i am using mysql for orthomcl software. when i use the command
orthomclLoadBlast my_orthomcl/orthomcl.config my_orthomcl/similarSequence.txt
it gives this error
Can't load '/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/DBD/mysql/mysql.so' for module DBD::mysql: libmysqlclient.so.15: cannot open shared object file: No such file or directory at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230, line 5. at /storage/home/cdac/OrthoMCL/orthomclSoftwarev2.0.8/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line48
Compilation failed in require at /storage/home/cdac/OrthoMCL/orthomclSoftware-v2.0.8/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 48, <F> line 5.
How to solve this problem ??
You could install a local perl in your home and you could leave vendor perl untouched.
You could use perlbrew or local::lib to maintain an up to date perl version without modifying the system installed perl.
Related
I'm having an issue with the DBD::mysql module. This question has been asked before on this forum but a solution was not posted so I thought I would repost it. Sorry if this is not appropriate for this forum. This is my first post.
You can find the original post from bLIGU here:
Error using perl module DBD::mysql in ActivePerl 5.28 on Windws10 64bits
I have the exact same problem. I'm just upgrading my Active Perl version. Nothing else changed. I'm running the same MySql server version and this script ran fine before the update and it runs fine if I go back to version 5.20.2.2002 and use PPM to download the packages.
Note that ActiveState now requires you to build a custom version of ActivePerl with the modules online and generates an install file for you. PPM is no longer supported.
Here's the error:
install_driver(mysql) failed: Can't load 'C:/Perl64/site/lib/auto/DBD/mysql/mysql.dll' for module DBD::mysql: load_file:The specified module could not be found at C:/Perl64/lib/DynaLoader.pm line 193.
at (eval 11) line 3.
Compilation failed in require at (eval 11) line 3.
Perhaps a required shared library or dll isn't installed where expected
at C:\E22_TE~1\ICTDEV~1\Scripts\UPDATE~1.PL line 136.strong text
The file C:/Perl64/site/lib/auto/DBD/mysql/mysql.dll is present so I'm wondering if the DLL is trying to load something else and returns an error.
I installed Apache Drill through the link in the Drill Documentation. Apache Drill works fine. I also installed and got Apache Superset running using docker. Superset also works totally fine.
But my goal is to integrate Superset and Drill together. The only tutorial I was able to find was a tutorial from Dataist. When following this tutorial they ask us to add a database.
Since I am running both Drill and Superset in my local machine they ask us to type drill+sadrill://localhost:8047/dfs/test?use_ssl=False as the SQLAlchemy URI. They ask us to test the connection by pressing test connection.
When pressing test connection I get an error message as follows.
ERROR: {"error": "Connection failed!\n\nThe error message returned was:\nCan't load plugin: sqlalchemy.dialects:drill.sadrill", "stacktrace": "Traceback (most recent call last):\n File \"/home/superset/superset/views/core.py\", line 1755, in testconn\n engine = database.get_sqla_engine(user_name=username)\n File \"/home/superset/superset/utils/core.py\", line 132, in __call__\n value = self.func(*args, **kwargs)\n File \"/home/superset/superset/models/core.py\", line 911, in get_sqla_engine\n return create_engine(url, **params)\n File \"/usr/local/lib/python3.6/site-packages/sqlalchemy/engine/__init__.py\", line 435, in create_engine\n return strategy.create(*args, **kwargs)\n File \"/usr/local/lib/python3.6/site-packages/sqlalchemy/engine/strategies.py\", line 61, in create\n entrypoint = u._get_entrypoint()\n File \"/usr/local/lib/python3.6/site-packages/sqlalchemy/engine/url.py\", line 172, in _get_entrypoint\n cls = registry.load(name)\n File \"/usr/local/lib/python3.6/site-packages/sqlalchemy/util/langhelpers.py\", line 240, in load\n \"Can't load plugin: %s:%s\" % (self.group, name)\nsqlalchemy.exc.NoSuchModuleError: Can't load plugin: sqlalchemy.dialects:drill.sadrill\n"}
Can someone figure out why I am getting this error. And also if there are any other tutorials to follow which give a better idea on how to set up Drill and superset.
I have encountered a similar issue while trying to connect elasticsearch. I guess the docker image you used was amancevice/superset. This issue cause because your image is not using the latest SQLAlchemy, SQLAlchemy-Utils packages. Upgrade or reinstall these packages to fix the issue.
To uninstall:
pip uninstall SQLAlchemy
pip uninstall SQLAlchemy-Utils
To install again (latest version):
pip install SQLAlchemy
pip install SQLAlchemy-Utils
I have reported this issue here https://github.com/amancevice/docker-superset/issues/158 maybe it get fixed with the upcoming images.
I have a problem starting Kamailio Version 4.3. I installed Kamailio from source, and the modules are stored in the default directory /usr/local/lib64/kamailio/modules. I am using the json module that Kamailio provides but it fails to load.
