Breakdancer Installation/Running Problems: Error/Suspicious Messages During Installation

Question

[tptacek3050]

This is a followup to an earlier question I had about an error I as getting while running breakdancer: Error running breakdancer-max: Max Kahan error: 0

I decided to try re-installing the program and watch carefully for errors or suspicious messages. Well, I found some messages that I can't explain.

First of all, according to the installation instructions (https://github.com/genome/breakdancer/blob/master/INSTALL.md), the last two lines you should see after making breakdancer are as follows:

Linking CXX executable ../../../../bin/breakdancer-max
[100%] Built target breakdancer-max

However, the last two lines I see are as follows:

Linking CXX executable ../../../../test-bin/TestConfigLib
[100%] Built target TestConfigLib

After this, I tried running a make test and got the following error messages:

Running tests...
Test project /home/tptacek/breakdancer/build
    Start 1: TestBdLib
1/5 Test #1: TestBdLib ........................   Passed    0.08 sec
    Start 2: TestCommonLib
2/5 Test #2: TestCommonLib ....................   Passed    0.02 sec
    Start 3: TestIoLib
3/5 Test #3: TestIoLib ........................   Passed    0.06 sec
    Start 4: TestConfigLib
4/5 Test #4: TestConfigLib ....................   Passed    0.02 sec
    Start 5: RunBreakDancer
5/5 Test #5: RunBreakDancer ...................***Failed    0.67 sec

80% tests passed, 1 tests failed out of 5

Label Time Summary:
integration    =   0.67 sec
unit           =   0.18 sec

Total Test time (real) =   0.92 sec

The following tests FAILED:
          5 - RunBreakDancer (Failed)
Errors while running CTest
make: *** [test] Error 8

Are these errors anything I should be concerned about, and if so, could the explain the error I was getting in the linked thread above?

Answer 1

[ernfrid]

We think there may be a bug. The released 1.4.2 version does seem to be functioning properly though. You can get that copy of the code by executing the following command after the initial git clone in the install instructions. git checkout v1.4.2

Then proceed with creating the build directory and compiling as normal.

[ernfrid]

We think this is now fixed in v1.4.4 that was just released to github. Let us know if it does not resolve the problem!

[tptacek3050]

I wish I had checked back earlier this week. Unfortunately, I can't dig into this now, but will attempt this by Monday. I'll let you know how things turned out. Thanks for your reply.

[raveancic]

I have v1.4.4 and I obtain the same thing at the end of the installation:

"[100%] Built target TestBdLib"

instead of:

"100% Built breakdancer-max"

in addition if I run the make test I obtain:

"100% tests passed, 0 tests failed out of 4".

What should I do to install brakdancer-max.pl? What could it miss for the final installation? Sorry but I am not a bioninformatic.

Thank you

Answer 2

[Philipp Bayer]

Hi,

I just installed breakdancer according to the instructions and "make test" ran fine, and in my case the last output line of the installation process is identical to yours not to what's in the INSTALL-instructions.

In the breakdancer-folder there's a folder called Testing, in which you'll find a directory Temporary. In there is a LastTest.log which tells you more about each step in the tests, could you please upload the part from

5/5 Testing: RunBreakDancer
5/5 Test: RunBreakDancer

to pastebin.com or something like that? I have a feeling you probably got some dependency missing, or there's a broken bash environment variable. Thanks!

[tptacek3050]

Sorry I didn't see this earlier. Thanks for your reply. Here's the log file from the point you specified: http://pastebin.com/T2eSsFLq