Bug 252965

Summary: biology/kallisto: failure with HDF5 1.12
Product: Ports & Packages Reporter: Thierry Thomas <thierry>
Component: Individual Port(s)Assignee: Jason W. Bacon <jwb>
Status: Closed FIXED    
Severity: Affects Only Me CC: thierry
Priority: --- Flags: bugzilla: maintainer-feedback? (jwb)
Version: Latest   
Hardware: Any   
OS: Any   
Bug Depends on:    
Bug Blocks: 251894    

Description Thierry Thomas freebsd_committer 2021-01-24 10:07:14 UTC
science/hdf5 should be upgraded to 1.12, but some ports are not compatible with this version, and it has been suggested to repocopy the actual port to science/hdf5-110.

PR 251894 propose a patch to do that, and an exp-run has been launched to detect the incompatibilities.

Unfortunately, your port biology/kallisto failed: see
http://package18.nyi.freebsd.org/data/121amd64-default-foo/2021-01-20_21h30m48s/logs/errors/kallisto-0.46.1,1.log
(this looks like a missing -lz?)

Could you please propose a patch, either to fix it with 1.12 or to switch to hdf5-110?
Comment 1 commit-hook freebsd_committer 2021-01-26 01:34:34 UTC
A commit references this bug:

Author: jwb
Date: Tue Jan 26 01:34:21 UTC 2021
New revision: 562627
URL: https://svnweb.freebsd.org/changeset/ports/562627

Log:
  biology/kallisto: Add -lz for pending hdf5 upgrade

  PR:             252965
  Submitted by:   thierry

Changes:
  head/biology/kallisto/Makefile
Comment 2 Jason W. Bacon freebsd_committer 2021-01-26 01:34:57 UTC
Thanks!