As I am trying to run Shapeit for GWAS imputation in a linux cluster, I've runned into this error message
/net/userpath/bin/shapeit: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /net/userpath/bin/shapeit)
/net/userpath/bin/shapeit: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /net/userpath/bin/shapeit)
When I run strings /usr/lib64/libstdc++.so.6 | grep GLIBC
I get
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBC_2.3
GLIBC_2.3.2
GLIBC_2.4
GLIBC_2.2.5
GLIBCXX_FORCE_NEW
Any idea how to get the rest of GLIBC_* into the linux cluser ?
This command will install required libraries for the same.
sudo apt-get install libstdc++6
Related
I am trying to upgrade my GitLab docker container from version 13.8.0 to 13.8.8 with ce edition.
I tried by download the Debian package for the ubuntu focal version from the below link:
https://packages.gitlab.com/gitlab/gitlab-ce/packages/ubuntu/focal/gitlab-ce_13.8.8-ce.0_amd64.deb
but while installing the package I am getting the following errors...
root#2d66229ecf41:/tmp#dpkg -i gitlab-ce_13.8.8-ce.0_amd64.deb
(Reading database ... 86705 files and directories currently installed.)
Preparing to unpack gitlab-ce_13.8.8-ce.0_amd64.deb ...
/opt/gitlab/embedded/bin/ruby: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not found (required by /opt/gitlab/embedded/lib/libruby.so.2.7)
/opt/gitlab/embedded/bin/ruby: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by /opt/gitlab/embedded/lib/libruby.so.2.7)
/opt/gitlab/embedded/bin/ruby: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.28' not found (required by /opt/gitlab/embedded/lib/libruby.so.2.7)
/opt/gitlab/embedded/bin/ruby: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.25' not found (required by /opt/gitlab/embedded/lib/libruby.so.2.7)
/opt/gitlab/embedded/bin/ruby: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.27' not found (required by /opt/gitlab/embedded/lib/libruby.so.2.7)
dpkg: error processing archive gitlab-ce_13.8.8-ce.0_amd64.deb (--install):
subprocess new pre-installation script returned error exit status 1
Errors were encountered while processing:
gitlab-ce_13.8.8-ce.0_amd64.deb
what I should I do?
My disc space is also free...
what is the problem?
can anyone help me to fix this?
Based on the error message, ruby needs xcrypt v2.0, glibc_2.xx and they are not installed or unable to be found.
This is the first step I would try, after performing a backup:
sudo apt-get update && sudo apt-get upgrade && sudo apt-get dist-upgrade
sudo apt-get install -f
https://ubuntuforums.org/showthread.php?t=2438576
how may i have my local glibc used instead of the root lib64 glibc? I've obtained a newer version of glibc and extracted to a local directory with ld_library_path written to point to that local path, but the application is still looking at the library in /lib64/.
How do I override this?
gate
gate: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /p/work/aapplasa/gate/usr/lib64/libproxy.so.1)
ldd --version
ldd (GNU libc) 2.11.3
rpm2cpio rpm/glibc-2.19-16.2.5.x86_64.rpm | cpio -idmv
setenv LD_LIBRARY_PATH /p/work/aapplasa/gate/usr/lib64
gate
gate: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /p/work/aapplasa/gate/usr/lib64/libproxy.so.1)
tl;dr
How to solve version 'GLIBCXX_3.4.15' not found when I cannot be root on the Linux server?
I'm tring to use PhantomJS on OpenShift. As explained in this article, PhantomJS GhostDriver binds on localhost only, while on OpenShift, you cannot bind anything on localhost (you need to specify the machine IP address). Paolo Bernardi (the author of the article) shares a patch that fixes PhantomJS, so that it's possible to bind on an IP address.
The problem is that the provided patch does not work on my OpenShift server: when running ./phantomjs -v on my patched PhantomJS installation, I catch a segmentation fault. So I decided to compile PhantomJS with the fix by myself on a Debian server I have, thanks to PhantomJS documentation:
sudo apt-get install build-essential g++ flex bison gperf ruby perl libsqlite3-dev libfontconfig1-dev libicu-dev libfreetype6 libssl-dev libpng-dev libjpeg-dev python ttf-mscorefonts-installer
git clone git://github.com/ariya/phantomjs.git
cd phantomjs
git checkout 1.9
# apply the fix
./build.sh
When running ./phantomjs -v on the compiled binary, I get 1.9.8: it worked.
