Public bug reported:
uncalled 2.3+ds-3build5, uploaded to stonking-proposed as a no-change
rebuild for the hdf5 2.2 transition, fails to build from source on all
architectures.
The link of the _uncalled extension fails:
/usr/bin/x86_64-linux-gnu-ld.bfd: cannot find -lhdf5: No such file or
directory
collect2: error: ld returned 1 exit status
The -lhdf5 comes from the setup.py hunk of debian/patches/debian_hdf5:
libraries = ["bwa", "hdf5", "z", "dl", "m"],
It used to resolve because pkg-config --libs hdf5-serial emitted
"-L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5" under hdf5 1.14, which
put the flavor directory on the linker search path. With hdf5 2.2 the
serial development symlink on the default multiarch path is
libhdf5_serial.so, and hdf5-serial.pc emits just "-lhdf5_serial". Plain
libhdf5.so only exists inside /usr/lib/<triplet>/hdf5/serial/, which the
linker does not search by default.
Fix: amend debian_hdf5 to link hdf5_serial instead of hdf5. While
touching the patch, drop the library_dirs pkg-config shell-out as well:
pkg-config --libs-only-L hdf5-serial now returns empty, so the shell-out
injects only a '-L ' into the link line.
Debian carries the same patch at 2.3+ds-3+b4 and will hit the
identical failure once its own hdf5 2.2 transition lands, so the
amendment should be forwarded there.
** Affects: uncalled (Ubuntu)
Importance: Undecided
Assignee: Valentin Haudiquet (vhaudiquet)
Status: In Progress
** Tags: ftbfs
** Description changed:
uncalled 2.3+ds-3build5, uploaded to stonking-proposed as a no-change
- rebuild for the hdf5 2.2 transition, fails to build on all architectures.
+ rebuild for the hdf5 2.2 transition, fails to build from source on all
architectures.
The link of the _uncalled extension fails:
- /usr/bin/x86_64-linux-gnu-ld.bfd: cannot find -lhdf5: No such file or
directory
- collect2: error: ld returned 1 exit status
+ /usr/bin/x86_64-linux-gnu-ld.bfd: cannot find -lhdf5: No such file or
directory
+ collect2: error: ld returned 1 exit status
The -lhdf5 comes from the setup.py hunk of debian/patches/debian_hdf5:
- libraries = ["bwa", "hdf5", "z", "dl", "m"],
+ libraries = ["bwa", "hdf5", "z", "dl", "m"],
It used to resolve because pkg-config --libs hdf5-serial emitted
"-L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5" under hdf5 1.14, which
put the flavor directory on the linker search path. With hdf5 2.2 the
serial development symlink on the default multiarch path is
libhdf5_serial.so, and hdf5-serial.pc emits just "-lhdf5_serial". Plain
libhdf5.so only exists inside /usr/lib/<triplet>/hdf5/serial/, which the
linker does not search by default.
Fix: amend debian_hdf5 to link hdf5_serial instead of hdf5. While
touching the patch, drop the library_dirs pkg-config shell-out as well:
pkg-config --libs-only-L hdf5-serial now returns empty, so the shell-out
injects only a '-L ' into the link line.
Debian carries the same patch at 2.3+ds-3+b4 and will hit the
identical failure once its own hdf5 2.2 transition lands, so the
amendment should be forwarded there.
--
You received this bug notification because you are a member of Ubuntu
Bugs, which is subscribed to Ubuntu.
https://bugs.launchpad.net/bugs/2167945
Title:
uncalled: FTBFS in stonking-proposed with hdf5 2.2: ld cannot find
-lhdf5
To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu/+source/uncalled/+bug/2167945/+subscriptions
--
ubuntu-bugs mailing list
[email protected]
https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
