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This PR adds the r-fdb-infiniummethylation-hg18 package and the needed
dependency of r-txdb-hsapiens-ucsc-hg18-knowngene.
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This PR adds an updated version to the r-rhtslib package as well as fix
the build.
- add patches to use compiler flags from R
- add variables for bzip2 and xz dependencies
- use the spack Makeconf file when building the in-tree htslib
- make patchelf available to allow R to remove reference to temporary
installation directory in htslib shared object
- Add new version of r-rsamtools as the r-rsamtools and r-rhtlib
packages are closely paired.
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As discussed in:
https://spackpm.slack.com/archives/C5VL7V81G/p1581394270058800
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* Fix run environment
Trying to install Avizo, i get "Error: NameError: name 'run_env' is not defined". Correcting it to be just "env"
* fix identation
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Starting with 2020, the tar files are named v2020.0.tar.gz,
v2020.1.tar.gz, etc, not 2020_U1.tar.gz.
https://github.com/intel/tbb/releases
The previous commit (7a10478708) fixed the checksum mismatch, but
didn't update url_for_version (my bad).
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UnifyFS no longer has an option to depend on numa. This removes the
numa variant, dependency, and associated conflict.
This commit also
- renames the `pmpi` variant to the more appropriate `auto-mount`
- changes the preferred version to the most recent release
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exceptions. (#14929)
* Replace direct call to patchelf with get_existing_elf_rpaths which handles exceptions.
* Remove unused patchelf definition.
* Convert to set.
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* macsio: cast from int to unsigned int
* macsio: apply a patch only when version is 1.1
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It's often useful to run a module with `python -m`, e.g.:
python -m pyinstrument script.py
Running a python script this way was hard, though, as `spack python` did
not have a similar `-m` option. This PR adds a `-m` option to `spack
python` so that we can do things like this:
spack python -m pyinstrument ./test.py
This makes it easy to write a script that uses a small part of Spack and
then profile it. Previously thee easiest way to do this was to write a
custom Spack command, which is often overkill.
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* Adding Intel LLVM compiler.
* Fixing some minor issues.
* Split build environment on run environment in intel-llvm.
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* Fix PYTHONPATH for static build.
* Only for the latest version.
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- fix a missing `env.` prefix in the build environment.
- rename development branch to same name as in git
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WarpX removed the `dev` branch in favor of a simpler,
`master`-centric development model.
`master` is the new development branch and there is no
stable branch anymore (we use tags and release branches
instead).
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Add patch for DDDigi's broken TBB support. The issue is fixed in
DD4hep master so the patch is only required for 1.11.0
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- `git -C` doesn't work on git before 1.8.5
- `working_dir` gets us the same effect
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* Add cpio package
* intel-mkl: Depend on cli tool needed during build
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* Fix QT4 platform name for linux clang
* Fix clang compiler flags on QT4
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Added python3 dependency
Added support for new CMake variables
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* Hydrogen now depends on `aluminum +nccl` vs. `aluminum +mpi_cuda`
* Hydrogen: Simplify Mac OS OpenMP-detection logic
* Aluminum: Add Mac OS OpenMP-detection logic
* LBANN: depend on conduit@0.4.0: instead of conduit@master
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Fixes #10019
If multiple instances of a package were installed in a single
instance of Spack, and they differed in terms of dependencies, then
"spack find" would not distinguish specs based on their dependencies.
For example if two instances of X were installed, one with Y and one
with Z, then "spack find X ^Y" would display both instances of X.
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This new version of libedit can make use of an ncurses dependency
built with +termlib (which moves some symbols into a separate
libtinfo).
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This PR will set the approriate library if ncurses is built with a
separate tinfo library.
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This PR creates the r-biomartr package as well as needed new packages
and updates.
- new dependency: r-philentropy
- update: r-curl
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* Adapt to ACTS v0.16
* ACTS uses the DD4hep XML components nowadays
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