Question: Trouble Installing Breakdancer 1.4.2: Boost Libraries Inexplicably Not Visible
1
gravatar for tptacek3050
5.0 years ago by
tptacek305060
United States
tptacek305060 wrote:

I am attempting to install Breakdancer 1.4.2 on a 64 bit Linux CentOS 5.6 cluster. I do not have root access: I'm am installing my own personal copy. I have been following the installation instructions as shown here: https://github.com/genome/breakdancer/blob/master/INSTALL.md.

I get to this step:

cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local

And I get the following output:

=====================

Score floating point type: double -- Found Samtools - Samtools include dirs: /share/apps/ngs-ccts/breakdancer-1.4.2/breakdancer/build/samtools-0.1.19;/usr/include - Samtools libraries: /share/apps/ngs-ccts/breakdancer-1.4.2/breakdancer/build/samtools-0.1.19/libbam.a;/usr/lib64/libz.so CMake Error at /share/apps/cmake/cmake-2.8.10.2-Linux-i386/share/cmake-2.8/Modules/FindBoost.cmake:1192 (message): Unable to find the requested Boost libraries.

Boost version: 1.52.0

Boost include path: /share/apps/ngs-ccts/boost_1_52_0

The following Boost libraries could not be found:

      boost_system
      boost_chrono

Some (but not all) of the required Boost libraries were found. You may need to install these additional Boost libraries. Alternatively, set BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT to the location of Boost. Call Stack (most recent call first): CMakeLists.txt:28 (find_package)

-- Configuring incomplete, errors occurred!

===================

However, in the /share/apps/ngs-ccts/boost_1_52_0/libs folder there are folders called system/ and chrono/ which I presume have the missing libraries in them. Is there a way I can redirect the compiler to the correct directories? Is this indicative of an error in the way Boost was installed on the cluster (i.e. do I need to call my tech support guys)?

Travis Ptacek

breakdancer • 2.8k views
ADD COMMENTlink modified 5.0 years ago by tgi.tabbott220 • written 5.0 years ago by tptacek305060

What do you see when you type echo $BOOST_LIBRARYDIR and echo $BOOST_ROOT?

ADD REPLYlink written 5.0 years ago by Dan D6.6k

I get blank lines.

ADD REPLYlink written 5.0 years ago by tptacek305060

can you do this and try again?: export BOOST_LIBRARYDIR=/share/apps/ngs-ccts/boost_1_52_0/libs export BOOST_ROOT=/share/apps/ngs-ccts/boost_1_52_0/

ADD REPLYlink written 5.0 years ago by Dan D6.6k

Just tried it, I get the same error message.

ADD REPLYlink written 5.0 years ago by tptacek305060

try typing yum install boost and then retry the installation.

ADD REPLYlink written 5.0 years ago by Dan D6.6k

I need to be root (not possible for me) to perform this command. Do I need to contact the cluster administrators?

ADD REPLYlink written 5.0 years ago by tptacek305060

Oops, I totally missed that in your initial post. Yes, I would contact the cluster administrators at this point. All of the other ideas I have would require you to be root.

ADD REPLYlink written 5.0 years ago by Dan D6.6k

What should I tell him? Is boost not installed correctly? Do I need to get him to install the software for me?

ADD REPLYlink written 5.0 years ago by tptacek305060

I would ask him to do a yum install boost. That's easy for him and likely to work for your app. If he balks, I would then explain that you tried to point your app to the specific path of the boost libs via setting specific environment variables, but that it didn't work and is indicative of a boost library installation that would also not suffice for other applications folks might want to install in the future.

ADD REPLYlink written 5.0 years ago by Dan D6.6k
1
gravatar for tgi.tabbott
5.0 years ago by
tgi.tabbott220
United States
tgi.tabbott220 wrote:

Hello. I just pushed a new version to master that includes the required parts of boost. If you update (git pull) from github, or simply reclone the repository, you should be able to proceed without having to explicitly install boost.

ADD COMMENTlink written 5.0 years ago by tgi.tabbott220

Just tried running it this morning and it worked. Thanks!

ADD REPLYlink written 5.0 years ago by tptacek305060
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