Original version: 16 October, 2023
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.
Commands such as am_available() should report no files
cached. The command
am_data("gene_hg38")
#> * [16:31:01][info] retrieving file name 'AlphaMissense_gene_hg38.tsv.gz' (247.7 Kb)
#> * [16:31:01][info] data licensed under 'CC-BY-4.0'
#> * [16:31:02][info] downloading or finding local file
#> adding rname 'AlphaMissense_gene_hg38.tsv.gz'
#> * [16:31:04][info] creating database table 'gene_hg38'
#> * [16:31:04][info] disconnecting all registered connections
#> # Source: table<gene_hg38> [?? x 2]
#> # Database: DuckDB v1.1.1 [biocbuild@Linux 6.8.0-47-generic:R 4.5.0//home/biocbuild/.cache/R/BiocFileCache/2f7e82265d846_2f7e82265d846]
#> 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.
Remember to disconnect and shutdown all managed DuckDB connections.
Database connections that are not closed correctly trigger warning messages.
sessionInfo()
#> R Under development (unstable) (2024-10-21 r87258)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.1 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.21-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_2.31.0 AnnotationFilter_1.31.0 GenomicFeatures_1.59.0
#> [4] AnnotationDbi_1.69.0 Biobase_2.67.0 GenomicRanges_1.59.0
#> [7] GenomeInfoDb_1.43.0 IRanges_2.41.0 S4Vectors_0.45.0
#> [10] ProteinGymR_0.99.7 gghalves_0.1.4 ggplot2_3.5.1
#> [13] ggdist_3.3.2 tidyr_1.3.1 ExperimentHub_2.15.0
#> [16] AnnotationHub_3.15.0 BiocFileCache_2.15.0 dbplyr_2.5.0
#> [19] BiocGenerics_0.53.0 AlphaMissenseR_1.3.0 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_4.5.0
#> [7] RSQLite_2.3.7 png_0.1-8
#> [9] vctrs_0.6.5 ProtGenerics_1.39.0
#> [11] pkgconfig_2.0.3 crayon_1.5.3
#> [13] fastmap_1.2.0 XVector_0.47.0
#> [15] labeling_0.4.3 utf8_1.2.4
#> [17] Rsamtools_2.23.0 promises_1.3.0
#> [19] rmarkdown_2.28 UCSC.utils_1.3.0
#> [21] purrr_1.0.2 bit_4.5.0
#> [23] xfun_0.48 zlibbioc_1.53.0
#> [25] cachem_1.1.0 queryup_1.0.5
#> [27] jsonlite_1.8.9 blob_1.2.4
#> [29] highr_0.11 later_1.3.2
#> [31] DelayedArray_0.33.0 BiocParallel_1.41.0
#> [33] parallel_4.5.0 spdl_0.0.5
#> [35] R6_2.5.1 bslib_0.8.0
#> [37] rtracklayer_1.67.0 jquerylib_0.1.4
#> [39] SummarizedExperiment_1.37.0 Rcpp_1.0.13
#> [41] knitr_1.48 BiocBaseUtils_1.9.0
#> [43] Matrix_1.7-1 httpuv_1.6.15
#> [45] tidyselect_1.2.1 abind_1.4-8
#> [47] yaml_2.3.10 codetools_0.2-20
#> [49] curl_5.2.3 rjsoncons_1.3.1
#> [51] lattice_0.22-6 tibble_3.2.1
#> [53] shiny_1.9.1 bio3d_2.4-4
#> [55] withr_3.0.2 KEGGREST_1.47.0
#> [57] evaluate_1.0.1 r3dmol_0.1.2
#> [59] Biostrings_2.75.0 pillar_1.9.0
#> [61] BiocManager_1.30.25 filelock_1.0.3
#> [63] MatrixGenerics_1.19.0 whisker_0.4.1
#> [65] distributional_0.5.0 generics_0.1.3
#> [67] RCurl_1.98-1.16 BiocVersion_3.21.1
#> [69] munsell_0.5.1 scales_1.3.0
#> [71] xtable_1.8-4 glue_1.8.0
#> [73] lazyeval_0.2.2 tools_4.5.0
#> [75] BiocIO_1.17.0 GenomicAlignments_1.43.0
#> [77] forcats_1.0.0 XML_3.99-0.17
#> [79] grid_4.5.0 colorspace_2.1-1
#> [81] GenomeInfoDbData_1.2.13 RcppSpdlog_0.0.18
#> [83] duckdb_1.1.1 restfulr_0.0.15
#> [85] cli_3.6.3 rappdirs_0.3.3
#> [87] shiny.gosling_1.3.0 fansi_1.0.6
#> [89] S4Arrays_1.7.0 viridisLite_0.4.2
#> [91] gtable_0.3.6 sass_0.4.9
#> [93] digest_0.6.37 SparseArray_1.7.0
#> [95] rjson_0.2.23 htmlwidgets_1.6.4
#> [97] farver_2.1.2 memoise_2.0.1
#> [99] htmltools_0.5.8.1 lifecycle_1.0.4
#> [101] httr_1.4.7 mime_0.12
#> [103] bit64_4.5.2