I'm getting the same error, but am running binary on CL (linux). Did you solve?

it's about time we updated the salmon dependency - it has a more sophisticated build setup now that should fix this cc @cboursnell

I am having the same problem running on ubuntu 16.04 LTS. Has any progress been made to address this issue? Thanks! Hannah

@blahah (cc @cboursnell)
Dear Richard,
I have started getting the same error since our nodes' system upgraded to Debian Stretch. The pre-compiled package of transrate-1.0.3 used to work fine with the older Debian. Any update regarding the salmon dependency? Thank you very much!!
Yui

I started on a v1.0.4 yesterday - hoping to get it out by the end of this week. I might need some help testing on different platforms - if anyone in this thread is willing to try the new build on their platform and report back before the release please add a thumbs up emoji to this comment :)

pls comment with any platforms you want it tested on and whether you can do that test

list of platforms we should test:

• debian stretch
• ubuntu 16.04
• ubuntu 14.04
• centOS 7

Great news! I can test the package with debian stretch and ubuntu 16.04; if I can get it by the Friday evening European time (going away from Saturday morning.).

Would it be possible to test it on Debian 10 (Buster)? I've had the same salmon issue with precompiled binaries as well as with trying to compile them on my system (newer versions of salmon work just fine).

Cheers,

J

I have the same problem but don't know how to solve it. Is v1.0.4 available now? Any update to solve salmon problem?

I have just downloaded the newest version on http://hibberdlab.com/transrate/installation.html and get salmon issues. Can anyone please advise?

As of May 2018, I'm also having this problem.
Any solution?

Deleting "librt.so.1" from the salmon lib file seems to get salmon running on Ubuntu 16.04

Same issue here on Ubuntu 16.04.4 LTS and Debian 9 (stretch). I can test it on both if requested.

I found a solution to this issue.
I removed salmon from <transrate_path>/lib and created a link to salmon 0.6.0 installed with conda.

I had any version of Salmon installed, so I installed salmon 0.6.0 using conda.

First I created a conda environment called transrate to avoid issues with other programs that might use latest versions of salmon.

$ conda create -n transrate

I entered the transrate environment and then installed salmon 0.6.0

$ conda install salmon=0.6.0

I got salmon's path with

$ whereis salmon
/home/vinicius/miniconda3/envs/transrate/bin/salmon

So, I entered transrate bin dir, removed salmon from there and created a link to conda's salmon

$ cd /home/prog/transrate-1.0.3-linux-x86_64/bin
$ rm salmon
$ ln -s /home/vinicius/miniconda3/envs/transrate/bin/salmon

And it works.

I'm also having this problem, but on Ubuntu 18.04.1 LTS.

@cooketho you can use the Oyster River version of transrate, in ~/Oyster_River-Protocol/software/orp-transrate/

Maybe this can help to solve the issue. And I have tested it.
Here: https://github.com/blahah/transrate/issues/215#issuecomment-453590406
Thanks @lmfaber

Hey all, I managed to solve this problem by renaming the librt.so.1 to librt.so.6. From what I have seen the problem seems to be the incompatibility of this version with the new systems.
This change can be simply done by executing "mv librt.so.1 librt.so.6" command in the /bin directory of Transrate program PATH_TO/transrate-1.0.3-linux-x86_64/bin.
Not sure if this is the correct way to do it but it seems to be working.
Cheers :)