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hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
http://bioconductor.org/packages/SC3
GNU General Public License v3.0
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Error in ED2(data) #64

Closed biosyssun closed 5 years ago

biosyssun commented 6 years ago

I met an error when i ran sc3 fuction. Error in ED2(data) : Not compatible with requested type: [type=list; target=double]

please help! thanks!

wikiselev commented 6 years ago

Could you provide your sessionInfo()?

rfarouni commented 5 years ago

I got the same problem.

Error in checkForRemoteErrors(val) : 3 nodes produced errors; first error: Error in ED2(data) : Not compatible with requested type: [type=S4; target=double].
12.
stop(count, " nodes produced errors; first error: ", firstmsg, domain = NA)
11.
checkForRemoteErrors(val)
10.
dynamicClusterApply(cl, fun, length(x), argfun)
9.
clusterApplyLB(cl, argsList, evalWrapper)
8.
e$fun(obj, substitute(ex), parent.frame(), e$data)
7.
structure(list(args = distances(.doRNG.stream = list(c(407L, -1161039318L, -490271325L, -1027984760L, -1775018263L, 1105057174L, -669866209L), c(407L, 1020159488L, 103857914L, 24429005L, -762343192L, 1999669063L, -1091817748L), c(407L, 224450330L, -1136206754L, ...
6.
do.call("%dopar%", list(obj, ex), envir = parent.frame())
5.
foreach::foreach(i = distances) %dorng% { try({ calculate_distance(dataset, i) }) ...
4.
sc3_calc_dists(object)
3.
sc3_calc_dists(object)
2.
sc3(sce10x_hg38_keep, ks = 2:4, biology = TRUE)
1.
sc3(sce10x_hg38_keep, ks = 2:4, biology = TRUE)

sessionInfo()

R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.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       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SC3_1.10.0                  bindrcpp_0.2.2              pheatmap_1.0.10             Rphenograph_0.99.1         
 [5] igraph_1.2.2                uwot_0.0.0.9008             Matrix_1.2-15               scran_1.10.1               
 [9] dbscan_1.1-3                forcats_0.3.0               stringr_1.3.1               dplyr_0.7.8                
[13] purrr_0.2.5                 readr_1.3.1                 tidyr_0.8.2                 tibble_1.4.2               
[17] tidyverse_1.2.1             DropletUtils_1.2.1          ensembldb_2.6.3             AnnotationFilter_1.6.0     
[21] GenomicFeatures_1.34.1      AnnotationDbi_1.44.0        scater_1.10.0               ggplot2_3.1.0              
[25] SingleCellExperiment_1.4.0  SummarizedExperiment_1.12.0 DelayedArray_0.8.0          BiocParallel_1.16.2        
[29] matrixStats_0.54.0          Biobase_2.42.0              GenomicRanges_1.34.0        GenomeInfoDb_1.18.1        
[33] IRanges_2.16.0              S4Vectors_0.20.1            BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
  [1] readxl_1.2.0             backports_1.1.3          plyr_1.8.4               lazyeval_0.2.1           digest_0.6.18           
  [6] foreach_1.4.4            htmltools_0.3.6          viridis_0.5.1            rsconnect_0.8.12         gdata_2.18.0            
 [11] magrittr_1.5             memoise_1.1.0            cluster_2.0.7-1          doParallel_1.0.14        ROCR_1.0-7              
 [16] limma_3.38.3             Biostrings_2.50.1        modelr_0.1.2             RcppParallel_4.4.2       prettyunits_1.0.2       
 [21] colorspace_1.3-2         rrcov_1.4-7              blob_1.1.1               rvest_0.3.2              WriteXLS_4.0.0          
 [26] haven_2.0.0              xfun_0.4                 crayon_1.3.4             RCurl_1.95-4.11          jsonlite_1.6            
 [31] bindr_0.1.1              iterators_1.0.10         glue_1.3.0               registry_0.5             gtable_0.2.0            
 [36] zlibbioc_1.28.0          XVector_0.22.0           Rhdf5lib_1.4.2           DEoptimR_1.0-8           HDF5Array_1.10.1        
 [41] scales_1.0.0             mvtnorm_1.0-8            rngtools_1.3.1           DBI_1.0.0                edgeR_3.24.2            
 [46] bibtex_0.4.2             Rcpp_1.0.0               xtable_1.8-3             viridisLite_0.3.0        progress_1.2.0          
 [51] bit_1.1-14               httr_1.4.0               gplots_3.0.1             RColorBrewer_1.1-2       pkgconfig_2.0.2         
 [56] XML_3.98-1.16            locfit_1.5-9.1           dynamicTreeCut_1.63-1    later_0.7.5              tidyselect_0.2.5        
 [61] labeling_0.3             rlang_0.3.0.1            reshape2_1.4.3           munsell_0.5.0            cellranger_1.1.0        
 [66] tools_3.5.2              cli_1.0.1                generics_0.0.2           RSQLite_2.1.1            broom_0.5.1             
 [71] evaluate_0.12            yaml_2.2.0               knitr_1.21               bit64_0.9-7              robustbase_0.93-3       
 [76] caTools_1.17.1.1         RANN_2.6                 doRNG_1.7.1              nlme_3.1-137             mime_0.6                
 [81] xml2_1.2.0               biomaRt_2.38.0           compiler_3.5.2           rstudioapi_0.8           beeswarm_0.2.3          
 [86] curl_3.2                 e1071_1.7-0              statmod_1.4.30           pcaPP_1.9-73             stringi_1.2.4           
 [91] RSpectra_0.13-1          lattice_0.20-38          ProtGenerics_1.14.0      pillar_1.3.1             BiocManager_1.30.4      
 [96] RcppAnnoy_0.0.11         BiocNeighbors_1.0.0      cowplot_0.9.3            bitops_1.0-6             irlba_2.3.2             
[101] httpuv_1.4.5.1           rtracklayer_1.42.1       R6_2.3.0                 promises_1.0.1           KernSmooth_2.23-15      
[106] gridExtra_2.3            vipor_0.4.5              codetools_0.2-16         gtools_3.8.1             assertthat_0.2.0        
[111] rhdf5_2.26.1             pkgmaker_0.27            withr_2.1.2              GenomicAlignments_1.18.0 Rsamtools_1.34.0        
[116] GenomeInfoDbData_1.2.0   mgcv_1.8-26              hms_0.4.2                grid_3.5.2               class_7.3-15            
[121] rmarkdown_1.11           DelayedMatrixStats_1.4.0 shiny_1.2.0              lubridate_1.7.4          base64enc_0.1-3         
[126] ggbeeswarm_0.6.0
rfarouni commented 5 years ago

Now it works! I think the problem was solved by restarting a new R session after installation.