I am getting a bunch of compile errors when I try to install the MySQL DBD::mysql Perl library. I am trying to install this library on OpenSuse linux (SUSE Linux Enterprise server 10 (x86_64) version 10, patch level 4)
The install fails when trying to compile dbdimp.h. There are hundreds of complile errors but I have reason to believe they all stem from the first 3:
dbdimp.h:23:49: error: mysql.h: No such file or directory
dbdimp.h:24:45: error: mysqld_error.h: No such file or directory
dbdimp.h:26:49: error: errmsg.h: No such file or directory
I believe that the reason I am getting the errors above is that I have no MySql Client installed. I do not know how to install mysql client (I believe I am supposed to get some version of libmysqlclient).
I am brand new to opensuse and vaguely familar with installing packages on Linux in general have used yum, yast, apt-get on ubuntu + centOS previously but the only package manager tools that seem to be on OpenSuse 10 are rpm and zypper. I have not managed to install the required mysql client using either of these. If anyone knows how to install MySql Client to resolve my issue I would greatly appreciate any recomendations
Thanks
You need to install MySQL or the MySQL client libraries, either through your system's package manager or by following the installation instructions from the source code.
It sounds like your question is really "How do I install MySQL on OpenSuse", which would be more appropriate for one of the other StackExchange sites.
I was able to resolve this to a point. In my original question, I stated that I had tried using YAST but that it had not worked. In fact, I did not fully explore the YAST install option but when I did, I managed to download install the required librarys by following an article I found (http://adminramble.com/install-mysql-yast/#chitika_close_button)
I was able to open the YAST GUI in the terminal window (not an X-window display) and navigate through the "software management" section wherein I was able to do a search for MySql. Amoung the search results were mysql client libraries, which I then selected and hit "Accept". The installation started and completed successully.
In order to complile the PERL DBD::mysql module, I had to create a new makefile with the ccflags specified so that the header files could be found:
perl Makefile.PL --cflags -I/usr/include/mysql
I say "to a point" at the top of this comment because I then ran into further problems compiling but my original issue posted has been partially resolved and getting this far may help someone else who is experiencing the same problem. Will update if I get a solution to the compile problem.
Related
I trying to get set up with Variant Effect Predictor (VEP) on the command line. I'm following the setup tutorial but I'm encountering some errors around dependencies. I'm also quite new to the command line so if anyone is able to break down the solution too then I'd be very grateful. Thanks!
Tutorial: https://www.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html
VEP requirements: http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements
I also have Perl v5.32.1.
What I've done:
I installed dependencies (listed in the requirements page) with the following commands:
- sudo -s cpanm DBI
- sudo -s cpanm Archive::Zip
- sudo -s cpanm DBD::mysql
For DBD:mysql, I got the follwoing message:
--> Working on DBD::mysql
Fetching http://www.cpan.org/authors/id/D/DV/DVEEDEN/DBD-mysql-4.050.tar.gz ... OK
Configuring DBD-mysql-4.050 ... N/A
! Configure failed for DBD-mysql-4.050. See /root/.cpanm/work/1626111140.5937/build.log for details.
Trying it out anyway, I ran perl INSTALL.pl (from the tutorial page) and got the message below. I would like VEP to run in online mode too if possible.
`WARNING: DBD::mysql module not found. VEP can only run in offline (--offline) mode without DBD::mysql installed
http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements
Hello! This installer is configured to install v104 of the Ensembl API for use by the VEP.
It will not affect any existing installations of the Ensembl API that you may have.
It will also download and install cache files from Ensembl's FTP server.
Checking for installed versions of the Ensembl API...done
Setting up directories
Destination directory ./Bio already exists.
Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? y
- fetching BioPerl
- unpacking ./Bio/tmp/release-1-6-924.zip
ERROR: Unable to unpack file ./Bio/tmp/release-1-6-924.zip without Archive::Extract or tar/unzip/gzip`
You show us this error:
Configure failed for DBD-mysql-4.050. See /root/.cpanm/work/1626111140.5937/build.log for details.
So looking in there will give you more clues about what the problems are. Without that, we can only guess.
But we can make educated guesses. The DBD::mysql distribution comes with a file called DBD::mysql::INSTALL which will talk you through some of the problems you'll find while installing this module.
