scde
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hms-dbmi
Error in vignette execution
When executing this code of the vignette, I run into an error during the model fitting.
SessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-conda-linux-gnu
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS/LAPACK: /path/to/homedir/miniforge3/envs/scde/lib/libopenblasp-r0.3.28.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_DE.UTF-8 LC_COLLATE=C.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Berlin
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] scde_2.34.0 flexmix_2.3-19 lattice_0.22-6
loaded via a namespace (and not attached):
[1] nlme_3.1-166 brew_1.0-10 MatrixModels_0.5-3
[4] pcaMethods_1.98.0 Cairo_1.6-2 statmod_1.5.0
[7] rjson_0.2.23 extRemes_2.2 nnet_7.3-19
[10] stats4_4.4.2 locfit_1.5-9.10 Biobase_2.66.0
[13] modeltools_0.2-23 grid_4.4.2 SparseM_1.84-2
[16] distillery_1.2-2 MASS_7.3-61 Lmoments_1.3-1
[19] compiler_4.4.2 Rook_1.2 codetools_0.2-20
[22] RColorBrewer_1.1-3 Rcpp_1.0.13-1 limma_3.62.1
[25] edgeR_4.4.0 mgcv_1.9-1 BiocParallel_1.40.0
[28] quantreg_5.99.1 RMTstat_0.3.1 parallel_4.4.2
[31] splines_4.4.2 Matrix_1.7-1 tools_4.4.2
[34] RcppArmadillo_14.2.0-1 BiocGenerics_0.52.0 survival_3.7-0
Code:
library(scde)
data(es.mef.small)
sg <- factor(gsub("(MEF|ESC).*", "\\1", colnames(es.mef.small)), levels = c("ESC", "MEF"))
names(sg) <- colnames(es.mef.small)
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)
Error:
Loading required package: flexmix
Loading required package: lattice
cross-fitting cells.
number of pairs: 190
number of pairs: 190
total number of pairs: 380
cross-fitting 380 pairs:
building individual error models.
adjusting library size based on 2000 entries
fitting ESC models:
1 : ESC_10
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
2 : ESC_11
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
3 : ESC_12
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
4 : ESC_13
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
5 : ESC_14
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
6 : ESC_15
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
7 : ESC_16
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
8 : ESC_17
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
9 : ESC_18
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
10 : ESC_19
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
11 : ESC_1
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
12 : ESC_20
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
13 : ESC_21
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
14 : ESC_22
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
15 : ESC_23
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
16 : ESC_24
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
17 : ESC_25
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
18 : ESC_26
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
19 : ESC_27
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
20 : ESC_28
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_10 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_11 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_12 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_13 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_14 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_15 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_16 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_17 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_18 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_19 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_1 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_20 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_21 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_22 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_23 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_24 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_25 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_26 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_27 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_28 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR fitting of 20 out of 20 cells resulted in errors reporting remaining 0 cells
fitting MEF models:
1 : MEF_49
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
2 : MEF_50
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
3 : MEF_51
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
4 : MEF_52
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
5 : MEF_53
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
6 : MEF_54
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
7 : MEF_55
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
8 : MEF_56
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
9 : MEF_57
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
10 : MEF_58
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
11 : MEF_59
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
12 : MEF_60
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
13 : MEF_61
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
14 : MEF_62
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
15 : MEF_63
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
16 : MEF_64
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
17 : MEF_65
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
18 : MEF_66
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
19 : MEF_67
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
20 : MEF_68
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_49 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_50 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_51 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_52 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_53 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_54 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_55 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_56 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_57 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_58 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_59 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_60 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_61 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_62 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_63 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_64 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_65 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_66 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_67 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_68 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR fitting of 20 out of 20 cells resulted in errors reporting remaining 0 cells
data frame with 0 columns and 0 rows
(scde) norm:~$ vim test_scde.R
(scde) norm:~$ Rscript test_scde.R
Loading required package: flexmix
Loading required package: lattice
cross-fitting cells.
number of pairs: 190
number of pairs: 190
total number of pairs: 380
cross-fitting 380 pairs:
building individual error models.
adjusting library size based on 2000 entries
fitting ESC models:
1 : ESC_10
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
2 : ESC_11
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
3 : ESC_12
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
4 : ESC_13
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
5 : ESC_14
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
6 : ESC_15
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
7 : ESC_16
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
8 : ESC_17
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
9 : ESC_18
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
10 : ESC_19
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
11 : ESC_1
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
12 : ESC_20
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
13 : ESC_21
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
14 : ESC_22
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
15 : ESC_23
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
16 : ESC_24
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
17 : ESC_25
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
18 : ESC_26
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
19 : ESC_27
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
20 : ESC_28
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_10 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_11 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_12 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_13 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_14 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_15 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_16 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_17 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_18 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_19 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_1 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_20 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_21 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_22 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_23 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_24 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_25 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_26 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_27 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell ESC_28 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR fitting of 20 out of 20 cells resulted in errors reporting remaining 0 cells
fitting MEF models:
1 : MEF_49
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
2 : MEF_50
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
3 : MEF_51
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
4 : MEF_52
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
5 : MEF_53
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
6 : MEF_54
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
7 : MEF_55
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
8 : MEF_56
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
9 : MEF_57
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
10 : MEF_58
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
11 : MEF_59
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
12 : MEF_60
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
13 : MEF_61
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
14 : MEF_62
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
15 : MEF_63
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
16 : MEF_64
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
17 : MEF_65
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
18 : MEF_66
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
19 : MEF_67
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
20 : MEF_68
Classification: weighted
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_49 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_50 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_51 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_52 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_53 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_54 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_55 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_56 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_57 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_58 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_59 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_60 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_61 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_62 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_63 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_64 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_65 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_66 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_67 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR encountered in building a model for cell MEF_68 - skipping the cell. Error:
Error in components[[i]]@logLik :
no applicable method for `@` applied to an object of class "function"
ERROR fitting of 20 out of 20 cells resulted in errors reporting remaining 0 cells
Hi @LeonHafner
Thanks for the issue.
The bug is somewhere here: https://github.com/hms-dbmi/scde/blob/main/R/functions.R#L139-L201
Others have mentioned this, e.g : https://github.com/hms-dbmi/scde/issues/88
System libraries need to be updated perhaps from 2016/2017.
Somehow, the package versions need to be modified and possibly a few lines in the source code need to be updated here. I just haven't had the bandwidth to do this. If you have the chance to find the bug, please create a PR.
Sorry I cannot be more helpful here.
