Comments (7)
That is correct. I have no issue with R4.0.5
from metacell.
R version 4.1.0 (2021-05-18)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.3 (Maipo)
Matrix products: default
BLAS/LAPACK: /storage/chen/home/zz4/miniconda3/lib/libopenblasp-r0.3.15.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] SingleCellExperiment_1.14.1 SummarizedExperiment_1.22.0
[3] Biobase_2.52.0 GenomicRanges_1.44.0
[5] GenomeInfoDb_1.28.0 IRanges_2.26.0
[7] S4Vectors_0.30.0 BiocGenerics_0.38.0
[9] MatrixGenerics_1.4.0 matrixStats_0.59.0
[11] metacell_0.3.6
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 lattice_0.20-44 tidyr_1.1.3
[4] png_0.1-7 zoo_1.8-9 assertthat_0.2.1
[7] digest_0.6.27 utf8_1.2.1 RSpectra_0.16-0
[10] IRdisplay_1.0 R6_2.5.0 repr_1.1.3
[13] evaluate_0.14 ggplot2_3.3.3 pillar_1.6.1
[16] zlibbioc_1.38.0 rlang_0.4.11 uuid_0.1-4
[19] Rgraphviz_2.36.0 Matrix_1.3-3 pdist_1.2
[22] reticulate_1.20 RCurl_1.98-1.3 igraph_1.2.6
[25] tgstat_2.3.16 munsell_0.5.0 umap_0.2.7.0
[28] DelayedArray_0.18.0 compiler_4.1.0 pkgconfig_2.0.3
[31] askpass_1.1 base64enc_0.1-3 htmltools_0.5.1.1
[34] openssl_1.4.4 tidyselect_1.1.1 GenomeInfoDbData_1.2.6
[37] tibble_3.1.2 tgconfig_0.1.2 fansi_0.5.0
[40] crayon_1.4.1 dplyr_1.0.6 bitops_1.0-7
[43] grid_4.1.0 tgutil_0.1.6 jsonlite_1.7.2
[46] gtable_0.3.0 lifecycle_1.0.0 DBI_1.1.1
[49] magrittr_2.0.1 scales_1.1.1 graph_1.70.0
[52] XVector_0.32.0 dbscan_1.1-8 ellipsis_0.3.2
[55] generics_0.1.0 vctrs_0.3.8 IRkernel_1.2
[58] lpSolveAPI_5.5.2.0-17.7 tools_4.1.0 glue_1.4.2
[61] purrr_0.3.4 yaml_2.2.1 colorspace_2.0-1
[64] cluster_2.1.2 pbdZMQ_0.3-5
from metacell.
I got this dead kernel when running mcell_mc_from_coclust_balanced(). It also shows
filtered NA left with NA based on co-cluster imbalance
from metacell.
Another issue is mcell_coclust_filt_by_k_deg(). I have to rename cell labels to "1", "2", .... or as.numeric(names(thresh_Kr)) will not work.
from metacell.
as.numeric(names(thresh_Kr)) should work with parsable strings, not just "1". However, this issue appears to happen to multiple users lately, possibly related to the R version 4.1.0. I haven't reproduced this issue yet, will write back quickly when we find a workaround. In the meantime, you can try to downgrade R.
from metacell.
Thanks for the info, will update
from metacell.
This issue should be solved now for 4.1.0 as well, please let us know if you encounter any other problems with the current R versions.
from metacell.
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from metacell.