Kept getting issue when using ImmGenData() in SingleR
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!!
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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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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()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...
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.