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GenomicsDB / GenomicsDB-R

Experimental R bindings to the native GenomicsDB library
GNU General Public License v2.0
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checking whether genomicsdb works... configure: error: GenomicsDB installation at /opt/GenomicsDB/ is not functional #17

Closed lima1 closed 8 months ago

lima1 commented 8 months ago

Hi @nalinigans ,

I think this happens due to the recent deprecation of genomics_db_version, although my naive attempt in fixing it by replacing it with genomicsdb::version().size > 0 did not work.

Thanks again, Markus

nalinigans commented 8 months ago

It is indeed replaced by genomicsdb::version() which returns std::string. So, you may have to do a genomicsdb::version().size().

I had forgotten to merge my changes from the develop branch to master. Sorry for the oversight. See https://github.com/GenomicsDB/GenomicsDB-R/blob/f3c8a897ce621b557f354390aebb03b20e40209b/src/genomicsdb_query.cpp#L87

Let me know if you are still seeing the issue.

lima1 commented 8 months ago

I think the particular configure check fails here: https://github.com/GenomicsDB/GenomicsDB-R/blob/master/configure.ac#L76C1-L86C106.

I tried it with both develop and master for GenomicsDB and GenomicsDB-R. Does installing GenomicsDB-R work for you? Then maybe my GenomicsDB is indeed not functional.

nalinigans commented 8 months ago

Just merged from develop into master and see that the GitHub Actions has failed. Just started looking at the failure, hopefully will get in a fix soon.

nalinigans commented 8 months ago

@lima1, seems to be fixed now. Please reopen if you still see issues. Thanks.