tanaylab / metacell

Metacell - Single-cell mRNA Analysis
https://tanaylab.github.io/metacell
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function `tgs_cor_graph()` is missing in package #90

Open TimelikeTachyon opened 9 months ago

TimelikeTachyon commented 9 months ago

Recently I found that the function mcell_add_cgraph_from_mat_bknn() of your package metacell is continue dying and has no respound at all to any other inputs. After a short test, it seems that due to the function tgs_cor_graph() is missing in the package.

In detail, The help info of this function could be viewed when using ?tgs_cor_graph command: tgs_cor_graph {metacell}: wrapping tgs functions to compute balanced graph from a matrix... but if we use metacell::tgs_cor_graph, it will Immediately throwout an error as: Error: 'tgs_cor_graph' is not an exported object from 'namespace:metacell' I have tested your package version 0.3.7 as well as 0.3.41, and both have the same issue. Any possible to fix it? Thanks.

TimelikeTachyon commented 9 months ago

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