It's important to note that DBD::mysql is a wrapper around MySQL's client libraries. They are written in C, so you'll need a C compiler installed in order to build DBD::mysql. You'll also need the client libraries and the development versions of the client libraries (for the C header files that you'll need to compile the module). On Ubuntu, those packages are called "libmysqlclient" and "libmysqlclient-dev". If you don't have a C compiler, then you'll want to install "gcc" too.
But this is all getting a bit complicated. There's another, simpler, approach. If you're using the system version of Perl (the version that was installed as part of the operating system and probably lives in /usr/bin/perl) then I'd recommend using the pre-build Ubuntu version of the package, which you can install by running:
$ sudo apt-get install libdbd-mysql-perl
Installing that version uses the OS's own package manager, and the package manager knows which other packages are needed in order for it to work - so it will install those as well.
People will probably complain that you're better off installing the modules from CPAN as it gives you more flexibility and allows you to use more up-to-date packages than the versions from your OS repos. And they're right. But, honestly, if you're a non-Perl programmer who just wants to get an application up and running, this is by far the simplest approach.
(But, as I said above, this is all guesswork as you haven't shared the most important errors with us.)
I'm new to collectd and Riemann. Im essentially trying to direct collectd logs to a riemann server instance. I understand that I need write_riemann plugin installed. I tried compiling the source files for write_riemann available online, but it includes a file called "riemann.pb-c.h", which is no where to be found. Please help!
Download the binary. After running the build script, while running the configure script include "--enable-write_riemann", this should install it. I had a lot of dependencies missing on CentOS, which threw a lot of errors. Once they were installed, write_riemann plugin was compiled and installed. Another issue you might face while installing the dependency is not able to find the right packages for protobuf-c.I was using yum package installer. Go to sudo vi /etc/yum.repos.d/epel.repo and change enabled from 0 to 1. After this, the protobuf-c processor was recognised while running the configure script. This solved my issue. Hope it does yours too!
I am trying to install the contrib/unaccent package for Postgresql 8.4 on my Ubuntu box. But I got the error message when I typed make:
/usr/lib/postgresql/8.4/lib/pgxs/src/makefiles/pgxs.mk: No such file or directory
Apparently PGXS is Postgresql's infrastructure for installing extensions, but I could not find the file pgxs.mk at all on my ubuntu box.
Following some leads on the Internet, I tried installing libpq-dev. Nonetheless, I couldn't find any pgxs.mk even after installing libpq-dev.
What's really frustrating is that I can't even find an example of pgxs.mk anywhere on the Internet. How do I install the PGXS infrastructure?
Probably you need to install postgresql-server-dev-8.4 package, which contains your missing makefile:
/usr/lib/postgresql/8.4/lib/pgxs/src/makefiles/pgxs.mk
I have installed Eclipse 3.5.2 and the plugin Subversion JavaHL Native Library Adapter 1.6.9.2 and this worked without any problems. However, this morning I was forced to change the password to logon to my Mac and since then I get the message that "Subversion native library not available" when I try to save any changes. Can anyone help? I have tried to add this line (-Djava.library.path=/usr/lib/jni) to the eclipse.ini file but this didn´t seem to make any difference.
Can anyone help?
Install MacPorts or HomeBrew, then run the following command:
For MacPorts, the commands to run are:
sudo port install subversion-javahlbindings +no_bdb +universal
For HomeBrew, the command is:
brew install --universal --java subversion
I was having a similar problem on Mac OS X Snow Leopard. I suspect your libraries are there but just need permissions changed, whereas I didn't have the libs at all.
The directory to check is /opt/subversion/lib, see if it has any libsvnjavahl files. In your case they may be there and just need new permissions.
To get the files I followed the the instructions they give for installing JavaHL on OS X, which is to download and install Open CollabNet. (login required, although it's free)
Then you just need to update your environment variable in .profile, something like:
export PATH=.:/opt/subversion/bin:$HOME/bin:$PATH
Then ran:
. .profile
Then I tested with javahltests.jar as mentioned here.
The easiest thing to do is download and install the OSX package that is provided on openCollabNet.
MacPorts also provides an easy Subversion and JavaHL package, however on Snow Leopard ?MacPorts is still compiling these packages as simple 32-bit binaries. If you use the default Snow Leopard JVM which is 64-bit you will get an error...
Failed to load JavaHL Library.
