mbox series

[bug#77357,0/1] Remove freebayes

Message ID cover.1743241966.git.andreas@enge.fr
Headers
Series Remove freebayes |

Message

Andreas Enge March 29, 2025, 9:52 a.m. UTC 
  I noticed that the package does not build when updating parallel.
It should be possible to somehow repair it, but apparently nobody has
noticed that the package does not build any more for almost two years:
   https://ci.guix.gnu.org/build/9529724/details
   first failure:
   https://ci.guix.gnu.org/build/1171985/details
So if there is no interest in it, there is maybe no point in spending
time on it.

I would suggest to remove it on or after April 29.

Andreas Enge (1):
  gnu: Remove freebayes.

 gnu/packages/bioinformatics.scm | 82 ---------------------------------
 1 file changed, 82 deletions(-)


base-commit: 67f4a2feadbb6cc04a61b5a3bc7b8f4bace2a0bb

Comments

Andreas Enge March 29, 2025, 10:01 a.m. UTC | #1 
I made a mistake in submitting the patch series; the (trivial) patch is
in #77358, which I have closed; we can continue the discussion here.

Andreas
Sebastian Dümcke March 30, 2025, 4:12 p.m. UTC | #2 
Dear Andreas,

I know I have a manifest somewhere depending on freebayes. However, I am 
unsure when was the last time I ran it. And even then I could use 
time-machine to get a working version of freebayes running. So removing 
it is not a big deal. However, it seems that upstream is aware of the 
failing test suite [1]. Unfortubnately building --with-latest=freebayes 
did not immediately lead me to success.

Perhaps what should be discussed is the potential overlap (at leat 
conceptually) between the guix channel bioinformatic tools (as found in 
bioinformatics.scm) and the many more tools in the guix-science channel. 
Would it make sense to move all these packages over to the guix-science 
channel?

Best
Sebastian

[1]: https://github.com/freebayes/freebayes/issues/786