Running Beast2 on Fedora 27

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Robin Cristofari

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Jan 24, 2018, 4:06:10 PM1/24/18
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Hello all,

I'm trying to run Beast2 on a (fresh) Fedora 27 distribution, with OpenJDK 1.8.0 installed. All runs until the actual conputation: BEAST crashes at the first step with the following error:

On Linux 64bit, you need additional support libraries.
You need to install libgfortran3.

For example for debian or Ubuntu, type "sudo apt-get install libgfortran3"

For more information, see https://github.com/mikiobraun/jblas/wiki/Missing-Libraries

However, the link provided tells me as expected to install libgfortran - but this is already present on my system as version libgfortran-7.2.1 (the standard on Fedora 27), and I can't find any legacy rpm for libgfortran3 apart for OpenSUSE or Mandriva but they won't install on Fedora.

Any idea of a workaround..?

Thank you !

Robin

Remco Bouckaert

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Jan 24, 2018, 4:52:59 PM1/24/18
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Hi Robin,

I wonder whether this is an issue with OpenJDK or whether this is due to one of the libraries used by BEAST depending on libgfortran3. As far as I know, none of the libraries used by BEAST (apache common-math, colt, antlr, beagle or jam) use fortran, but I might be wrong. Do you have BEAST packages installed?

Perhaps you could install Oracle’s version of the JDK, at least to confirm this is a problem with OpenJDK.

Cheers,
Remco


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Andrés Parada

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Jan 24, 2018, 5:08:39 PM1/24/18
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Adding to what Remco answered, I always follow these instructions to install OpenJDK http://www.webupd8.org/2012/01/install-oracle-java-jdk-7-in-ubuntu-via.html
Modify or update as required

Cheers
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Instituto de Cs Ambientales y Evolutivas
Universidad Austral de Chile
Campus Isla Teja s/n
Valdivia, Chile

Robin Cristofari

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Jan 26, 2018, 2:30:05 PM1/26/18
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Thank you very much for this fast answer !

I tested now running Oracle Java 8 - however the error is the same.

However, the good news is that indeed, removing the MultiTypeTree package fixed the issue... so this is not such a big problem after all (although this might be worth fixing some day - I unfortunately don't have the skills for that...)

Thank you again for your help !

Best,

Robin

Tim Vaughan

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Jan 30, 2018, 11:46:06 AM1/30/18
to beast...@googlegroups.com, Remco Bouckaert
Hi Robin,

I've looked into this a bit: it seems that Fedora 26 removed libgfortran3, which is necessary for the jblas library that MultiTypeTree uses, from their repositories.  There's an issue relating to this open on the jblas github page (https://github.com/mikiobraun/jblas/issues/87), so hopefully the jblas programmer will release a version that supports the new library soon.  In the meantime, it seems the only way around the problem is to install an older version of the gfortran package (or whichever Fedora package owns libgfortran) and extract the libgfortran.so.3 binary from that package.

Luckily Debian/Ubuntu/etc supply both libgfortran3 and 4 concurrently, so there's currently no issue on those systems.

All the best,
Tim

Naoki Takebayashi

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Nov 23, 2022, 9:24:12 PM11/23/22
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This is an old thread, but I came to this problem with BEAST 2.6.7 with Fedora 35.  I'm posting this, so others can solve the problem (with Fedora 34-37).

You can install old libgfortran.so.3 from this page:


Basically you can do

dnf copr enable kwizart/compat-libgfortran-48
dnf install compat-libgfortran-48

as a super user.

Naoki
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