error message: libstdc++.so.6: version `GLIBCXX_3.4.17' not found (required by sailfish)

[ying chen]

Hi guys,

I got the error messages when I tried to do a simple index:

[brainiac0860]$ sailfish index -t Homo_sapiens.GRCh37.75.cdna.all.fa -o SailfishIndex -k 20

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.17' not found (required by sailfish)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by sailfish)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.13' not found (required by sailfish)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by sailfish)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.3' not found (required by sailfish)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.14' not found (required by sailfish)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by sailfish)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.5' not found (required by sailfish)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by /myhps/users/c135523/local/bin/Sailfish_0_6_3/lib/libsailfish_core.so)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.5' not found (required by /myhps/users/c135523/local/bin/Sailfish_0_6_3/lib/libsailfish_core.so)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.14' not found (required by /myhps/users/c135523/local/bin/Sailfish_0_6_3/lib/libsailfish_core.so)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.17' not found (required by /myhps/users/c135523/local/bin/Sailfish_0_6_3/lib/libsailfish_core.so)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.13' not found (required by /myhps/users/c135523/local/bin/Sailfish_0_6_3/lib/libsailfish_core.so)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /myhps/users/c135523/local/bin/Sailfish_0_6_3/lib/libsailfish_core.so)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /myhps/users/c135523/local/bin/Sailfish_0_6_3/lib/libsailfish_core.so)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /myhps/users/c135523/local/bin/Sailfish_0_6_3/lib/libboost_program_options.so.1.54.0)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /myhps/users/c135523/local/bin/Sailfish_0_6_3/lib/libboost_serialization.so.1.54.0)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /myhps/users/c135523/local/bin/Sailfish_0_6_3/lib/libboost_serialization.so.1.54.0)

sailfish: /myhps/users/c135523/local/bin/gistic2/MATLAB_Component_Runtime/v714/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /myhps/users/c135523/local/bin/Sailfish_0_6_3/lib/libjellyfish-1.1.so.1)

[brainiac0860]$ 

Why Sailfish index call gistic2 Matlab runtime library?

Thanks a lot for the help!

Ying

[ying chen]

Sorry, it turned out that I got the error because I did not set the path for /usr/lib and /usr/lib64. It has nothing to do with Sailfish.                Ying

[Craig Monger]

Hi all,

I'm getting a similar error when trying to run salmon

salmon: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by salmon)

I have tried to set environment variables and am still getting this error, am I missing something? Sorry I know something like setting these paths should be simple but I cant get it to work and my googlefu is failing me. 

I have set the following in my /etc/profile in my attempts to solve this

PATH="/usr/local/bin:/usr/bin:/bin:/usr/local/games:/mnt/work/software/SalmonBeta/bin:/usr/lib:/usr/lib/x86_64-linux-gnu/"

LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:/usr/lib:/usr/local/lib:/mnt/work/software/SalmonBeta/lib"

Thanks for reading, look forward to being able to try this piece of software out in my analyses! 

 

 

[Rob]

Hi Craig,

  Could you let us know what version of salmon you're tying to use (e.g. one of the binaries from the latest release? which one?), as well as what operating system you're on?  The type of error you're
seeing is typical of your OS having too old of a libc for the executable.  This is likely to happen if you're using the executable compiled for a newer version of linux than you have (e.g. if you're on
Ubuntu 12.04, or RHEL 5 and try to use the Ubuntu 14.04 executable).  In such a case, one thing to try is to use the older binary (I have one compiled on ubuntu 10.04 under the latest releases).
The other option is to compile it from source yourself (but this will require a reasonably recent c++ compiler which won't be available by default unless you're on a relatively new linux distro).

--Rob

[Craig Monger]

Hi Rob,

We are running on on Debian 7 and I was trying to use the latest binary release of Salmon. I'll give compiling from source a go and let you know how I get on. 

Thanks for the quick response and advice.