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spatstat update breaks spatstat::markvario dependency #4243

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innesbre opened this issue Mar 17, 2021 · 2 comments
Closed

spatstat update breaks spatstat::markvario dependency #4243

innesbre opened this issue Mar 17, 2021 · 2 comments
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@innesbre
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Updating spatstat seems to have misplaced "markvario", resulting in the following error when trying to attach Seurat:

library(Seurat)
Error: package or namespace load failed for ‘Seurat’:
 object ‘markvario’ is not exported by 'namespace:spatstat'
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

loaded via a namespace (and not attached):
  [1] nlme_3.1-152           spatstat.sparse_2.0-0  matrixStats_0.58.0     RcppAnnoy_0.0.18       RColorBrewer_1.1-2    
  [6] httr_1.4.2             sctransform_0.3.2      tools_4.0.3            utf8_1.2.1             R6_2.5.0              
 [11] irlba_2.3.3            rpart_4.1-15           KernSmooth_2.23-18     mgcv_1.8-34            DBI_1.1.1             
 [16] lazyeval_0.2.2         colorspace_2.0-0       withr_2.4.1            tidyselect_1.1.0       gridExtra_2.3         
 [21] compiler_4.0.3         cli_2.3.1              plotly_4.9.3           scales_1.1.1           lmtest_0.9-38         
 [26] spatstat.data_2.0-0    ggridges_0.5.3         pbapply_1.4-3          goftest_1.2-2          spatstat_2.0-1        
 [31] stringr_1.4.0          digest_0.6.27          spatstat.utils_2.1-0   rmarkdown_2.7          pkgconfig_2.0.3       
 [36] htmltools_0.5.1.1      sessioninfo_1.1.1      parallelly_1.24.0      fastmap_1.1.0          htmlwidgets_1.5.3     
 [41] rlang_0.4.10           shiny_1.6.0            generics_0.1.0         zoo_1.8-9              jsonlite_1.7.2        
 [46] ica_1.0-2              dplyr_1.0.5            magrittr_2.0.1         spatstat.linnet_1.65-3 patchwork_1.1.1       
 [51] Matrix_1.3-2           Rcpp_1.0.6             munsell_0.5.0          fansi_0.4.2            abind_1.4-5           
 [56] reticulate_1.18        lifecycle_1.0.0        stringi_1.5.3          yaml_2.2.1             MASS_7.3-53.1         
 [61] Rtsne_0.15             plyr_1.8.6             grid_4.0.3             parallel_4.0.3         listenv_0.8.0         
 [66] promises_1.2.0.1       ggrepel_0.9.1          crayon_1.4.1           deldir_0.2-10          miniUI_0.1.1.1        
 [71] lattice_0.20-41        cowplot_1.1.1          splines_4.0.3          tensor_1.5             knitr_1.31            
 [76] pillar_1.5.1           igraph_1.2.6           spatstat.geom_1.65-5   future.apply_1.7.0     reshape2_1.4.4        
 [81] codetools_0.2-18       leiden_0.3.7           glue_1.4.2             evaluate_0.14          SeuratObject_4.0.0    
 [86] data.table_1.14.0      vctrs_0.3.6            png_0.1-7              httpuv_1.5.5           spatstat.core_1.65-5  
 [91] polyclip_1.10-0        gtable_0.3.0           RANN_2.6.1             purrr_0.3.4            tidyr_1.1.3           
 [96] scattermore_0.7        future_1.21.0          assertthat_0.2.1       ggplot2_3.3.3          xfun_0.22             
[101] mime_0.10              xtable_1.8-4           later_1.1.0.1          survival_3.2-10        viridisLite_0.3.0     
[106] tibble_3.1.0           cluster_2.1.1          globals_0.14.0         fitdistrplus_1.1-3     ellipsis_0.3.1        
[111] ROCR_1.0-11    
@innesbre innesbre added the bug Something isn't working label Mar 17, 2021
@innesbre
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@samuel-marsh
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See #4226 (comment)

@mojaveazure mojaveazure added the duplicate This issue or pull request already exists label Mar 17, 2021
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