# E. Issues & Solutions

Original version: 16 October, 2023

    library(AlphaMissenseR)

# 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")
    #> * [18:21:52][info] retrieving file name 'AlphaMissense_gene_hg38.tsv.gz' (247.7 Kb)
    #> * [18:21:52][info] data licensed under 'CC-BY-4.0'
    #> * [18:21:53][info] downloading or finding local file
    #> adding rname 'AlphaMissense_gene_hg38.tsv.gz'
    #>
    #> * [18:22:00][info] creating database table 'gene_hg38'
    #> * [18:22:00][info] disconnecting all registered connections
    #> # Source:   table<gene_hg38> [?? x 2]
    #> # Database: DuckDB 1.4.2 [biocbuild@Darwin 21.6.0:R 4.5.2//Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/114a06d21e531_114a06d21e531]
    #>    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 rows

will 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' vignette

This 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()
    #> * [18:22:03][info] disconnecting all registered connections

Database connections that are not closed correctly trigger warning messages.

# Session information

    sessionInfo()
    #> R version 4.5.2 (2025-10-31)
    #> Platform: x86_64-apple-darwin20
    #> Running under: macOS Monterey 12.7.6
    #>
    #> Matrix products: default
    #> BLAS:   /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib
    #> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
    #>
    #> locale:
    #> [1] C/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] stats4    stats     graphics  grDevices utils     datasets  methods
    #> [8] base
    #>
    #> other attached packages:
    #>  [1] ensembldb_2.34.0        AnnotationFilter_1.34.0 GenomicFeatures_1.62.0
    #>  [4] AnnotationDbi_1.72.0    Biobase_2.70.0          GenomicRanges_1.62.0
    #>  [7] Seqinfo_1.0.0           IRanges_2.44.0          S4Vectors_0.48.0
    #> [10] ggplot2_4.0.1           ggdist_3.3.3            tidyr_1.3.1
    #> [13] ExperimentHub_3.0.0     AnnotationHub_4.0.0     BiocFileCache_3.0.0
    #> [16] dbplyr_2.5.1            BiocGenerics_0.56.0     generics_0.1.4
    #> [19] AlphaMissenseR_1.6.1    dplyr_1.1.4
    #>
    #> loaded via a namespace (and not attached):
    #>   [1] DBI_1.2.3                   bitops_1.0-9
    #>   [3] httr2_1.2.1                 rlang_1.1.6
    #>   [5] magrittr_2.0.4              otel_0.2.0
    #>   [7] matrixStats_1.5.0           compiler_4.5.2
    #>   [9] RSQLite_2.4.4               png_0.1-8
    #>  [11] vctrs_0.6.5                 ProtGenerics_1.42.0
    #>  [13] pkgconfig_2.0.3             crayon_1.5.3
    #>  [15] fastmap_1.2.0               XVector_0.50.0
    #>  [17] labeling_0.4.3              utf8_1.2.6
    #>  [19] Rsamtools_2.26.0            promises_1.5.0
    #>  [21] rmarkdown_2.30              UCSC.utils_1.6.0
    #>  [23] purrr_1.2.0                 bit_4.6.0
    #>  [25] xfun_0.54                   cachem_1.1.0
    #>  [27] cigarillo_1.0.0             GenomeInfoDb_1.46.1
    #>  [29] jsonlite_2.0.0              blob_1.2.4
    #>  [31] later_1.4.4                 DelayedArray_0.36.0
    #>  [33] BiocParallel_1.44.0         parallel_4.5.2
    #>  [35] spdl_0.0.5                  R6_2.6.1
    #>  [37] bslib_0.9.0                 RColorBrewer_1.1-3
    #>  [39] rtracklayer_1.70.0          jquerylib_0.1.4
    #>  [41] SummarizedExperiment_1.40.0 Rcpp_1.1.0
    #>  [43] knitr_1.50                  BiocBaseUtils_1.12.0
    #>  [45] Matrix_1.7-4                httpuv_1.6.16
    #>  [47] tidyselect_1.2.1            abind_1.4-8
    #>  [49] dichromat_2.0-0.1           yaml_2.3.10
    #>  [51] codetools_0.2-20            curl_7.0.0
    #>  [53] rjsoncons_1.3.2             lattice_0.22-7
    #>  [55] tibble_3.3.0                shiny_1.11.1
    #>  [57] bio3d_2.4-5                 withr_3.0.2
    #>  [59] KEGGREST_1.50.0             S7_0.2.1
    #>  [61] evaluate_1.0.5              r3dmol_0.1.2
    #>  [63] Biostrings_2.78.0           pillar_1.11.1
    #>  [65] BiocManager_1.30.27         filelock_1.0.3
    #>  [67] MatrixGenerics_1.22.0       whisker_0.4.1
    #>  [69] distributional_0.5.0        RCurl_1.98-1.17
    #>  [71] BiocVersion_3.22.0          scales_1.4.0
    #>  [73] xtable_1.8-4                glue_1.8.0
    #>  [75] lazyeval_0.2.2              tools_4.5.2
    #>  [77] BiocIO_1.20.0               GenomicAlignments_1.46.0
    #>  [79] XML_3.99-0.20               grid_4.5.2
    #>  [81] colorspace_2.1-2            RcppSpdlog_0.0.23
    #>  [83] duckdb_1.4.2                restfulr_0.0.16
    #>  [85] cli_3.6.5                   rappdirs_0.3.3
    #>  [87] shiny.gosling_1.6.0         S4Arrays_1.10.0
    #>  [89] viridisLite_0.4.2           gtable_0.3.6
    #>  [91] sass_0.4.10                 digest_0.6.39
    #>  [93] SparseArray_1.10.3          rjson_0.2.23
    #>  [95] htmlwidgets_1.6.4           farver_2.1.2
    #>  [97] memoise_2.0.1               htmltools_0.5.8.1
    #>  [99] lifecycle_1.0.4             httr_1.4.7
    #> [101] mime_0.13                   bit64_4.6.0-1