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matsengrp / sumrep

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libgfortran.so.4 #10

Closed Pezhvuk closed 5 years ago

Pezhvuk commented 6 years ago

libgfortran.so.3 is no longer functional for the igraph package, which is kind of a "master dependency" for sumrep and its dependencies. The relevant library must be updated through apt-get before proceeding, as the most up to date version is libgfortran.so.4.

BrandenOlson commented 5 years ago

Hey @Pezhvuk -- thanks for the heads up and sorry for the very late reply. I'm not sure where the igraph dependency comes from. I may have removed this as a necessary library at some point. Do you remember where you encountered it?

javh commented 5 years ago

Both alakazam and shazam depend on igraph, so the shazam install will require an igraph install.

Pezhvuk commented 5 years ago

Hi @BrandenOlson. no problem! @javh is right, it is required by Shazam and Alakazam, and I think the problem was that, for reasons that I cannot remember, libgfortran.so.3 was being used/installed for some X dependency of probably Shazam/Alakazam (I think). Though libgfortran.so.3 seemed to had been deprecated for igraph, and was causing kind of a catch-22 situation where that X dependency would build on libgfortran.so.3, and either disallow libgfortran.so.3 to be overwritten by .so.4, or that dependency then was needed for igraph, rendering the update of libgfortran.so.3 mid-process impossible. Ultimately, I resolved the problem by enforcing the installation of libgfortran.so.4 through apt-get before letting that X dependency install .so.3 and causing all the downstream issues (I still occasionally get nightmares).

javh commented 5 years ago

Hehe. My first guess would be to blame numpy for the libgfortran.so.3 requirement. If so, it can probably be fixed by using a newer numpy version. That's just a wild guess though.

Pezhvuk commented 5 years ago

That could very well be. It's relatively easy to ignore, or be unaware of, a Numpy update.

BrandenOlson commented 5 years ago

@Pezhvuk -- Wow, sounds like quite the hassle, but glad you got it figured out. I'd be happy to put a warning of some sort in the README, but it sounds like the cause and solution are not entirely known. Perhaps I can say something like "if you encounter problems with libgfortran.so.3 or igraph during the installation of alakazam or shazam, issue #10 might help" ?

Pezhvuk commented 5 years ago

@BrandenOlson, That sounds like a good idea.