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matsen / pplacer

Phylogenetic placement and downstream analysis
http://matsen.fredhutch.org/pplacer/
GNU General Public License v3.0
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Is it difficult to remove the OCaml <= 4.01 requirement? #354

Open wwood opened 7 years ago

wwood commented 7 years ago

Hi,

First off, thanks for writing pplacer, it has become a quite central tool for our group, even if we don't use it directly instead via tools which I'll refrain from advertising.

Accordingly, we are wanting to package pplacer for the GNU Guix package manager / OS, and I've got it working locally: http://lists.gnu.org/archive/html/guix-devel/2017-02/msg00273.html

However, it would simplify maintenance of the package if the newest version of OCaml could be used rather than 4.01 (and this would presumably be true for others building from source too). Without having a great amount of experience with OCaml, is updating likely to be a difficult thing? Thanks, ben.

rekado commented 5 years ago

Meanwhile, pplacer has been removed from Guix due to its dependency on OCaml 4.01, which is affected by an unfixed CVE.

rekado commented 5 years ago

I patched the sources to build with OCaml 4.02. Here's the patch series to add pplacer to GNU Guix again: https://issues.guix.info/issue/35207

rekado commented 5 years ago

I've patched pplacer to build with OCaml 4.07.1. Here's the patch adding it to Guix: https://git.savannah.gnu.org/cgit/guix.git/commit/?id=36f4f1e297941877439eca77f24d7400da3a51f9

matsen commented 5 years ago

Hey @rekado thanks for this!

I've been away so am just catching up. Does this require pplacer code changes, or just packaging changes? If the former, would you like to submit a PR against the main repo?