When copying this binary on OpenShift and running ./phantomjs -v, I catch an error:
./phantomjs: /usr/lib64/libstdc++.so.6: version 'GLIBCXX_3.4.15' not found (required by ./phantomjs)
Any idea how to solve this? What's the reason of this error? Please excuse my lack of system knownledge :)
Update (and solution):
Thanks to moleculartear, I compiled a patched binary on an RHEL OS: no error anymore!
The working PhantomJS binary: https://github.com/jrestful/server/blob/master/seo/phantomjs-1.9.8-patched.tar.gz?raw=true
More details:
I cannot update GLIBC version on OpenShift since I cannot be root (unless there are some workarounds).
I cannot compile PhantomJS on OpenShift directly since I don't have enough space for the sources on that server.
My OpenShift cartridges: Tomcat 7 (JBoss EWS 2.0) + MongoDB 2.4 + RockMongo 1.1.
On my Debian server:
$ uname -a
Linux servername 3.2.0-4-amd64 #1 SMP Debian 3.2.41-2 x86_64 GNU/Linux
$ strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBC
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBC_2.2.5
GLIBC_2.3
GLIBC_2.3.2
GLIBCXX_DEBUG_MESSAGE_LENGTH
On my OpenShift server:
$ uname -a
Linux servername 2.6.32-504.3.3.el6.x86_64 #1 SMP Fri Dec 12 16:05:43 EST 2014 x86_64 x86_64 x86_64 GNU/Linux
$ strings /usr/lib/libstdc++.so.6 | grep GLIBC
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBC_2.0
GLIBC_2.3
GLIBC_2.4
GLIBC_2.1
GLIBC_2.1.3
GLIBC_2.3.2
GLIBC_2.2
GLIBCXX_FORCE_NEW
GLIBCXX_DEBUG_MESSAGE_LENGTH
Since OpenShift Online runs on RHEL, you should be able to install CentOS into a VM on your local machine (or run one in the cloud somewhere) and compile a version of PhantomJS with the patch and then upload it to your OpenShift server and use it.
If you can't do that please use the contact us form at help.openshift.com and reference this stackoverflow question.
I am a system, hundreds 5:11
I'm trying to run a game server and I'm a mistake, says I lack the lib. GLIBCXX_3.4.11
[root#571 ~]# strings /usr/lib/libstdc++.so.6 | grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_FORCE_NEW
Error: Failed (/usr/lib/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required
If anyone can help me, please. I will be very grateful.
sudo yum install libstdc++.x86_64
Is anyone succesfully running robomongo on centos machine.
I got this result when try to excuting it
> ./robomongo.sh
./bin/robomongo: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./bin/robomongo)
./bin/robomongo: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by ./bin/robomongo)
./bin/robomongo: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./lib/libqscintilla2.so.8)
./bin/robomongo: /lib64/libc.so.6: version `GLIBC_2.15' not found (required by ./lib/libQtGui.so.4)
./bin/robomongo: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./lib/libQtGui.so.4)
./bin/robomongo: /lib64/libc.so.6: version `GLIBC_2.15' not found (required by ./lib/libQtCore.so.4)
./bin/robomongo: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./lib/libQtCore.so.4)
>
I have been try to update glibc from yum command
> yum list installed | grep glibc
glibc.x86_64 2.12-1.107.el6_4.2 #updates
glibc-common.x86_64 2.12-1.107.el6_4.2 #updates
glibc-devel.x86_64 2.12-1.107.el6_4.2 #updates
glibc-headers.x86_64 2.12-1.107.el6_4.2 #updates
> sudo yum update glibc.x86_64
Loaded plugins: fastestmirror, refresh-packagekit
Loading mirror speeds from cached hostfile
* base: centos.biz.net.id
* epel: kartolo.sby.datautama.net.id
* extras: centos.biz.net.id
* rpmforge: kartolo.sby.datautama.net.id
* updates: centos.biz.net.id
Setting up Update Process
No Packages marked for Update
>
please, is anyone could solve this problem?
-Mardi
According to this issue, Robomongo supports CentOS starting from 0.8.1. Download the latest version - and it will work for you.
It looks like robomongo is build against a different glibc than you have, and hence it's not working. I would suggest you just compile it yourself from GitHub.
windows and MAC binaries are available if you want to add scons, cmake, QT5 and build robomongo on your centos box
i think you should run:
sudo yum install -y glibc.i686 libstdc++.i686 libgcc.i686
goodluck!
Go to this link and download the latest version of robomongo.
http://app.robomongo.org/download.html
Example: 64 bit .tar.gz
Then extract the zip file. and goto extracted_folder_path/bin/
Then start robomongo.sh using command
./robomongo.sh