Re: [wgs-assembler-users] /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.10' not found (required by /share/work/lhuang/my_apps/wgs-8.1/Linux-amd64/bin/gatekeeper)

[Walenz, B. <wa...@nb...>]

You might still be compiling with the older compiler.  Try adding the new compiler to the start of your path, or set environment variables CC and CXX to point to the new version.

Your glibc package might be ancient, try updating it.

This isn’t a problem specific to the assembler.  Searching for ‘GLIBCXX_3.4.10 not found’ gives lots of other suggestions.  For example: https://bbs.archlinux.org/viewtopic.php?pid=1065388

b


From: wuk...@16... [mailto:wuk...@16...]
Sent: Tuesday, September 23, 2014 9:07 AM
To: Brian Walenz
Cc: wgs-assembler-users
Subject: Re: [wgs-assembler-users] /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.10' not found (required by /share/work/lhuang/my_apps/wgs-8.1/Linux-amd64/bin/gatekeeper)

Hi,
I compile it from source code like:

bzip2 -dc wgs-8.1.tar.bz2 | tar -xf - cd wgs-8.1 cd kmer && make install && cd .. cd samtools && make && cd .. cd src && make && cd .. cd ..


The old gcc version is 4.1.2, and I  install a new version of gcc 4.5.1 on own account.



________________________________
Best,

Kai Wu

From: Brian Walenz<mailto:th...@gm...>
Date: 2014-09-23 20:58
To: wuk...@16...<mailto:wuk...@16...>
CC: wgs-assembler-users<mailto:wgs...@li...>
Subject: Re: [wgs-assembler-users] /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.10' not found (required by /share/work/lhuang/my_apps/wgs-8.1/Linux-amd64/bin/gatekeeper)
Hi-

Did you compile this yourself, or is it the pre-compiled version from sourceforge?  Try compiling yourself.  How old is 'too old'?

b

On Sun, Sep 21, 2014 at 2:14 AM, wuk...@16...<mailto:wuk...@16...> <wuk...@16...<mailto:wuk...@16...>> wrote:
Dear colleagues,

When I run the command "runCA -p ipagpj029hmc001 -d ipagpj029hmc001_raw useGrid=1 scriptOnGrid=1 doOBT=1 unitigger=bogart /home/kwu/workdir/my_projects/ipag_pj029/data/CA_data/ipagpj029hmc001_1.1.frg /home/kwu/workdir/my_projects/ipag_pj029/data/CA_data/ipagpj029hmc001_2.1.frg"
After a while, the error massege of ipagpj029hmc001.gkpStore.err is:
/share/work/lhuang/my_apps/wgs-8.1/Linux-amd64/bin/gatekeeper: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.10' not found (required by /share/work/lhuang/
my_apps/wgs-8.1/Linux-amd64/bin/gatekeeper)

I don't know why it? I know my gcc version is too old. So, I install a new version of gcc on my own account. And I set the environment variable:
export LD_LIBRARY_PATH=/home/kwu/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/home/kwu/lib64:$LD_LIBRARY_PATH

But, it seem can't find it.

________________________________
Best,

Kai Wu

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