---
title: "E. Issues & Solutions"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{E. 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()
```