Building error

[tgac]

Building error

[maplesond]

Hi Andrew, thanks for the raising this and providing the detailed logs. I'll look into this today and get back to you. In the meantime you could try cloning directly from github and see if you can install that way.

Best regards,
Dan Mapleson

[maplesond]

I've taken a look on my build machines and all seem to compile fine (both from distributable and git clone), although I don't have quite the same environment setup:

Desktop (s):
OS: Mint 17.2
GCC: 4.8.4
Boost: 1.55.0
libtool: 2.4.2

Cluster:
OS: CentOS release 6.7
GCC: 4.9.1
Boost: 1.59.0
libtool: 2.4.2

Out of interest have you tried installing any earlier versions of KAT? If so did they succeed or fail? Also could you send me your config.log files. Both for jellyfish (./deps/jellyfish-2.2.0/config.log) and kat (./config.log) please. This might help me work out what's happening on your system.

As an aside, I noticed that there was a check failing for gnuplot, which I've now fixed and is currently head of the develop branch. This shouldn't affect your main problem however.

[maplesond]

Another thing to check for is whether or not libtool (./deps/jellyfish-2.2.0/libtool) is created by the configure script. It should be there after untarring the distributable (or cloning the repo), but should be after running the configure script.

If this doesn't work, one thing to try would be modifying how jellyfish calls libtool. To do this you'll need to work from the cloned repo (not the distributable). Firstly, open the jellyfish configure.ac (./deps/jellyfish-2.2.0/configure.ac) file. Then change line 8 from "AC_PROG_LIBTOOL" to "LT_INIT". (AC_PROG_LIBTOOL is a deprecated way of initialising libtool, LT_INIT is the currently recommended way). Then go back to the kat root dir, run "./autogen.sh", then do the "./configure". Then check to see if the "libtool" script has been made in the jellyfish dir. If it has then hopefully make will work properly now.

[andrewjrobinson]

Thanks for all the suggestions Daniel,

The libtool file didn't exist in the repo versions of source (before running ./autogen.sh) but did in release versions (and after running ./autogen.sh on repo versions) so appears to be all ok.

I have tried:

1. Changing the LT_INIT line: same error
2. Installing from latest head of repo: same error
3. Installing an older version (2.0.1): same error
4. Installing with an older version of libtool (2.4.2): same error

I had already installed jellyfish v2.2.3 on this system and it worked so I tried installing jellyfish v2.2.0 which showed the similar errors to what I was getting with the KAT version of jellyfish. So the error seems to be with the jellyfish v2.2.0 on my system.

I should have mentioned that this is a HPC and uses "Environment Modules" to bring particular versions of software into users PATH (that are installed in NON-standard prefixes).

I tried to upgrade the version of jellyfish in the latest head of KAT but was getting errors with swig and now it wants valgrind. Do you do any alterations to jellyfish that you embed? and is it possible to tell it to use and external version of jellyfish (from the PATH)?

[maplesond]

Hi Andrew, thanks for the feedback. It sounds like the jellyfish authors have fixed a few issues and made the software more portable since v2.2.0. I'll update the jellyfish version in KAT for a future release.

With regard to jellyfish modifications, I have made some small changes in the jellyfish configure.ac file, to remove some checks which are unnecessary for use within KAT (the swig and valgrind checks for example).

For KAT V2 we made the decision to embed jellyfish within KAT, and therefore prevent version mismatches, as we think this improves stability of the system. Previously we were running into issues where hashes made with different versions of jellyfish were not compatible (even from dot releases), so embedding jellyfish avoids that problem completely. Also we make extensive use of the jellyfish library's API, and would like to avoid and potential issues when changes to the API occur. So unfortunately there's noway of overriding the embedded version of jellyfish in KAT.

Hope that helps. I'll leave the ticket open for now. I'll close it when I've embedded a newer version of jellyfish.

[maplesond]

Should be fixed in the latest release: https://github.com/TGAC/KAT/releases/tag/Release-2.1.0. Please reopen if there are any issues.