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ShellyCoder / cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor
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Error when run getHyperPathway #38

Open tqh003 opened 1 year ago

tqh003 commented 1 year ago

Hi, When I tried to run the pathway activity analysis using example data. I encountered a error as follow:

pathway.hyper.list <- lapply(colnames(n), function(i){ print(i) tmp <- getHyperPathway(data = n, object = mt, cella_cellb = i, Org="Homo sapiens") return(tmp) }) Error in parse(text = elt) : :1:7: unexpected symbol 1: Using an ^

Does anyone has any idea what cause this error? Thanks in advance.

BTW, my sessioninfo is: R version 3.6.3 (2020-02-29) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages: [1] stats graphics grDevices utils datasets methods
[7] base
other attached packages: [1] stringi_1.7.8 forcats_0.5.2 dplyr_1.0.9 purrr_0.3.4
[5] readr_2.1.2 tidyr_1.2.0 tibble_3.1.8 ggplot2_3.3.6
[9] tidyverse_1.3.2 networkD3_0.4 stringr_1.4.1 cellcall_1.0.7

tqh003 commented 1 year ago

Interestingly, when I installed the cellcall in Ubuntu20.04 LTS and tried to run cellcall on the example data, everything worked well. Is there anybody knows the possible reasons for the error in Windows 10?

BTW, my sessionInfo is as follow: R version 4.2.2 Patched (2022-11-10 r83330) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] cellcall_1.0.7