An error when installing BamM

[minsookim1983]

Hello,

I am trying to install BamM; however, I got an error.
The error message is attached.
install error.txt
Please, let me know what is wrong with me.
Thank you.

Min-Soo

[wwood]

Hi Min-Soo,
That's a pain. Can I ask how you downloaded BamM? The recommended way is to use the realeses page https://github.com/Ecogenomics/BamM/releases or better yet, using the version that has been packaged in GNU Guix https://www.gnu.org/software/guix/ . It won't work if you use the "Download zip" on the front GitHub page https://github.com/Ecogenomics/BamM

Hope that helps.
ben

[minsookim1983]

Thank you for your comment.
As you response, I downloaded BamM from https://github.com/Ecogenomics/BamM/releases. I think I forget the installation of 'libcfu' and 'htslib'. I installed 'htslib' safely, but not 'libcfu'. First, I can find 'libcfu v0.0.3', not 'v1.0.3', and it is hard to install 'libcfu v0.0.3'. Would you please let me know how to install libcfu safely?

Min-Soo

[wwood]

Both libcfu and htslib are bundled with BamM, so you don't need to worry about those (if you don't want to, htslib can be included as a shared library but it is probably easiest just not to bother). Would you mind sending a log of what is going wrong for you including the commands that you ran please?
Thanks, ben

[minsookim1983]

I am sorry for late answer. Here is the error message I got.
Error.txt
Thank you.

Min-Soo

[hhollandmoritz]

Hi,
I'm getting the same error as Min-Soo after trying the steps above. The only difference is I don't have admin privileges so all of my commands are run without sudo. I was looking through the other threads for hints and so I tried running ./autgen.sh and I get this error:

[hollandh@microbe c]$ ./autogen.sh
configure.ac:1: error: m4_defn: undefined macro: _m4_divert_diversion
configure.ac:1: the top level
autom4te: /usr/bin/m4 failed with exit status: 1
aclocal: autom4te failed with exit status: 1
autoreconf: aclocal failed with exit status: 1

I've tried this on both version 1.7.3 and 1.7.2 in case it was a bug introduced between versions but I get the same error in both. I'm running this code on a RedHat operating system (which I've read is similar to CentOS) which may mean I have the same issues as the user trying to run it on CentOS.

Do you have any suggestions on how to proceed from here?
Thanks,
Hannah

[timbalam]

I've managed to reproduce a similar error to Hannah's on a CentOS 6 virtual box. We'll try to fix it, however it might take a while. In the meantime, we have recently produced a docker image https://hub.docker.com/r/timbalam/bamm/. If it is possible to use docker on your system, it'd be great to have some people try that. If you do try it, please let us know of any issues using that.

[hhollandmoritz]

Unfortunately, docker is not an option on my system, but I will keep trying to find a work-around as you work on a permanent fix. Thanks so much!

[jvollme]

I think a work-around to this problem was found in #39