Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Error in vignette execution #94

Open
LeonHafner opened this issue Dec 5, 2024 · 1 comment
Open

Error in vignette execution #94

LeonHafner opened this issue Dec 5, 2024 · 1 comment
Labels
help wanted

Comments

@LeonHafner
Copy link

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
@evanbiederstedt
Copy link
Collaborator

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 : #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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
help wanted
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@evanbiederstedt @LeonHafner