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libmongoc requires pkg-config to detect several of its dependencies.
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* libunwind: add version 1.3-rc1 and variant xz
Version 1.3-rc1 is the latest published snapshot from libunwind.
Variant xz adds spack-built support for reading compressed symbol
tables, or else disables this feature. Without the variant, libunwind
will look for liblzma in /usr/lib.
* Add preferred=True to version 1.2.1 as the last official stable
release.
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* gperftools@2.7: new version
* gperftools: update homepage & url
The URL in the homepage field of the gperftools package redirects to
its GitHub repo, and the URL for version 2.3 returns a 404 error. This
commit updates both fields to the most recent sensible values.
* gperftools: update commit hashes to sha256
This commit deletes the url field for all listed versions because it
is no longer needed as a result of updating the package url field. In
addition, all commit hashes are updated to SHA256.
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* initial atk update
* Add coreqs
* Fixed flake8 errors
* corrected gnome's version URLs
* Added correct list_url's
* Changed list_depth
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- `imp` is deprecated and seems to have started having some weird
issues on certain Linux versions.
- In particular, the file argument to `load_source` is ignored on
arch linux with Python 3.7.
- `imp` is the only way to do imports in 2.6, so we'll keep it around for
now and use it if importlib won't work.
- `importlib` is the new import system, and it allows us to get
lower-level access to the import implementation.
- This consolidates all import logic into `spack.util.imp`, and make it
use `importlib` if it's avialable.
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* added relion 3 beta - WIP
* added relion 3 beta - WIP
* more relion changes - still WIP
* more changes for relion
* more changes
* now correctly handling cuda_arch
* now correctly handling cuda_arch
* fixed flake8 syntax errors
* fixed flake8 syntax errors
* merge
* fixed flake8 errors again
* relion 3 finished
* added print message to cuda_arch exception
* relion - shortened explination
* still need tag=2.0.3 for v 2.0.3 - removed @develop since it no longer exists
* correct cuda versions now used properly
* relion 3 done
* added tags back
* fixed exception message
* relion - added develop back as master
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- foam_add_lib() must be used instead of the undefined foamAddLib()
for adding VTK
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* Fix spack versions behavior when no URL
* Unit test packages without URLs or safe versions
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* add gcc8 patch for python 2.7.14
Change-Id: I48cb5e717577d8158d1f7f1fe270156a01940d8a
* add explaining comment
Change-Id: Ia46168e2269d7de47d7ec8d0bf9e3b7696ea8e31
* remove unnecessary part of the patch
Change-Id: Iee763effe2439f0f160c1547640eca4bb9451a68
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Replace use of `shutil.copytree` with `copy_tree` and `install_tree` functions in `llnl.util.filesystem`.
- `copy_tree` copies without setting permissions. It should be used to copy files around in the build directory.
- `install_tree` copies files and sets permissions. It should be used to copy files into the installation directory.
- `install` and `copy` are analogous single-file functions.
- add more extensive tests for these functions
- update packages to use these functions.
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* zoltan: fix building with Intel compilers
- building with the Intel compilers may require explicit linking
with the Intel Fortran library (libifcore)
* simplify code; get rid of format() for static strings
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- dependency patching test didn't attempt to apply patches; just to see
whether they were on the spec.
- it applies the patch now and verifies that that patch was applied.
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* Change bzip2 download URL
* bzip2.org -> bzip.org
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* r-rots: new package
* r-rots: hash is a commit
* r-rots: dep types
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* r-argparse: new package
* r-argparse: dep types
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* r-genelendatabase: new package
* r-genelendatabase: git not url
* r-genelendatabase: add runtime deps and fix package type
* r-genelendatabase: dep type
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* r-glimma: new package
* r-glimma: git not url
* r-glimma: adding runtime deps
* r-glimma: dep types
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* r-ctc: new package
* r-ctc: fixing package directory name
* r-ctc: git not url
* r-ctc: dep types
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* Add smtools 1.9.
* Add hstlib 1.9.
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* Install sam.h and libbam.a for legacy apps.
* Install bam.h.
* Remove which(mkdir).
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* Add package for fasta
Add a package for the fasta sequence alignment tools.
The build system is novel (fasta is "venerable", so...). The source
tree includes nearly 50 variant Makefiles, the installer is expected
to pick one that's appropriate and then edit the "XDIR" variable to
specify the installation path. I can only test 64 bit darwin and
linux, so that's all I've included. I'm also assuming that every
64bit x86 system we'll see supports the SSE2 extensions. Other
situations can be dealt with when someone has a test case.
* Switch to MakefilePackage and clean up a bit
- Clean up the description
- Switch to MakefilePackage
- generalize the path to the chosen Makefile
- implement separate `edit`, `build`, and `install` phases.
* Fix call to format()
* Fix broken if logic
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* r-bindrcpp: add new version
* r-bindrcpp: version ordering and removing r version restriction
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* r-biasedurn: new package
* r-biasedurn: add list_url
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* r-amap: new package
* r-amap: add list_url
* r-amap: dep type
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* r-fastcluster: new package
* r-fastcluster: add list_url
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* packages/phist: new version 1.6.1
* packages/phist: depends on Python 3.x for generating Fortran and C++ bindings
* packages/phist: new version 1.7.2
* phist: depend on python@3 only for versions later than 1.7
* packages/phist: depend on python@3: rather than 3
* phist: python dependency is type='build', thans @adamjstewart
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* Branch with the meson build-system
* Fix build_environment for dual loads and add create code
* Add documentation
* Fixed option list
* Update build_system_guess for meson
* Fixed documentation errors
* Added meson to build and configure and updated documentation
* fix typos
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