Original version: 16 October, 2023
Updating duckdb to 0.9.1
The R duckdb client version 0.9.1 cannot read databases created with previous versions of the package. The duckdb error message indicates
am_available() Error in h(simpleError(msg, call)) : error in evaluating the argument ‘drv’ in selecting a method for function ‘dbConnect’: rapi_startup: Failed to open database: IO Error: Trying to read a database file with version number 51, but we can only read version 64.
The database file was created with DuckDB version v0.8.0 or v0.8.1.
The storage of DuckDB is not yet stable; newer versions of DuckDB cannot read old database files and vice versa. The storage will be stabilized when version 1.0 releases.
For now, we recommend that you load the database file in a supported version of DuckDB, and use the EXPORT DATABASE command followed by IMPORT DATABASE on the current version of DuckDB.
See the storage page for more information: https://duckdb.org/internals/storage
but in practice the most straight-forward solution is to remove existing AlphaMissenseR data resources and ‘start again’.
The following attempts to identify AlphaMissenseR data resources cached locally
am_rids <-
bfcinfo() |>
dplyr::filter(
grepl("zenodo", rname) |
startsWith(rname, "AlphaMissense_")
) |>
pull(rid)After verifying that these resources have not been created outside AlphaMissenseR, remove them.
BiocFileCache::bfcremove(rids = am_rids)Commands such as am_available() should report no files
cached. The command
am_data("gene_hg38")
#> # Source: table<gene_hg38> [?? x 2]
#> # Database: DuckDB v1.1.1 [mtmorgan@Darwin 23.6.0:R 4.5.0//Users/mtmorgan/Library/Caches/org.R-project.R/R/BiocFileCache/121787f1dafbc_121787f1dafbc]
#> transcript_id mean_am_pathogenicity
#> <chr> <dbl>
#> 1 ENST00000000233.10 0.742
#> 2 ENST00000000412.8 0.378
#> 3 ENST00000001008.6 0.422
#> 4 ENST00000001146.6 0.467
#> 5 ENST00000002125.9 0.351
#> 6 ENST00000002165.11 0.406
#> 7 ENST00000002501.10 0.320
#> 8 ENST00000002596.6 0.471
#> 9 ENST00000002829.8 0.524
#> 10 ENST00000003084.10 0.405
#> # ℹ more rowswill re-download the file and insert it into a database that functions with duckdb 0.9.1.
Resource temporarily unavailable
Trying to access a data resource with am_data() may
sometimes result in a DuckDB errors about “Resource unavailable”.
> am_data("hg38")
* [10:05:09][warning] error in evaluating the argument 'drv' in selecting a
method for function 'dbConnect': rapi_startup: Failed to open database:
IO Error: Could not set lock on file
".../Caches/org.R-project.R/R/BiocFileCache/1ec5157ddaa2_1ec5157ddaa2":
Resource unavailable
Error in value[[3L]](cond) :
failed to connect to DuckDB database, see 'Issues & Solutions' vignetteThis occures when the database is being used by an independent
R process. The solution is to identify the process and
disconnect from the database using, e.g.,
db_disconnect_all().
Finally
Remember to disconnect and shutdown all managed DuckDB connections.
db_disconnect_all()
#> * [09:26:57][info] disconnecting all registered connectionsDatabase connections that are not closed correctly trigger warning messages.
Session information
sessionInfo()
#> R Under development (unstable) (2024-07-31 r86945)
#> Platform: aarch64-apple-darwin23.4.0
#> Running under: macOS Sonoma 14.6.1
#>
#> Matrix products: default
#> BLAS: /Users/mtmorgan/bin/R-devel/lib/libRblas.dylib
#> LAPACK: /Users/mtmorgan/bin/R-devel/lib/libRlapack.dylib; LAPACK version 3.12.0
#>
#> 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/New_York
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] AlphaMissenseR_1.1.10 dplyr_1.1.4
#>
#> loaded via a namespace (and not attached):
#> [1] sass_0.4.9 utf8_1.2.4 generics_0.1.3
#> [4] spdl_0.0.5 RSQLite_2.3.7 digest_0.6.37
#> [7] magrittr_2.0.3 evaluate_1.0.1 grid_4.5.0
#> [10] fastmap_1.2.0 blob_1.2.4 jsonlite_1.8.9
#> [13] whisker_0.4.1 DBI_1.2.3 httr_1.4.7
#> [16] purrr_1.0.2 fansi_1.0.6 scales_1.3.0
#> [19] textshaping_0.4.0 jquerylib_0.1.4 duckdb_1.1.1
#> [22] cli_3.6.3 rlang_1.1.4 dbplyr_2.5.0
#> [25] munsell_0.5.1 bit64_4.5.2 withr_3.0.1
#> [28] cachem_1.1.0 yaml_2.3.10 BiocBaseUtils_1.7.3
#> [31] tools_4.5.0 memoise_2.0.1 colorspace_2.1-1
#> [34] ggplot2_3.5.1 filelock_1.0.3 curl_5.2.3
#> [37] rjsoncons_1.3.1 vctrs_0.6.5 R6_2.5.1
#> [40] BiocFileCache_2.13.2 lifecycle_1.0.4 RcppSpdlog_0.0.18
#> [43] fs_1.6.4 htmlwidgets_1.6.4 bit_4.5.0
#> [46] ragg_1.3.3 pkgconfig_2.0.3 desc_1.4.3
#> [49] pkgdown_2.1.1 pillar_1.9.0 bslib_0.8.0
#> [52] gtable_0.3.6 Rcpp_1.0.13 glue_1.8.0
#> [55] systemfonts_1.1.0 xfun_0.48 tibble_3.2.1
#> [58] tidyselect_1.2.1 knitr_1.48 htmltools_0.5.8.1
#> [61] rmarkdown_2.28 compiler_4.5.0