last biocoductor version

[dibbelab]

I am not able to reproduce the tutorial example with last scde version from bioconductor. About one week ago it was working fine.

# load example dataset
data(es.mef.small)

# factor determining cell types
sg <- factor(gsub("(MEF|ESC).*", "\\1", colnames(es.mef.small)), levels = c("ESC", "MEF"))
# the group factor should be named accordingly
names(sg) <- colnames(es.mef.small)  
table(sg)

cd <- clean.counts(es.mef.small, min.lib.size=1000, min.reads = 1, min.detected = 1)

o.ifm <- scde.error.models(counts = cd, groups = sg, n.cores = 1, threshold.segmentation = TRUE, save.crossfit.plots = FALSE, save.model.plots = FALSE, verbose = 1)

The error I get:

20 : MEF_68
Classification: weighted 
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots
ERROR encountered in building a model for cell MEF_49 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_50 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_51 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_52 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_53 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_54 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_55 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_56 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_57 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_58 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_59 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_60 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_61 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_62 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_63 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_64 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_65 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_66 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_67 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR encountered in building a model for cell MEF_68 - skipping the cell. Error:
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

ERROR fitting of 20 out of 20 cells resulted in errors reporting remaining 0 cells

[arsenepkao]

Hi,

I have the exact same problem here. With the scde version 2.12.0 from Bioconductor, the scde.expression.prior() and knn.error.models() both give the same error as reported above. I tried previous suggestions, but neither flexmix version 2.3-13 nor an older scde package works. Could anyone please tell me how to make it work?

Below are my sessioninfo

sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] scde_2.12.0 devtools_2.2.1 usethis_1.5.1 boot_1.3-23
[5] flexmix_2.3-13 lattice_0.20-38 ggfortify_0.4.8 irlba_2.3.3
[9] Matrix_1.2-18 shiny_1.4.0 DESeq2_1.24.0 dplyr_0.8.3
[13] ggplot2_3.2.1 monocle3_0.2.0 SingleCellExperiment_1.6.0 SummarizedExperiment_1.14.1
[17] DelayedArray_0.10.0 BiocParallel_1.18.1 matrixStats_0.55.0 GenomicRanges_1.36.1
[21] GenomeInfoDb_1.20.0 IRanges_2.18.3 S4Vectors_0.22.1 Biobase_2.44.0
[25] BiocGenerics_0.30.0 rlang_0.4.3

loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 RSQLite_2.2.0 AnnotationDbi_1.46.1 htmlwidgets_1.5.1
[5] grid_3.6.2 Rtsne_0.15 munsell_0.5.0 codetools_0.2-16
[9] units_0.6-5 withr_2.1.2 colorspace_1.4-1 knitr_1.28
[13] rstudioapi_0.10 distillery_1.0-6 pbmcapply_1.5.0 labeling_0.3
[17] slam_0.1-47 GenomeInfoDbData_1.2.1 bit64_0.9-7 farver_2.0.3
[21] extRemes_2.0-11 rprojroot_1.3-2 coda_0.19-3 LearnBayes_2.15.1
[25] vctrs_0.2.2 xfun_0.12 R6_2.4.1 locfit_1.5-9.1
[29] RcppArmadillo_0.9.800.4.0 bitops_1.0-6 assertthat_0.2.1 promises_1.1.0
[33] scales_1.1.0 nnet_7.3-12 gtable_0.3.0 Cairo_1.5-10
[37] processx_3.4.1 MatrixModels_0.4-1 genefilter_1.66.0 splines_3.6.2
[41] lazyeval_0.2.2 acepack_1.4.1 brew_1.0-6 checkmate_1.9.4
[45] BiocManager_1.30.10 yaml_2.2.0 reshape2_1.4.3 crosstalk_1.0.0
[49] backports_1.1.5 httpuv_1.5.2 Hmisc_4.3-0 tools_3.6.2
[53] spData_0.3.2 ellipsis_0.3.0 RColorBrewer_1.1-2 proxy_0.4-23
[57] sessioninfo_1.1.1 Rcpp_1.0.3 plyr_1.8.5 base64enc_0.1-3
[61] zlibbioc_1.30.0 classInt_0.4-2 purrr_0.3.3 RCurl_1.98-1.1
[65] ps_1.3.0 prettyunits_1.1.1 rpart_4.1-15 deldir_0.1-23
[69] viridis_0.5.1 ggrepel_0.8.1 cluster_2.1.0 fs_1.3.1
[73] magrittr_1.5 data.table_1.12.8 RSpectra_0.16-0 SparseM_1.78
[77] gmodels_2.18.1 RANN_2.6.1 pcaMethods_1.76.0 pkgload_1.0.2
[81] mime_0.8 xtable_1.8-4 XML_3.99-0.3 jpeg_0.1-8.1
[85] RMTstat_0.3 gridExtra_2.3 testthat_2.3.1 compiler_3.6.2
[89] tibble_2.1.3 KernSmooth_2.23-16 crayon_1.3.4 htmltools_0.4.0
[93] mgcv_1.8-31 later_1.0.0 spdep_1.1-3 Formula_1.2-3
[97] tidyr_1.0.2 geneplotter_1.62.0 expm_0.999-4 RcppParallel_4.4.4
[101] DBI_1.1.0 MASS_7.3-51.4 sf_0.8-0 cli_2.0.1
[105] gdata_2.18.0 igraph_1.2.4.2 pkgconfig_2.0.3 foreign_0.8-72
[109] sp_1.3-2 plotly_4.9.1 annotate_1.62.0 XVector_0.24.0
[113] stringr_1.4.0 callr_3.4.1 digest_0.6.23 RcppAnnoy_0.0.14
[117] Rook_1.1-1 htmlTable_1.13.3 uwot_0.1.5 edgeR_3.26.8
[121] DelayedMatrixStats_1.6.1 curl_4.3 Lmoments_1.3-1 gtools_3.8.1
[125] quantreg_5.54 modeltools_0.2-22 rjson_0.2.20 lifecycle_0.1.0
[129] nlme_3.1-142 jsonlite_1.6 desc_1.2.0 viridisLite_0.3.0
[133] limma_3.40.6 fansi_0.4.1 pillar_1.4.3 fastmap_1.0.1
[137] httr_1.4.1 pkgbuild_1.0.6 survival_3.1-8 glue_1.3.1
[141] remotes_2.1.0 png_0.1-7 bit_1.1-15.1 class_7.3-15
[145] stringi_1.4.4 blob_1.2.1 latticeExtra_0.6-29 memoise_1.1.0
[149] e1071_1.7-3

[JulioLeonIncio]

I got the same problem!

[wir963]

I am also getting the same problem

[mercegari]

Any chance of what can be the problem here? I am also having the same problem:

library(scde)
data(pollen)
cd <- clean.counts(pollen)
knn <- knn.error.models(cd, k=ncol(cd)/4, n.cores=10, min.count.threshold=2, min.nonfailed=5, max.model.plots=10)

I am getting lots of the following error:

Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

followed by:

Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots

My session info:

R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bullseye/sid

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so

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

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

other attached packages:
[1] scde_2.18.0     flexmix_2.3-17  lattice_0.20-41

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6               conquer_1.0.2           
 [3] edgeR_3.32.1             BiocGenerics_0.36.0     
 [5] splines_4.0.4            MASS_7.3-53.1           
 [7] BiocParallel_1.24.1      rjson_0.2.20            
 [9] brew_1.0-6               RcppArmadillo_0.10.2.2.0
[11] distillery_1.2           Rook_1.1-1              
[13] Lmoments_1.3-1           tools_4.0.4             
[15] nnet_7.3-15              parallel_4.0.4          
[17] RMTstat_0.3              grid_4.0.4              
[19] Biobase_2.50.0           nlme_3.1-152            
[21] mgcv_1.8-34              quantreg_5.85           
[23] modeltools_0.2-23        MatrixModels_0.5-0      
[25] matrixStats_0.58.0       Matrix_1.3-2            
[27] RColorBrewer_1.1-2       extRemes_2.1            
[29] limma_3.46.0             compiler_4.0.4          
[31] pcaMethods_1.82.0        stats4_4.0.4            
[33] locfit_1.5-9.4           SparseM_1.81            
[35] Cairo_1.5-12.2