These are the errors that were encountered:
no libsvnjavahl-1 in java.library.path
no svnjavahl-1 in java.library.path
/opt/local/lib/libsvnjavahl-1.0.0.0.dylib: no suitable image found. Did find: /opt/local/lib/libsvnjavahl-1.0.0.0.dylib: mach-o, but wrong architecture
Note the error about wrong architecture. This is because the 64-bit JVM cannot load a 32-bit native library. The ?CollabNet binaries for OSX do not have this problem because they include both 32-bit and 64-bit versions.
Source: subclipse.tigris.org
Here is a blog entry that gives a solution:
http://blog.mattwoodward.com/getting-rid-of-subversion-native-library-not
I don't know whether this will work in your particular situation, but it's worth a try.
(Edited to fix link that became broken after I posted. The link became broken sometime between May 3 and June 1.)
In case you already have subversion installed I'd recommend performing first a brew uninstall and then the install again. And follow the steps to create the links indicated after the install concludes. This worked for me. Regards
I fixed it installing the SVNKit Client Adapter (not required) package.
How can I get PDO to work on my mac (os x 10.5)? I'm using the built in php and php in Zend/Eclipse. Can't seem to find useful drivers for it at all.
I had to install the PDO_PGSQL driver recently on Leopard, and I ran across a multitude of problems. In my search for answers, I stumbled across this question. Now I have it successfully installed, and so, even though this question is quite old, I hope that what I've found can help others (like myself) who will undoubtedly run into similar problems.
The first thing you'll need to do is install PEAR, if you haven't done so already, since it doesn't come installed on Leopard by default.
Once you do that, use the PECL installer to download the PDO_PGSQL package:
$ pecl download pdo_pgsql
$ tar xzf PDO_PGSQL-1.0.2.tgz
(Note: you may have to run pecl as the superuser, i.e. sudo pecl.)
After that, since the PECL installer can't install the extension directly, you'll need to build and install it yourself:
$ cd PDO_PGSQL-1.0.2
$ phpize
$ ./configure --with-pdo-pgsql=/path/to/your/PostgreSQL/installation
$ make && sudo make install
If all goes well, you should have a file called "pdo_pgsql.so" sitting in a directory that should look something like "/usr/lib/php/extensions/no-debug-non-zts-20060613/" (the PECL installation should have outputted the directory it installed the extension to).
To finalize the installation, you'll need to edit your php.ini file. Find the section labeled "Dynamic Extensions", and underneath the list of (probably commented out) extensions, add this line:
extension=pdo_pgsql.so
Now, assuming this is the first time you've installed PHP extensions, there are two additional steps you need to take in order to get this working. First, in php.ini, find the extension_dir directive (under "Paths and Directories"), and change it to the directory that the pdo_pgsql.so file was installed in. For example, my extension_dir directive looks like:
extension_dir = "/usr/lib/php/extensions/no-debug-non-zts-20060613"
The second step, if you're on a 64-bit Intel Mac, involves making Apache run in 32-bit mode. (If there's a better strategy, I'd like to know, but for now, this is the best I could find.) In order to do this, edit the property list file located at /System/Library/LaunchDaemons/org.apache.httpd.plist. Find these two lines:
<key>ProgramArguments</key>
<array>
Under them, add these three lines:
<string>arch</string>
<string>-arch</string>
<string>i386</string>
Now, just restart Apache, and PDO_PGSQL will be up and running.
Take a look at this PECL package: PDO_PGSQL
I haven't tried it myself, but I've been interested in playing with Postgres as an alternative to MySQL. If I have a chance to try it soon, I'll throw my results up here in case it helps.
I'm not sure this will help with the PDO drivers specifically, but you might look into BitNami's MAPPStack.
I had a ton of trouble with Postgres, PHP, and Apache on my Mac, some of it having to do with 64- vs 32-bit versions of some or all of them. So far, the BitNami MAPPStack install is working nicely in general. Maybe it will help with your PDO issues as well.
Install new php version via brew and restart server, and php -v, all issues are removed.
This is what worked for me
brew install php55-pdo-pgsql
This installs PHP 5.5.32 and PostgreSQL 9.5. I already had PostgreSQL 9.4 installed so I uninstalled the homebrew version with:
brew uninstall postgres
You then have to update /etc/apache2/httpd.conf to point to the correct PHP version and restart Apache:
LoadModule php5_module /usr/local/Cellar/php55/5.5.32/libexec/apache2/libphp5.so
My OSX version is Yosemite.