Error: 'clusterCall' is not an exported object from 'namespace:BiocGenerics'

[dheo1201]

When I try to run fit_models for DEG, I get the following error: Error: 'clusterCall' is not an exported object from 'namespace:BiocGenerics'

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

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

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

other attached packages:
 [1] ggiraph_0.7.10              ggrepel_0.9.1               ggbiplot_0.55               scales_1.1.1                plyr_1.8.6                 
 [6] forcats_0.5.1               purrr_0.3.4                 readr_2.1.0                 tidyr_1.2.0                 tibble_3.1.6               
[11] tidyverse_1.3.1             zeallot_0.1.0               knitr_1.36                  DropletUtils_1.14.1         RColorBrewer_1.1-2         
[16] viridis_0.6.2               viridisLite_0.4.0           pheatmap_1.0.12             stringr_1.4.0               Rtsne_0.15                 
[21] reshape2_1.4.4              VGAM_1.1-5                  mclust_5.4.8                ggplot2_3.3.5               dplyr_1.0.7                
[26] magrittr_2.0.1              reticulate_1.22             monocle3_1.0.0              SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0
[31] GenomicRanges_1.46.1        GenomeInfoDb_1.30.0         IRanges_2.28.0              S4Vectors_0.32.3            MatrixGenerics_1.6.0       
[36] matrixStats_0.61.0          Biobase_2.54.0              BiocGenerics_0.40.0        

loaded via a namespace (and not attached):
 [1] colorspace_2.0-2          ellipsis_0.3.2            rprojroot_2.0.2           scuttle_1.4.0             XVector_0.34.0           
 [6] fs_1.5.0                  rstudioapi_0.13           remotes_2.4.2             fansi_0.5.0               lubridate_1.8.0          
[11] xml2_1.3.2                R.methodsS3_1.8.1         sparseMatrixStats_1.6.0   cachem_1.0.6              pkgload_1.2.4            
[16] jsonlite_1.7.3            RhpcBLASctl_0.21-247.1    broom_0.7.12              dbplyr_2.1.1              png_0.1-7                
[21] R.oo_1.24.0               HDF5Array_1.22.1          compiler_4.1.2            httr_1.4.2                dqrng_0.3.0              
[26] backports_1.4.0           assertthat_0.2.1          Matrix_1.3-4              fastmap_1.1.0             limma_3.50.0             
[31] cli_3.1.0                 htmltools_0.5.2           prettyunits_1.1.1         tools_4.1.2               gtable_0.3.0             
[36] glue_1.5.0                GenomeInfoDbData_1.2.7    Rcpp_1.0.7                cellranger_1.1.0          vctrs_0.3.8              
[41] rhdf5filters_1.6.0        DelayedMatrixStats_1.16.0 xfun_0.28                 ps_1.6.0                  rvest_1.0.2              
[46] testthat_3.1.1            beachmat_2.10.0           lifecycle_1.0.1           devtools_2.4.3            edgeR_3.36.0             
[51] zlibbioc_1.40.0           hms_1.1.1                 parallel_4.1.2            rhdf5_2.38.0              curl_4.3.2               
[56] memoise_2.0.1             gridExtra_2.3             stringi_1.7.5             desc_1.4.0                pkgbuild_1.3.1           
[61] BiocParallel_1.28.1       systemfonts_1.0.3         rlang_0.4.12              pkgconfig_2.0.3           bitops_1.0-7             
[66] lattice_0.20-45           Rhdf5lib_1.16.0           htmlwidgets_1.5.4         processx_3.5.2            tidyselect_1.1.1         
[71] R6_2.5.1                  generics_0.1.2            DelayedArray_0.20.0       DBI_1.1.2                 pillar_1.7.0             
[76] haven_2.4.3               withr_2.4.3               RCurl_1.98-1.5            modelr_0.1.8              crayon_1.5.0             
[81] uuid_1.0-3                utf8_1.2.2                tzdb_0.2.0                usethis_2.1.5             readxl_1.3.1             
[86] locfit_1.5-9.4            callr_3.7.0               digest_0.6.29             reprex_2.0.1              R.utils_2.11.0    

[vicscott]

it means the version of BiocGenerics could be wrong, try another old version like this install.packages("https://www.bioconductor.org/packages//2.12/bioc/src/contrib/BiocGenerics_0.6.0.tar.gz",repos=NULL,type="source") and restart R

[aburgosru]

I have the same problem... I'm also using R version 4.1.2

[jordan841220]

Same problem here. Currently I can only work around it with cores=1.

[jonoave]

I would agree with you @JordanCTLin . I had a smaller cds_subset that ran pretty quickly without any issues with the default 1 cores.

However when I want to compare between 2 clusters, using 1 cores take forever (more than an hour and never completes). And when I increased this cores, I encountered this error.

Then I went back to cds_subset and reran it, but increasing the cores and the same error pops up. So @vicscott , I don't think the version of Biocgenerics is the issue.

What a pity that that there doesn't seem to be any more active development on this software, with almost no replies to any issues/bugs reported here.