These are chat archives for cboursnell/transfuse

2nd
Nov 2016
Matt MacManes
@macmanes
Nov 02 2016 10:41
when downloading the 0.5.0 release from the above link
/home/ubuntu/transfuse-0.5.0-linux-x86_64/lib/ruby/bin.real/ruby: relocation error: /home/ubuntu/transfuse-0.5.0-linux-x86_64/lib/librt.so.1: symbol __vdso_clock_gettime, version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
this is Ubuntu 16.04, ruby 2.3.0p0 (2015-12-25 revision 53290) [x86_64-linux], gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 20160609
Chris Boursnell
@cboursnell
Nov 02 2016 10:49
Well the version of ruby you have installed isn't used, because the package uses travelling-ruby so contains a version of ruby
So the problem is something in Ubuntu 16.04 I guess? I thought I tested the package in a 16.04 VM, so I'll have another look and see if I can reproduce.
Matt MacManes
@macmanes
Nov 02 2016 10:50
if helpful, this is ami-40d28157
and
sudo apt-get update && sudo apt-get -y upgrade && sudo apt-get -y dist-upgrade
sudo apt-get -y install build-essential git python-pip python-numpy python-matplotlib 

wget https://keybase.io/mpapis/key.asc
gpg --import key.asc
\curl -sSL https://get.rvm.io | bash -s stable --ruby
source /home/ubuntu/.rvm/scripts/rvm

curl -LO https://github.com/cboursnell/transfuse/releases/download/v0.5.0/transfuse-0.5.0-linux-x86_64.tar.gz
tar -zxf transfuse-0.5.0-linux-x86_64.tar.gz
PATH=$PATH:/home/ubuntu/transfuse-0.5.0-linux-x86_64/
this will reprouce the issue.
Chris Boursnell
@cboursnell
Nov 02 2016 10:53
Thanks
Matt MacManes
@macmanes
Nov 02 2016 10:53
(might as well make it easy for you) :)
Chris Boursnell
@cboursnell
Nov 02 2016 11:04
Ok, I reproduced on my machine in a vagrant 16.04 VM
Chris Boursnell
@cboursnell
Nov 02 2016 11:19
Ok, this is strange:
I installed salmon-0.4 and then when I ran it I got:
salmon: relocation error: /home/ubuntu/.rvm/gems/ruby-2.3.0/bin/librt.so.1: symbol __vdso_clock_gettime, version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
Chris Boursnell
@cboursnell
Nov 02 2016 11:30
So I don't think it's a problem with transfuse, but something with that ubuntu
Matt MacManes
@macmanes
Nov 02 2016 11:31
you can't reproduce the issue on another 16.04 AMI?
Chris Boursnell
@cboursnell
Nov 02 2016 11:31
./salmon: relocation error: /home/ubuntu/SalmonBeta-0.4.0_DebianSqueeze/bin/../lib/librt.so.1: symbol __vdso_clock_gettime, version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
The same on a completely clean VM just trying to run salmon
Matt MacManes
@macmanes
Nov 02 2016 11:36
hmm. I get the same error when trying to install on my own machine, which is also 16.04
/bin/bash: relocation error: /home/macmanes/transfuse_test/transfuse-0.5.0-linux-x86_64/lib/librt.so.1: symbol __vdso_clock_gettime, version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
so it looks like all 16.04
but for me, Salmon (installed from LinuxBrew), works fine
 salmon                                                                                                                                                                                                         ⏎ master ◼
Salmon v0.7.2

Usage:  salmon -h|--help or
        salmon -v|--version or
        salmon [--no-version-check] <COMMAND> [-h | options]

Commands:
     index Create a salmon index
     quant Quantify a sample
     swim  Perform super-secret operation
where did you get your Salmon from, I’ll try and reproduce that on my end - or is this the Salmon bundled with transfuse?
bundled salmon works fine
~/transfuse-0.5.0-linux-x86_64/bin$ ./salmon --help
Allowed Options:
  -v [ --version ]      print version string
  --no-version-check    don't check with the server to see if this is the
                        latest version
  -h [ --help ]         produce help message

    Salmon v0.4.2
    ===============

    Please invoke salmon with one of the following commands {index, quant, swim}.
    For more inforation on the options for theses particular methods, use the -h
    flag along with the method name.  For example:

    salmon index -h

    will give you detailed help information about the index command.
Chris Boursnell
@cboursnell
Nov 02 2016 11:42
It was the salmon from here:
https://github.com/COMBINE-lab/salmon/releases/download/v0.4.0/SalmonBeta-0.4.0_DebianSqueeze.tar.gz
that gave the error. I don't know why i used that version. lemme check 0.4.2
But the fact that it gave the same error implies there's a larger issue than something specific to transfuse :(
Matt MacManes
@macmanes
Nov 02 2016 11:46
yep, I get that same error with that version of Salmon
Chris Boursnell
@cboursnell
Nov 02 2016 11:46
Yup, same. weird...
Matt MacManes
@macmanes
Nov 02 2016 11:46
What you think, @rob-p?
yep.
Chris Boursnell
@cboursnell
Nov 02 2016 11:47
That should be the exact same one that was bundled with transfuse though
Matt MacManes
@macmanes
Nov 02 2016 11:48
right. which brings me to my next question, mostly for another day.. What are chances of getting updated transfuse with recent version of Salmon and TransRate?
Chris Boursnell
@cboursnell
Nov 02 2016 11:50
Yup, I will get on that. I've been writing up the paper so haven't done any work on the software recently.
Matt MacManes
@macmanes
Nov 02 2016 11:51
great news about the paper! I’ll stay tuned for updates