Kept getting issue when using ImmGenData() in SingleR
1
1
Entering edit mode
11 months ago
leranwangcs ▴ 60

Hi,

I'm trying to use SingleR to annotate my Seurat object, but the ImmGenData() keeps throwing me errors:

Error in UseMethod("filter_") : 
  no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"

Based on some post, I have downgraded dplyr to version 0.8.0, but it doesn't help. My sessionInfo:

R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] AnnotationHub_2.18.0        BiocFileCache_1.10.2        dbplyr_2.1.0               
 [4] SingleR_1.0.6               SummarizedExperiment_1.16.1 DelayedArray_0.12.3        
 [7] BiocParallel_1.20.1         matrixStats_0.58.0          Biobase_2.46.0             
[10] GenomicRanges_1.38.0        GenomeInfoDb_1.22.1         IRanges_2.20.2             
[13] S4Vectors_0.24.4            BiocGenerics_0.32.0         data.table_1.14.0          
[16] randomForest_4.6-14         dendroTools_1.1.1           forcats_0.5.1              
[19] stringr_1.4.0               dplyr_0.8.0                 purrr_0.3.4                
[22] readr_1.4.0                 tidyr_1.1.2                 tibble_3.0.6               
[25] tidyverse_1.3.0             pairwiseAdonis_0.0.1        cluster_2.1.1              
[28] forestmangr_0.9.3           vegan_2.5-7                 lattice_0.20-41            
[31] permute_0.9-5               rstatix_0.7.0               tidylog_1.0.2              
[34] janitor_2.1.0               tximport_1.14.2             ggpubr_0.4.0               
[37] phyloseq_1.30.0             plotly_4.9.3                ggplot2_3.3.3              

