Please reopen "Problem with initializeScenic() #168"

[huhayahoo]

This issue #168 has started occurring again..

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Motif databases selected: mm10_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather mm10_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather [1] "The index column 'features' is not available in the file." [1] "The index column 'features' is not available in the file." Using the column '0610005C13Rik' as feature index for the ranking database. Error in dplyr::pull(): ! Can't extract columns that don't exist. x Column features doesn't exist. Run rlang::last_error() to see where the error occurred. Warning messages: 1: In initializeScenic(org = org, dbDir = dbDir, dbs = dbs, datasetTitle = myDatasetTitle, : It was not possible to load the following databses; check whether they are downloaded correctly: mm10_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather mm10_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather 2: In RcisTarget::importRankings(dbFile, columns = rnktype) : The following columns are missing from the database: features

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• Already checked sha1sums and they are ok
• Already using latest version of arrow and dplyr

  packageVersion("arrow") [1] '10.0.1' packageVersion("dplyr") [1] '1.0.10'

Could it be that dplyr::pull() has changed in recent versions of dplyr?? here is detailed output of error..

rlang::last_error() <error/vctrs_error_subscript_oob> Error in dplyr::pull(): ! Can't extract columns that don't exist. x Column features doesn't exist.

Backtrace:

1. SCENIC::initializeScenic(...)
2. SCENIC::checkAnnots(object, motifAnnot)
3. base::lapply(...)
4. SCENIC (local) FUN(X[[i]], ...)
5. dplyr:::pull.data.frame(nRnks, rnktype) Run rlang::last_trace() to see the full context.

rlang::last_trace() <error/vctrs_error_subscript_oob> Error in dplyr::pull(): ! Can't extract columns that don't exist. x Column features doesn't exist.

Backtrace: x

1. +-SCENIC::initializeScenic(...)
2. | -SCENIC::checkAnnots(object, motifAnnot)
3. | -base::lapply(...)
4. | -SCENIC (local) FUN(X[[i]], ...)
5. | +-dplyr::pull(nRnks, rnktype)
6. | -dplyr:::pull.data.frame(nRnks, rnktype)
7. | -tidyselect::vars_pull(names(.data), !!enquo(var))
8. | -tidyselect:::pull_as_location2(...)
9. | +-tidyselect:::with_subscript_errors(...)
10. | | -rlang::try_fetch(...)
11. | | -base::withCallingHandlers(...)
12. | -vctrs::vec_as_location2(...)
13. | +-vctrs:::result_get(...)
14. | -vctrs:::vec_as_location2_result(...)
15. | +-base::tryCatch(...)
16. | | -base (local) tryCatchList(expr, classes, parentenv, handlers)
17. | | -base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
18. | | -base (local) doTryCatch(return(expr), name, parentenv, handler)
19. | -vctrs::vec_as_location(i, n, names = names, arg = arg, call = call)
20. -vctrs (local) <fn>()
21. -vctrs:::stop_subscript_oob(...)
22. -vctrs:::stop_subscript(...)
23. -rlang::abort(...)

Please advice how to proceed as few others have reported same issue after #168 has been closed...

[ZachLW]

Hi, I think the major problem happen on the database downloaded. Feather v1 format is compatible and you can find databases in the feather v1 format in the 'old' directory here: "https://resources.aertslab.org/cistarget/databases/old/" Hope this helps

[jwg054000]

I am having the same issue. Please advise on how to run this with R4.2+