Set the path to javah via the JAVAH environment variable. If it is
a version of java that does not have javah it will fall back to `javac
-h`. Without specifying this the build could pick up a javah from the
system.
- add version 3.4.0
- add patch for bam2wig when version 3.4.0
- url format changed again, hopefully stable now
- added missing python dependency when version >3.3.1
- have older version compile with htslib, samtools ,bcftools
- new dependencies for version 3.4.0
- sqlite
- mysql-client
- mysqlpp
- lp-solve
- suite-sparse
- refactored filtering code
- set python interpreter in scripts
This is as much a question as it is a minor fine-tuning of the docs. I've been known to add things to an environment by editing the `spack.yaml` file directly. When I read the previous version of this sentence, I was afraid that `spack add` was actually doing *two* things, modifying the `spack.yaml` and updating something else that defined the roots of the Environment. A bit of experimentation suggests that editing the `spack.yaml` file is sufficient to change the roots.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This adds that new version to the package, updates the url, and
updates the hash of v0.0.3 for the new url.
This also updates the KVTree dependency as MPI is required to be
enabled in KVTree for er to work.
rankstr is now also required by er for recently added tests.
PR #22864 added a patch to hpctoolkit to fix an issue with gcc 10.x, and the patch was applied to all revs unconditionally. But this was fixed in hpctoolkit master on Aug 11, 2020, so the patch should only apply to old revs.
Fixes#22951.
Update package with 4.1 sha keys.
Use variant to disable openmp in the build of llvm-amdgpu.
Set CPATH, LIBRARY_PATH so that clang knows to look in the rocm-openmp-extras for headers/libraries.
Disable flang warnings as Spack thinks they are errors.
In ROCm 4.1, the plugin changed names from hsa -> amdgpu.
Update HSA_INCLUDE for 4.1.0.
Clingo has been released on PyPI, so there
are no more concerns on our CI depending
on pypy.test for installing the wheel.
Apparently we have parts of Spack which
are not compatible with kcov > 3.4
UnifyFS has been integrated with updated versions of its mochi-margo
dependency (and mochi-margo's mercury and libfabric dependencies).
This removes support for version 0.9.0
fixes#22786
Trying to get optimization flags for a specific target from
a compiler may trigger warnings. In the context of constructing
facts for the ASP-based solver we don't want to show these
warnings to the user, so here we simply ignore them.
These were deprecated when the custom cuda_arch list was
removed. Also fixed up the Aluminum dependencies for Hydrogen and
DiHydrogen. Turns out that Aluminum v0.6.0 didn't have a correct
version in CMake and thus the interaction with older versions of
Hydrogen and DiHydrogen needed to be corrected.
This isn't a significant issue, but I noticed that the docstring incorrectly references "tty.fail" and I wanted to quickly fix it to reflect the correct command, tty.die. I also wanted to fix the docstrings to not be large clumps, to what @tgamblin suggested after I wrote this - having one line at the top that is a quick summary, and more verbose after that.
