Select() issue

[LucasMcNU]

Hi there, I thought I had fixed this issue when I updated AnnotationHub and Bioconductor, but it came back. When I try to use Select(), I get the following error:

Error: 'select' is not an exported object from 'namespace:AnnotationHub'

[lshep]

sessionInfo()

[LucasMcNU]

R version 4.3.3 (2024-02-29) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.2.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

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

time zone: America/Chicago tzcode source: internal

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

other attached packages: [1] BiocManager_1.30.22 stringr_1.5.1 forcats_1.0.0 tximport_1.30.0
[5] magrittr_2.0.3 dplyr_1.1.4 ggplot2_3.5.0 DESeq2_1.42.1
[9] SummarizedExperiment_1.32.0 MatrixGenerics_1.14.0 matrixStats_1.3.0 ensembldb_2.26.0
[13] AnnotationFilter_1.26.0 GenomicFeatures_1.54.4 AnnotationDbi_1.64.1 Biobase_2.62.0
[17] GenomicRanges_1.54.1 GenomeInfoDb_1.38.8 IRanges_2.36.0 S4Vectors_0.40.2
[21] AnnotationHub_3.10.1 BiocFileCache_2.10.2 dbplyr_2.5.0 BiocGenerics_0.48.1

loaded via a namespace (and not attached): [1] DBI_1.2.2 bitops_1.0-7 biomaRt_2.58.2 rlang_1.1.3
[5] compiler_4.3.3 RSQLite_2.3.6 png_0.1-8 vctrs_0.6.5
[9] ProtGenerics_1.34.0 pkgconfig_2.0.3 crayon_1.5.2 fastmap_1.1.1
[13] XVector_0.42.0 utf8_1.2.4 Rsamtools_2.18.0 promises_1.3.0
[17] tzdb_0.4.0 pracma_2.4.4 purrr_1.0.2 bit_4.0.5
[21] zlibbioc_1.48.2 cachem_1.0.8 progress_1.2.3 blob_1.2.4
[25] later_1.3.2 DelayedArray_0.28.0 BiocParallel_1.36.0 interactiveDisplayBase_1.40.0 [29] parallel_4.3.3 prettyunits_1.2.0 R6_2.5.1 stringi_1.8.3
[33] rtracklayer_1.62.0 Rcpp_1.0.12 readr_2.1.5 httpuv_1.6.15
[37] Matrix_1.6-5 tidyselect_1.2.1 rstudioapi_0.16.0 abind_1.4-5
[41] yaml_2.3.8 codetools_0.2-20 curl_5.2.1 lattice_0.22-6
[45] tibble_3.2.1 withr_3.0.0 shiny_1.8.1.1 KEGGREST_1.42.0
[49] xml2_1.3.6 Biostrings_2.70.3 pillar_1.9.0 filelock_1.0.3
[53] generics_0.1.3 vroom_1.6.5 RCurl_1.98-1.14 BiocVersion_3.18.1
[57] hms_1.1.3 munsell_0.5.1 scales_1.3.0 xtable_1.8-4
[61] glue_1.7.0 lazyeval_0.2.2 tools_4.3.3 BiocIO_1.12.0
[65] locfit_1.5-9.9 GenomicAlignments_1.38.2 XML_3.99-0.16.1 grid_4.3.3
[69] colorspace_2.1-0 GenomeInfoDbData_1.2.11 restfulr_0.0.15 cli_3.6.2
[73] rappdirs_0.3.3 fansi_1.0.6 S4Arrays_1.2.1 gtable_0.3.4
[77] digest_0.6.35 SparseArray_1.2.4 rjson_0.2.21 memoise_2.0.1
[81] htmltools_0.5.8.1 lifecycle_1.0.4 httr_1.4.7 mime_0.12
[85] bit64_4.0.5

[lshep]

can you should the full code (with any output) you are trying to use that leads up to the ERROR as well?

[LucasMcNU]

Here you are! Error starts when using Select() near the bottom.

`library("AnnotationHub") ah <- AnnotationHub() ## Connect to Annotation Hub

db <- query(ah, c("EnsDb","Homo sapiens","111"))[[1]] ## Make a query to your organism/database results <- data.frame(res.pol1)

keys <- keys(db, c("TXID","GENEID", "TXNAME"))

annotations <- select(db, keys, c("GENEID", "TXNAME", "SYMBOL", "GENENAME","GENEBIOTYPE","TXBIOTYPE", "SEQNAME", "TXSEQSTART","TXSEQEND","EXONID","EXONSEQSTART", "EXONSEQEND"), "TXID") `

[lshep]

I can't reproduce this. But a guess, do you have the package ensembldb installed? It is a required package for this resources, so do you have that installed/loaded?

[LucasMcNU]

I loaded EnsemblDB and it made no difference in the problem. Looking at this older issue from Bioconductor, it looks like this has been a problem before?

[lshep]

So it looks like the solution was posted https://support.bioconductor.org/p/p132709/#p134760 likely you have both dplyr and AnnotationDbi and need to specify which one to use

[LucasMcNU]

No, that doesn't solve the issue. There seems to be something else wrong with AnnotationHub, as calling the function specifically using AnnotationHub::Select() produces the same error.

[lshep]

There is no annotationhub::select function

[mtmorgan]

try, in your original incantation, calling traceback() after the error occurs.

annotations <- select(db, keys, c("GENEID", "TXNAME", "SYMBOL", "GENENAME","GENEBIOTYPE","TXBIOTYPE", "SEQNAME", "TXSEQSTART","TXSEQEND","EXONID","EXONSEQSTART", "EXONSEQEND"), "TXID")

## error, so try...
traceback()

[LucasMcNU]

How would you specify that you're using select() from annotation hub then? is this actually select() from dplyr?

To be clear, these lines of code worked fine until today.

[lshep]

there is no such function. there is not a select method defined in annotationhub. it is select like from annotationDbi or dplyr as the link above indicates

[LucasMcNU]

well, that was my problem - Thank you! And sorry for wasting your time

[lshep]

No worries. Glad we could figure it out.
Is this in a vignette or documentation somewhere that you found? if so we can update it to try to be more explicit about where select comes from

[LucasMcNU]

It's in the main vignette here with no explicit reference to AnnotationDbi and no loading of AnnotationDBI, although it is in the session info at the bottom. I just assumed they were one and the same.

[lshep]

Thanks! I'll look at adding a line to the vignette to show the appropriate AnnotationDbi call. Sorry for the confusion.

[lshep]

Reopening to remind to add AnnotationDbi library call and :: to vignette for more explicit calls to avoid confusion with conflicting dplyr select method that can occur.

[LiNk-NY]

FWIW @LucasMcNU You can use the conflicted package to resolve these issues:

library(conflicted)
## [... code above]
annotations <- select(db, keys, c("GENEID", "TXNAME", "SYMBOL", "GENENAME","GENEBIOTYPE","TXBIOTYPE", "SEQNAME", "TXSEQSTART","TXSEQEND","EXONID","EXONSEQSTART", "EXONSEQEND"), "TXID")
Error:
! [conflicted] select found in 2 packages.
Either pick the one you want with `::`:
• dplyr::select
• ensembldb::select
Or declare a preference with `conflicts_prefer()`:
• `conflicts_prefer(dplyr::select)`
• `conflicts_prefer(ensembldb::select)`
Run `rlang::last_trace()` to see where the error occurred.

The generic lives in AnnotationDbi but the specific method is coming from ensembldb.