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tanaylab / metacell

Metacell - Single-cell mRNA Analysis
https://tanaylab.github.io/metacell
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Error Occured when Running metacell Usage Guide Page #89

Open TimelikeTachyon opened 9 months ago

TimelikeTachyon commented 9 months ago

Got an error when running the usage guide page of metacell:

https://tanaylab.github.io/metacell/articles/a-basic_pbmc8k.html

mcell_import_scmat_10x("test", base_dir="http://www.wisdom.weizmann.ac.il/~atanay/metac_data/pbmc_8k/") mat = scdb_mat("test") print(dim(mat@mat))

What I got is:

summing up total of 0 paralog genes into 0 unique genes Error in rbind.Matrix(x, y, deparse.level = 0L) : cannot get a slot ("p") from an object of type "logical"

I guess it is may due to function scmat_read_scmat_10x read the wrong column of data. Could you please double check this issue? Thanks.

TimelikeTachyon commented 9 months ago

Not sure if the package version cause this kind of issue yet.. I triedmetacell 0.3.7 and 0.3.41 as well as package Matrix 1.6.1, 1.5.1, package Seurat 4.4.0, 5.1.0, etc, but still have the same issue. The sessioninfo is below:

sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so; LAPACK version 3.7.1

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Asia/Shanghai tzcode source: system (glibc)

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

loaded via a namespace (and not attached): [1] vctrs_0.6.5 cli_3.6.2 knitr_1.45 rlang_1.1.3 xfun_0.42 SCopeLoomR_0.13.0 processx_3.8.3
[8] purrr_1.0.2 assertthat_0.2.1 glue_1.7.0 bit_4.0.5 htmltools_0.5.7 ps_1.7.6 pkgbuild_1.4.3
[15] rmarkdown_2.25 grid_4.3.2 evaluate_0.23 fastmap_1.1.1 yaml_2.3.8 lifecycle_1.0.4 tgconfig_0.1.2
[22] compiler_4.3.2 pbapply_1.7-2 rstudioapi_0.15.0 lattice_0.22-5 digest_0.6.34 R6_2.5.1 tidyselect_1.2.0 [29] parallel_4.3.2 callr_3.7.5 magrittr_2.0.3 Matrix_1.5-1 hdf5r_1.3.9 tools_4.3.2 bit64_4.0.5
[36] arrow_14.0.0.2 remotes_2.4.2.1

myushen commented 4 weeks ago

same issue here, did you find a solution?