Kamailio's documentation on the json module is found here:
http://www.kamailio.org/docs/modules/3.4.x/modules/json.html
The documentation states that before the module is loaded you need the required library libjson, which I installed. When I start kamailio and cat the log file via kamailio start; cat /var/log/kamailio.log | grep error I am getting the following error:
Jan 8 12:43:53 localhost kamailio: ERROR: <core> [sr_module.c:576]: load_module(): could not open module </usr/local/lib64/kamailio/modules/json.so>: /usr/local/lib64/kamailio/modules/json.so: undefined symbol: is_error
Jan 8 12:43:53 localhost kamailio: : <core> [cfg.y:3432]: yyerror_at(): parse error in config file /usr/local/etc/kamailio/kamailio.cfg, line 109, column 12-20: failed to load module
Line 109 is obviously correct:
loadmodule "json.so"
More information:
ldd json.so
linux-vdso.so.1 => (0x00007ffc33e97000)
libjson-c.so.2 => /lib64/libjson-c.so.2 (0x00007f24d8110000)
libc.so.6 => /lib64/libc.so.6 (0x00007f24d7d7c000)
/lib64/ld-linux-x86-64.so.2 (0x00007f24d8527000)
Has anyone else experienced a similar issue, or does anyone know a solution? It is also worth mentioning I am running kamailio on CentOS 6.7.
is_error(p) should be a macro, look inside your json.h file (perhaps at /usr/include/json-c/json.h) and see if it includes "bits.h" from the same folder. Inside bits.h should be defined the macro is_error().
If you don't have that, maybe it is a customized library.
As a side note, an alternative for json operations in kamailio.cfg is using jansson module.
I would like to ask, how can I load new module in Kamailio 4.1.2?
Actually, I have an issue, when I tried to compile my kamaiio.cfg
I've got error:
root#kamailio:/usr/local/# kamailio -c kamailio.cfg
loading modules under /usr/local/lib64/kamailio/modules/
0(25392) ERROR: <core> [sr_module.c:587]: load_module(): ERROR: load_module: could not find module <websocket> in </usr/local/lib64/kamailio/modules/>
0(25392) : <core> [cfg.y:3408]: yyerror_at(): parse error in config file /usr/local/etc/kamailio/kamailio.cfg, line 323, column 12-25: failed to load module
0(25392) ERROR: <core> [cfg.y:3272]: yyparse(): cfg. parser: failed to find command ws_handle_handshake
0(25392) : <core> [cfg.y:3411]: yyerror_at(): parse error in config file /usr/local/etc/kamailio/kamailio.cfg, line 1083, column 27: unknown command, missing loadmodule?
ERROR: bad config file (2 errors)
when I look physically to the /usr/local/lib64/kamailio/modules/ there is some modules, but websocket.so is missing.
So, how can I get and load module in Kamailio?
Thank you for help!
You haven't installed the module websocket. Edit modules.lst file in the source code directory and add websocket to include_modules variable. If you don't have modules.lst, just do:
make cfg
Alternative is to do:
make cfg include_modules="websocket"
By default, the build system for kamailio compiles and install only the modules that have the same dependencies as the core of the application. For websocket you need to install libunistring and openssl (libssl) devel packages.
Steps to load new module to Kamailio server. (Try if above answer is not working for you)
Check the modules is exist in the default module directly /usr/local/lib64/kamailio/modules.
If found, add loadmodule "module_name.so" in load module section in kamailio.cfg file.
If the module is not found in default module directory, you can check for the source code of that module in the default module source code directory /usr/local/src/kamailio-4.4/kamailio/modules.
If source code found, enter to the module directory. Then create modules' shared object file(.so) by following commands.
./configure
make
make test
make install
Then you will get a shared object file(.so). Copy that file into the default module directory. and load this module from the kamailio.cfg file as mentioned in step 1.
If module source code does not exist in the default source code directory, You need to download the source code from the web. And follow step 3 and 4.
When I run a perl script which uses DBD::mysql , I get the error message:
install_driver(mysql) failed: Can't load '/home/y/lib/perl5/site_perl/5.8/i686-linux-64int/auto/DBD/mysql/mysql.so'
for module DBD::mysql: libmysqlclient.so.16: cannot open shared object file: No such file or directory
at /home/y/lib/perl5/5.8/i686-linux-64int/DynaLoader.pm line 230. at (eval 30) line 3
I am new to perl, but from what I understand it needs mysql.so and it knows the path.
/home/y/lib/perl5/site_perl/5.8/i686-linux-64int/auto/DBD/mysql/mysql.so is present.
Then why the problem?
The file that is missing is libmysqlclient.so.16, not mysql.so. It comes with the mysqlclient package on some distributions.
Make sure /etc/ld.so.conf contains /usr/local/mysql/lib/mysql and /usr/local/mysql/ . If not, add them and run ldconfig.