2.1    Matrix_1.2-18      
 [37] cli_2.0.2           later_1.0.0         visNetwork_2.0.9    htmltools_0.4.0     prettyunits_1.1.1   tools_4.0.0        
 [43] ncdfFlow_2.34.0     rsvd_1.0.3          gtable_0.3.0        glue_1.4.1          reshape2_1.4.4      dplyr_0.8.5        
 [49] Rcpp_1.0.4.6        Biobase_2.48.0      vctrs_0.3.0         changepoint_2.2.2   xfun_0.14           stringr_1.4.0      
 [55] ps_1.3.3            testthat_2.3.2      mime_0.9            lifecycle_0.2.0     gtools_3.8.2        devtools_2.3.0     
 [61] XML_3.99-0.3        DEoptimR_1.0-8      zlibbioc_1.34.0     MASS_7.3-51.6       zoo_1.8-8           scales_1.1.1       
 [67] EmbedSOM_2.1.1      RProtoBufLib_2.1.0  promises_1.1.0      parallel_4.0.0      RBGL_1.64.0         RColorBrewer_1.1-2 
 [73] yaml_2.2.1          curl_4.3            reticulate_1.15     memoise_1.1.0       ggplot2_3.3.1       latticeExtra_0.6-29
 [79] stringi_1.4.6       desc_1.2.0          pcaPP_1.9-73        flowClust_3.26.0    flowAI_1.19.1       BiocGenerics_0.35.2
 [85] pkgbuild_1.0.8      flowViz_1.53.0      rlang_0.4.6         pkgconfig_2.0.3     matrixStats_0.56.0  evaluate_0.14      
 [91] fda_5.1.4           lattice_0.20-41     purrr_0.3.4         ks_1.11.7           htmlwidgets_1.5.1   processx_3.4.2     
 [97] tidyselect_1.1.0    plyr_1.8.6          magrittr_1.5        R6_2.4.1            pillar_1.4.4        withr_2.2.0        
[103] tibble_3.0.1        crayon_1.3.4        KernSmooth_2.23-17  ellipse_0.4.2       rhandsontable_0.3.7 rmarkdown_2.1      
[109] jpeg_0.1-8.1        usethis_1.6.1       grid_4.0.0          data.table_1.12.8   callr_3.4.3         Rgraphviz_2.32.0   
[115] digest_0.6.25       xtable_1.8-4        tidyr_1.1.0         httpuv_1.5.2        R.utils_2.9.2       flowStats_4.1.0    
[121] openssl_1.4.1       RcppParallel_5.0.1  stats4_4.0.0        munsell_0.5.0       askpass_1.1         sessioninfo_1.1.1
software error flow cytometry ggcyto flowAI • 241 views
Entering edit mode

I cannot reproduce this using the current versions of flowCore, flowWorkspace, openCyto, ggcyto, CytoExploreR, and flowAI in any load order I've tried. Can you please provide an exact reproducible example from a new R session? I need to know all of the calls before library(ggcyto).


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