marbl / Winnowmap

Long read / genome alignment software

Other

235 stars 22 forks source link

Build of meryl fails (sys/sysctl.h missing in gcc 7.5) #28

Closed giesselmann closed 2 years ago

giesselmann commented 2 years ago

Hi,

I tried building winnowmap on a linux 5.10 with gcc 7.5.0. The winnowmap executable is build, but meryl fails. It is missing 'sys/sysctl.h' `utility/src/utility/system.C:37:10: fatal error: sys/sysctl.h: No such file or directory

include <sys/sysctl.h>

      ^~~~~~~~~~~~~~

compilation terminated. `

I could successfully build the master of https://github.com/marbl/meryl giving me a functional meryl binary. I wonder if this will work, are there any version dependencies between winnowmap and meryl?

Thank you for your help, Pay

brianwalenz commented 2 years ago

As far as I'm aware, there are no differences that should matter to winnowmap, but I'm not 100% sure.

The problem is that Linux 5.5 removed the sysctl() interface, but this version of meryl is still using it. The latest version is not using it.

What distribution of Linux is that, out of curiosity?

giesselmann commented 2 years ago

Cool, thanks for the quick help, I'll use a standalone meryl then. It's called Mariux, in-house build but somewhat ubuntu-like.

cjain7 commented 2 years ago

Hi @giesselmann , Winnowmap code is also revised to have latest version of Meryl (commit: f9a4c1a). Please feel free to re-try and let us know if it works fine.

giesselmann commented 2 years ago

pulled, build, works. Thank you!