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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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* perl6-slurp: new package
* perl-perl6-slurp: changing perl version dependency
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* libiberty: new package
The libiberty.a library from GNU binutils. Libiberty provides
demangling and support functions for the GNU toolchain.
This package uses the binutils tarfile but only builds the libiberty
subdirectory. This is useful for other packages that want the
demangling functions without the rest of binutils.
Add variant 'fpic' to compile with -fPIC.
Addresses some issues raised in PR #8806.
* libiberty: change variant name to 'pic'.
Allow libiberty to install the library in lib64 and don't try to copy
it to lib.
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* update of veloc & dep versions (replace old non-working versions)
* veloc doesn't work with gcc <= 4.9.3
* explicitly pass MPI to CMake for veloc build
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* elfutils: update version and add variants
Add latest version 0.173.
Add variants bzip2, xz and zlib to support reading compressed DWARF
sections, default True.
Move maintainer-mode to a variant with default False. This is only
useful for developers who want to modify the source for generated
files.
* Add dependency on zlib for reading compressed DWARF sections.
Add variants to use bzip2 and xz for compressed sections.
Remove maintainer mode and the dependencies on flex and bison.
These are not used for one-time builds.
Be sure to squash both the commits and the commit messages.
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Also fix dependency version in glvis package.
Fixes build errors mentioned in #8454.
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This commit continues the changes discussed in #8823 by creating a new
"apple-libunwind" placeholder package that supplies instructions for
how to configure packages.yaml to register Apple's libunwind
implementation with spack. This package also provides the "unwind"
virtual package representing the libunwind base API. The clang-apple
compiler version should be specified in packages.yaml so that
apple-unwind is only used with Apple's clang compiler, not the stock
LLVM compiler.
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This commit begins addressing the ideas discussed in #8823. The
libunwind library now provides the "unwind" virtual package, which
represents the "libunwind base API" common to LLVM libunwind, Apple's
LLVM libunwind, and non-GNU libunwind.
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* py-crossmap: needs py-setuptools
* py-crossmap: additional deps
* py-crossmap: make bx build/run
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* libtool: add version 'develop'.
* libtool: patch: correct parsing of compiler output when collecting predeps and postdeps.
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limited features (#8886)
* Switch to perf_event backend to allow user installations but with limited features.
* Fix flake8 issues
* Fix flake8 issues remove filter for INSTALL_CHOWN
* Incorporate the comments
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