RStudio crash when importing anndata2ri

[JLiLab]

While other python packages work fine, importing anndata2r1 crashes RStudio. Any suggests how to fix this problem? Here is the session info:

R version 4.0.0 (2020-04-24) Platform: x86_64-apple-darwin17.0 (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/4.0/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] stats graphics grDevices utils datasets methods base

other attached packages: [1] Seurat_3.1.5 ggplot2_3.3.0 reticulate_1.15

loaded via a namespace (and not attached): [1] httr_1.4.1 tidyr_1.1.0 jsonlite_1.6.1 viridisLite_0.3.0 splines_4.0.0 leiden_0.3.3
[7] assertthat_0.2.1 ggrepel_0.8.2 sessioninfo_1.1.1 globals_0.12.5 pillar_1.4.4 lattice_0.20-41
[13] glue_1.4.1 digest_0.6.25 RColorBrewer_1.1-2 colorspace_1.4-1 cowplot_1.0.0 htmltools_0.4.0
[19] Matrix_1.2-18 plyr_1.8.6 pkgconfig_2.0.3 tsne_0.1-3 listenv_0.8.0 purrr_0.3.4
[25] patchwork_1.0.0 scales_1.1.1 RANN_2.6.1 Rtsne_0.15 tibble_3.0.1 ellipsis_0.3.1
[31] withr_2.2.0 ROCR_1.0-11 pbapply_1.4-2 lazyeval_0.2.2 cli_2.0.2 survival_3.1-12
[37] magrittr_1.5 crayon_1.3.4 future_1.17.0 fansi_0.4.1 nlme_3.1-147 MASS_7.3-51.5
[43] ica_1.0-2 tools_4.0.0 fitdistrplus_1.1-1 data.table_1.12.8 lifecycle_0.2.0 stringr_1.4.0
[49] plotly_4.9.2.1 munsell_0.5.0 cluster_2.1.0 irlba_2.3.3 compiler_4.0.0 rsvd_1.0.3
[55] rlang_0.4.6 grid_4.0.0 ggridges_0.5.2 rstudioapi_0.11 RcppAnnoy_0.0.16 htmlwidgets_1.5.1 [61] igraph_1.2.5 gtable_0.3.0 codetools_0.2-16 reshape2_1.4.4 R6_2.4.1 gridExtra_2.3
[67] zoo_1.8-8 knitr_1.28 dplyr_0.8.5 uwot_0.1.8 future.apply_1.5.0 KernSmooth_2.23-16 [73] ape_5.3 stringi_1.4.6 parallel_4.0.0 Rcpp_1.0.4.6 vctrs_0.3.0 sctransform_0.2.1 [79] png_0.1-7 tidyselect_1.1.0 xfun_0.14 lmtest_0.9-37

[flying-sheep]

anndata2ri is a python package. how do you import it “in RStudio”? With reticulate? Or can RStudio run a Python interpreter now?

[JLiLab]

I used the reticulate package, as shown in Scanpy in R (https://github.com/theislab/scanpy-in-R)

From: "Philipp A." notifications@github.com Reply-To: theislab/anndata2ri reply@reply.github.com Date: Sunday, May 24, 2020 at 10:29 AM To: theislab/anndata2ri anndata2ri@noreply.github.com Cc: "Li,James" jali@uchc.edu, Author author@noreply.github.com Subject: Re: [theislab/anndata2ri] RStudio crash when importing anndata2ri (#45)

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anndata2ri is a python package. how do you import it?

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[flying-sheep]

Duplicate of #20 or rstudio/reticulate#208 then. I don’t know of a way to properly use reticulate and rpy2 together.

[flying-sheep]

Fixed in https://github.com/rstudio/reticulate/pull/1188

[flying-sheep]

Fixed in https://github.com/rstudio/reticulate/pull/1188