could not find function "calculate_distance" #108
Description
Hi,
I am trying to use SC3 but running into the following error repeatedly. Please help to resolve this.
sce <- readRDS("data/deng/deng-sce.rds")
sce <- sc3(sce, ks = 10, biology = TRUE, n_cores = 1)
Setting SC3 parameters...
Calculating distances between the cells...
starting worker pid=41321 on localhost:11646 at 20:55:46.804
Loading required package: SC3
Loading required package: foreach
Loading required package: rngtools
Error in calculate_distance(dataset, i) :
could not find function "calculate_distance"
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘SC3’
Error in calculate_distance(dataset, i) :
could not find function "calculate_distance"
Error in calculate_distance(dataset, i) :
could not find function "calculate_distance"
Error in checkForRemoteErrors(val) :
3 nodes produced errors; first error: Error in calculate_distance(dataset, i) :
could not find function "calculate_distance"
Here is the session info:
sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /general/sw/eb/sw/FlexiBLAS/3.0.4-GCC-11.2.0/lib64/libflexiblas.so.3.0
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] SC3_1.26.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8.3 mvtnorm_1.1-3
[3] lattice_0.20-45 class_7.3-20
[5] assertthat_0.2.1 digest_0.6.29
[7] foreach_1.5.2 SingleCellExperiment_1.20.0
[9] utf8_1.2.2 mime_0.12
[11] R6_2.5.1 GenomeInfoDb_1.34.2
[13] WriteXLS_6.4.0 stats4_4.2.0
[15] pcaPP_1.9-74 e1071_1.7-9
[17] ggplot2_3.3.5 pillar_1.7.0
[19] zlibbioc_1.44.0 rlang_1.0.2
[21] S4Vectors_0.36.0 Matrix_1.5-1
[23] pheatmap_1.0.12 RCurl_1.98-1.6
[25] munsell_0.5.0 proxy_0.4-26
[27] shiny_1.7.1 DelayedArray_0.24.0
[29] httpuv_1.6.5 compiler_4.2.0
[31] pkgconfig_2.0.3 BiocGenerics_0.44.0
[33] htmltools_0.5.2 tidyselect_1.1.2
[35] SummarizedExperiment_1.28.0 tibble_3.1.6
[37] GenomeInfoDbData_1.2.9 IRanges_2.32.0
[39] codetools_0.2-18 matrixStats_0.62.0
[41] fansi_1.0.3 later_1.3.0
[43] crayon_1.5.1 rrcov_1.7-0
[45] dplyr_1.0.8 bitops_1.0-7
[47] grid_4.2.0 xtable_1.8-4
[49] gtable_0.3.0 lifecycle_1.0.1
[51] DBI_1.1.2 magrittr_2.0.3
[53] scales_1.2.0 cli_3.3.0
[55] XVector_0.38.0 ROCR_1.0-11
[57] promises_1.2.0.1 doRNG_1.8.2
[59] doParallel_1.0.17 robustbase_0.95-0
[61] ellipsis_0.3.2 generics_0.1.2
[63] vctrs_0.4.1 RColorBrewer_1.1-3
[65] iterators_1.0.14 tools_4.2.0
[67] Biobase_2.58.0 glue_1.6.2
[69] DEoptimR_1.0-11 purrr_0.3.4
[71] MatrixGenerics_1.10.0 rngtools_1.5.2
[73] fastmap_1.1.0 parallel_4.2.0
[75] colorspace_2.0-3 cluster_2.1.3
[77] GenomicRanges_1.50.1
I