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rahnaman
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10
@user-24168
Last seen 4.1 years ago
Hello,
I have installed the AnnotationHub and loading the library does not show any errors, however, I get the error below when trying to run AnnotationHub function.
Please note that I can not upgrade to R 4.0 to re-install the latest version of the package, and instead tried to remove and downgrade dplyr and plyr packages which did not solve the problem. Is there any way that I can use AnnotationHub with R 3.6.3?
Thank You,
NF
library(AnnotationHub) # no errors created here
hub <- AnnotationHub() # error created here
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')"
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
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_2.16.1 BiocFileCache_1.8.0 dplyr_1.0.2 plyr_1.8.6 dbplyr_2.0.0
[6] GenomicRanges_1.36.1 GenomeInfoDb_1.20.0 IRanges_2.18.3 S4Vectors_0.22.1 BiocGenerics_0.30.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 later_1.1.0.1 BiocManager_1.30.10 pillar_1.4.7
[5] compiler_3.6.3 XVector_0.24.0 bitops_1.0-6 tools_3.6.3
[9] zlibbioc_1.30.0 digest_0.6.27 bit_4.0.4 RSQLite_2.2.1
[13] memoise_1.1.0 lifecycle_0.2.0 tibble_3.0.4 pkgconfig_2.0.3
[17] rlang_0.4.9 shiny_1.5.0 DBI_1.1.0 rstudioapi_0.13
[21] yaml_2.2.1 curl_4.3 fastmap_1.0.1 GenomeInfoDbData_1.2.1
[25] httr_1.4.2 generics_0.1.0 vctrs_0.3.5 rappdirs_0.3.1
[29] bit64_4.0.5 tidyselect_1.1.0 Biobase_2.44.0 glue_1.4.2
[33] R6_2.5.0 AnnotationDbi_1.46.1 purrr_0.3.4 blob_1.2.1
[37] magrittr_2.0.1 promises_1.1.1 htmltools_0.5.0 ellipsis_0.3.1
[41] assertthat_0.2.1 xtable_1.8-4 mime_0.9 interactiveDisplayBase_1.22.0
[45] httpuv_1.5.4 RCurl_1.98-1.2 crayon_1.3.4
Thanks a lot for your reply. I was actually following that exact example, but to no avail. However, following your comment I went back and realized the reason was that there was a typo in there (marked below) that forwarded installation to the archive of dplyr package instead of dbplyr. After downgrading dbplyr it worked. Many Thanks!