# 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")
    #> # Source:   table<gene_hg38> [?? x 2]
    #> # Database: DuckDB v1.1.2 [biocbuild@Linux 6.8.0-47-generic:R 4.4.1//media/volume/teran2_disk/biocbuild/.cache/R/BiocFileCache/37a63916299483_37a63916299483]
    #>    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()
    #> * [17:36:16][info] disconnecting all registered connections

Database connections that are not closed correctly trigger warning messages.

# Session information

    sessionInfo()
    #> R version 4.4.1 (2024-06-14)
    #> Platform: x86_64-pc-linux-gnu
    #> Running under: Ubuntu 24.04.1 LTS
    #>
    #> Matrix products: default
    #> BLAS:   /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so
    #> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
    #>
    #> locale:
    #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    #>  [3] LC_TIME=en_GB              LC_COLLATE=C
    #>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
    #>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
    #>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
    #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
    #>
    #> time zone: America/New_York
    #> tzcode source: system (glibc)
    #>
    #> attached base packages:
    #> [1] stats4    stats     graphics  grDevices utils     datasets  methods
    #> [8] base
    #>
    #> other attached packages:
    #>  [1] ensembldb_2.30.0        AnnotationFilter_1.30.0 GenomicFeatures_1.58.0
    #>  [4] AnnotationDbi_1.68.0    Biobase_2.66.0          GenomicRanges_1.58.0
    #>  [7] GenomeInfoDb_1.42.0     IRanges_2.40.0          S4Vectors_0.44.0
    #> [10] gghalves_0.1.4          ggplot2_3.5.1           ggdist_3.3.2
    #> [13] tidyr_1.3.1             ExperimentHub_2.14.0    AnnotationHub_3.14.0
    #> [16] BiocFileCache_2.14.0    dbplyr_2.5.0            BiocGenerics_0.52.0
    #> [19] AlphaMissenseR_1.2.0    dplyr_1.1.4
    #>
    #> loaded via a namespace (and not attached):
    #>   [1] DBI_1.2.3                   bitops_1.0-9
    #>   [3] rlang_1.1.4                 magrittr_2.0.3
    #>   [5] matrixStats_1.4.1           compiler_4.4.1
    #>   [7] RSQLite_2.3.7               png_0.1-8
    #>   [9] vctrs_0.6.5                 ProtGenerics_1.38.0
    #>  [11] pkgconfig_2.0.3             crayon_1.5.3
    #>  [13] fastmap_1.2.0               XVector_0.46.0
    #>  [15] labeling_0.4.3              utf8_1.2.4
    #>  [17] Rsamtools_2.22.0            promises_1.3.0
    #>  [19] rmarkdown_2.28              UCSC.utils_1.2.0
    #>  [21] purrr_1.0.2                 bit_4.5.0
    #>  [23] xfun_0.48                   zlibbioc_1.52.0
    #>  [25] cachem_1.1.0                jsonlite_1.8.9
    #>  [27] blob_1.2.4                  highr_0.11
    #>  [29] later_1.3.2                 DelayedArray_0.32.0
    #>  [31] BiocParallel_1.40.0         parallel_4.4.1
    #>  [33] spdl_0.0.5                  R6_2.5.1
    #>  [35] bslib_0.8.0                 rtracklayer_1.66.0
    #>  [37] jquerylib_0.1.4             SummarizedExperiment_1.36.0
    #>  [39] Rcpp_1.0.13                 knitr_1.48
    #>  [41] BiocBaseUtils_1.8.0         Matrix_1.7-1
    #>  [43] httpuv_1.6.15               tidyselect_1.2.1
    #>  [45] abind_1.4-8                 yaml_2.3.10
    #>  [47] codetools_0.2-20            curl_5.2.3
    #>  [49] rjsoncons_1.3.1             lattice_0.22-6
    #>  [51] tibble_3.2.1                shiny_1.9.1
    #>  [53] bio3d_2.4-5                 withr_3.0.2
    #>  [55] KEGGREST_1.46.0             evaluate_1.0.1
    #>  [57] r3dmol_0.1.2                Biostrings_2.74.0
    #>  [59] pillar_1.9.0                BiocManager_1.30.25
    #>  [61] filelock_1.0.3              MatrixGenerics_1.18.0
    #>  [63] whisker_0.4.1               distributional_0.5.0
    #>  [65] generics_0.1.3              RCurl_1.98-1.16
    #>  [67] BiocVersion_3.20.0          munsell_0.5.1
    #>  [69] scales_1.3.0                xtable_1.8-4
    #>  [71] glue_1.8.0                  lazyeval_0.2.2
    #>  [73] tools_4.4.1                 BiocIO_1.16.0
    #>  [75] GenomicAlignments_1.42.0    XML_3.99-0.17
    #>  [77] grid_4.4.1                  colorspace_2.1-1
    #>  [79] GenomeInfoDbData_1.2.13     RcppSpdlog_0.0.18
    #>  [81] duckdb_1.1.2                restfulr_0.0.15
    #>  [83] cli_3.6.3                   rappdirs_0.3.3
    #>  [85] shiny.gosling_1.2.0         fansi_1.0.6
    #>  [87] S4Arrays_1.6.0              viridisLite_0.4.2
    #>  [89] gtable_0.3.6                sass_0.4.9
    #>  [91] digest_0.6.37               SparseArray_1.6.0
    #>  [93] rjson_0.2.23                htmlwidgets_1.6.4
    #>  [95] farver_2.1.2                memoise_2.0.1
    #>  [97] htmltools_0.5.8.1           lifecycle_1.0.4
    #>  [99] httr_1.4.7                  mime_0.12
    #> [101] bit64_4.5.2