Dependencies are missing: - salmon (0.6.0)

Question

Dependencies are missing: - salmon (0.6.0)

brunolouro opened this issue 8 years ago · comments

I've installed the packaged binary version on Ubuntu 16.04 LTS. Running just the basic assembly metrics is OK, but once it needs dependencies in the read-based run it states:

Dependencies are missing: - salmon (0.6.0)

Executing the salmon in the bin directory, it states:

./salmon: relocation error: /opt/transrate-1.0.3-linux-x86_64/bin/librt.so.1: symbol __vdso_clock_gettime, version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference

By checking /lib/x86_64-linux-gnu/libc.so.6 it states:

GNU C Library (Ubuntu GLIBC 2.23-0ubuntu3) stable release version 2.23, by Roland McGrath et al.

So is pointing to recent version...is there any basic solution to this?

I'm running transrate in a PC because I run into problems also with shared libraries in our clustered server, but there is because the libc are old versions.

Thanks,
Bruno

Sara Oppenheim · Answer 1 · Wed Oct 05 2016 00:24:22 GMT+0800 (China Standard Time)

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

Rik · Answer 2 · Thu Apr 06 2017 02:39:51 GMT+0800 (China Standard Time)

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

Hannah E Marx · Answer 3 · Wed May 17 2017 03:41:53 GMT+0800 (China Standard Time)

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

yuisato · Answer 4 · Wed Jul 05 2017 22:47:38 GMT+0800 (China Standard Time)

@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

Rik · Answer 5 · Wed Jul 05 2017 23:51:01 GMT+0800 (China Standard Time)

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

yuisato · Answer 6 · Thu Jul 06 2017 02:10:54 GMT+0800 (China Standard Time)

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.).

xibalbanus · Answer 7 · Thu Oct 26 2017 07:42:10 GMT+0800 (China Standard Time)

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

AsterChen · Answer 8 · Wed Nov 01 2017 16:39:11 GMT+0800 (China Standard Time)

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?

Emily Stander · Answer 9 · Wed Nov 08 2017 16:46:51 GMT+0800 (China Standard Time)

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

Cristobal Balladares · Answer 10 · Fri May 25 2018 03:31:18 GMT+0800 (China Standard Time)

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

sdbaney · Answer 11 · Wed Jul 11 2018 23:28:54 GMT+0800 (China Standard Time)

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

Jan Oppelt · Answer 12 · Fri Jul 20 2018 19:06:23 GMT+0800 (China Standard Time)

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

Vinícius H. Franceschini-Santos · Answer 13 · Thu Jan 24 2019 23:48:18 GMT+0800 (China Standard Time)

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.

cooketho · Answer 14 · Wed Jan 30 2019 01:20:40 GMT+0800 (China Standard Time)

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

Matt MacManes · Answer 15 · Wed Jan 30 2019 01:32:05 GMT+0800 (China Standard Time)

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

Zhaoweishan · Answer 16 · Mon Jul 06 2020 22:23:43 GMT+0800 (China Standard Time)

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

ljudevitluka · Answer 17 · Fri Dec 25 2020 20:55:18 GMT+0800 (China Standard Time)

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 :)