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bioperl / bioperl-live

Core BioPerl 1.x code
http://bioperl.org
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db.h dependency #350

Open lskatz opened 4 years ago

lskatz commented 4 years ago

In my own CI unit testing, I install bioperl as a dependency. However, it is difficult to make sure that bioperl installs. I am pretty sure that that BerkeleyDB (Ubuntu:libberkeleydb-perl) and ubuntu:libdb-dev is a dependency. Could it be documented somewhere?

https://packages.ubuntu.com/bionic/libberkeleydb-perl https://packages.ubuntu.com/bionic/libdb-dev

cjfields commented 3 years ago

Can you confirm that you are running into issues when either of these is not installed? We have largely switched to AnyDBM_File but it's possible DB_File is still in there somewhere (it's still showing up as a dependency); BerkeleyDB shouldn't be required though. See this page:

https://metacpan.org/release/BioPerl

carandraug commented 3 years ago

Looking at the Changes files, I see that in version 1.6.924 the dependency on DB_File was demoted from "required" to "recommended". My guess is that demotion was lost in version 1.7.3 with the move to dzil.

However, looking at the code and despite this demotion, there's modules (and programs as well) that still use DB_File without working around its absence so I'm not sure if that demotion is correct.