--- title: "Issues & Solutions" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Issues & Solutions} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- ```{r, include = FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ``` Original version: 16 October, 2023 ```{r setup, message = FALSE} 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 ```{r, eval = FALSE} 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. ```{r, eval = FALSE} BiocFileCache::bfcremove(rids = am_rids) ``` Commands such as `am_available()` should report no files cached. The command ```{r} am_data("gene_hg38") ``` will re-download the file and insert it into a database that functions with duckdb 0.9.1. [duckdb]: https://CRAN.R-project.org/package=duckdb # 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. ```{r db_disconnect_all} db_disconnect_all() ``` Database connections that are not closed correctly trigger warning messages. # Session information {.unnumbered} ```{r} sessionInfo() ```