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ropensci / taxadb

:package: Taxonomic Database
https://docs.ropensci.org/taxadb
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MonetDBLite removed from CRAN #52

Closed poldham closed 4 years ago

poldham commented 5 years ago

Hi Carl and collaborators, I was watching the recent rOpenSci community call and was very excited to give taxadb a whirl.

It seems there is a dependency on MonetDBLite and it is not available for R 3.5.3 (or 3.6 I guess). The CRAN status on the package reveals that it has been removed from CRAN and archived in April 2019 at the request of the maintainer.

I see now that you have spotted this here: https://github.com/MonetDB/MonetDBLite-R/issues/38 and mentioned the development of duckdb as an alternative.

Leaving this here for others who will have this question. taxadb looks great from Kari's presentation and I'll look forward to using taxadb when there has been some time to address the dependency issue.

All the best,

Paul

cboettig commented 5 years ago

Hi @poldham, yup, thanks for the note. For the moment I've just added MonetDBLite under Remotes, so taxadb should continue to install successfully with devtools::install_github().

As you've noted, MonetDBLite was removed from CRAN, and the maintainer intends to replace MonetDBLite with duckdb, so we'll plan to migrate to that as well. They are all DBI-based interfaces, so the changes required are pretty minimal. (taxadb already supports user-selected databases anyway, MonetDBLite is just provided as the default since it is easier to install and faster than alternatives like Postgres). We'll have to wait until duckdb is on CRAN to get taxadb to CRAN, but hopefully it is soon.

cboettig commented 4 years ago

Now accessible via additionalRepositories (as is duckdb). 

install.packages("taxadb", dep = TRUE)

Should allow both to install (from source, requires cmake). We still hope to see duckdb on CRAN soon.