Issue with AnnotationHub
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rahnaman ▴ 10
@user-24168
Last seen 10 months 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
AnnotationHub • 554 views
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Entering edit mode
shepherl 2.8k
@lshep
Last seen 4 hours ago
United States

Please see this post. Remember to downgrade both the dplyr and Bioconductor packages. Comment: ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for '

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Entering edit mode

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!

devtools::install_url("http://cran.r-project.org/src/contrib/Archive/**dplyr**/**dbplyr**1.3.0.tar.gz") 
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