loaded via a namespace (and not attached):
  [1] utf8_1.1.4                    tidyselect_1.1.0              RSQLite_2.2.3                
  [4] AnnotationDbi_1.48.0          htmlwidgets_1.5.3             grid_3.6.3                   
  [7] Rtsne_0.15                    devtools_2.3.2                speedyseq_0.5.3.9001         
 [10] munsell_0.5.0                 codetools_0.2-18              units_0.6-7                  
 [13] withr_2.4.1                   colorspace_2.0-0              knitr_1.31                   
 [16] rstudioapi_0.13               ggsignif_0.6.1                GenomeInfoDbData_1.2.2       
 [19] mnormt_2.0.2                  bit64_4.0.5                   rhdf5_2.30.1                 
 [22] rprojroot_2.0.2               brnn_0.8                      vctrs_0.3.6                  
 [25] generics_0.1.0                xfun_0.21                     R6_2.5.0                     
 [28] locfit_1.5-9.4                bitops_1.0-6                  microbiome_1.8.0             
 [31] cachem_1.0.4                  assertthat_0.2.1              promises_1.2.0.1             
 [34] scales_1.1.1                  nnet_7.3-15                   gtable_0.3.0                 
 [37] Cubist_0.2.3                  processx_3.4.5                oce_1.3-0                    
 [40] rlang_0.4.10                  clisymbols_1.2.0              genefilter_1.68.0            
 [43] splines_3.6.3                 lazyeval_0.2.2                broom_0.7.5                  
 [46] checkmate_2.0.0               yaml_2.2.1                    BiocManager_1.30.10          
 [49] reshape2_1.4.4                abind_1.4-5                   modelr_0.1.8                 
 [52] backports_1.2.1               httpuv_1.5.5                  Hmisc_4.4-2                  
 [55] usethis_2.0.1                 tools_3.6.3                   psych_2.0.12                 
 [58] ellipsis_0.3.1                biomformat_1.14.0             RColorBrewer_1.1-2           
 [61] sessioninfo_1.1.1             Rcpp_1.0.6                    plyr_1.8.6                   
 [64] base64enc_0.1-3               progress_1.2.2                zlibbioc_1.32.0              
 [67] classInt_0.4-3                RCurl_1.98-1.2                ps_1.5.0                     
 [70] prettyunits_1.1.1             rpart_4.1-15                  viridis_0.5.1                
 [73] haven_2.3.1                   ggrepel_0.9.1                 fs_1.5.0                     
 [76] magrittr_2.0.1                openxlsx_4.2.3                reprex_1.0.0                 
 [79] truncnorm_1.0-8               tmvnsim_1.0-2                 pkgload_1.2.0                
 [82] mime_0.10                     hms_1.0.0                     xtable_1.8-4                 
 [85] XML_3.99-0.3                  rio_0.5.16                    jpeg_0.1-8.1                 
 [88] readxl_1.3.1                  gridExtra_2.3                 testthat_3.0.2               
 [91] compiler_3.6.3                KernSmooth_2.23-18            crayon_1.4.1                 
 [94] htmltools_0.5.1.1             later_1.1.0.1                 mgcv_1.8-34                  
 [97] gsw_1.0-5                     Formula_1.2-4                 geneplotter_1.64.0           
[100] lubridate_1.7.9.2             DBI_1.1.1                     ExperimentHub_1.12.0         
[103] rappdirs_0.3.3                MASS_7.3-53.1                 sf_0.9-7                     
[106] boot_1.3-27                   Matrix_1.3-2                  ade4_1.7-16                  
[109] car_3.0-10                    cli_2.3.1                     igraph_1.2.6                 
[112] pkgconfig_2.0.3               foreign_0.8-75                xml2_1.3.2                   
[115] foreach_1.5.1                 annotate_1.64.0               multtest_2.42.0              
[118] XVector_0.26.0                rvest_0.3.6                   snakecase_0.11.0             
[121] callr_3.5.1                   digest_0.6.27                 MLmetrics_1.1.1              
[124] Biostrings_2.54.0             cellranger_1.1.0              htmlTable_2.1.0              
[127] DelayedMatrixStats_1.8.0      curl_4.3                      shiny_1.6.0                  
[130] lifecycle_1.0.0               nlme_3.1-152                  jsonlite_1.7.2               
[133] Rhdf5lib_1.8.0                BiocNeighbors_1.4.2           carData_3.0-4                
[136] desc_1.2.0                    viridisLite_0.3.0             fansi_0.4.2                  
[139] pillar_1.5.0                  pkgbuild_1.2.0                fastmap_1.1.0                
[142] httr_1.4.2                    survival_3.2-7                remotes_2.2.0                
[145] interactiveDisplayBase_1.24.0 glue_1.4.2                    zip_2.1.1                    
[148] png_0.1-7                     iterators_1.0.13              BiocVersion_3.10.1           
[151] bit_4.0.4                     class_7.3-18                  stringi_1.5.3                
[154] blob_1.2.1                    DESeq2_1.26.0                 latticeExtra_0.6-29          
[157] memoise_2.0.0                 e1071_1.7-4                   ape_5.4-1

Thank you very much!!

R SingleR • 755 views
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1
Entering edit mode

I think i saw this error when there's a package conflict. Try calling the function with the package name it comes from e.g. dplyr::filter()

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2
Entering edit mode

Thanks, but it doesn't seem to be the solution.... After digging into varies forums, the only way for me to go seemly is to update my mac version, then install R 4.0, then install the higher version of AnnotationHub which has fixed the bugs. I obviously don't want to update my mac version...

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0
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Hello leranwangcs!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/9134984/

This is typically not recommended as it runs the risk of annoying people in both communities.

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1
Entering edit mode
11 months ago
leranwangcs ▴ 60

Thanks, but it doesn't seem to be the solution.... After digging into varies forums, the only way for me to go seemly is to update my mac version, then install R 4.0, then install the higher version of AnnotationHub which has fixed the bugs. I obviously don't want to update my mac version...

ADD COMMENT
1
Entering edit mode

Are you referring to upgrading macOS? Is R v.4.0 not supported for your current version of macOS?

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