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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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* perl6-slurp: new package
* perl-perl6-slurp: changing perl version dependency
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- cc cleanup caused a parsing regression in flag handling
- We added proper quoting to array expansions, but flag variables were
never actually converted to arrays. Old code relied on this.
This commit:
- Adds reads to convert flags to arrays.
- Makes the cc test check for improper space handling to prevent future
regressions.
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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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- flags were prepended in reverse order to args, but this makes it hard
to see what order they'll be in on the final command line.
- add them in the order they'll appear to make cc easier to maintain.
- simplify code for assembling the command line
- fix separator used in SPACK_SYSTEM_DIRS test
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- Add back ccache support to the wrapper.
- Add a regression test to make sure ccache is working properly.
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- This corrects most of the issues found by shellcheck
- This also uses ':' as the delimiter for SPACK_SYSTEM_DIRS, for
consistency with other variables.
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- filtering using sed causes most builds to slow down quite a bit, as the
compiler wrapper has to run sed many times, and *it* runs many times
- do the system directory parsing directly in bash
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- Add tests to ensure that RPATHs are not added in cc mode, which can
cause some builds to fail.
- Change cc.py to use pytest style
- Instead of writing out all the flags, break the flags down into
variables so that it's easy to read what each test is supposed to
check. This should make cc.py more maintainable in the future.
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- Adding -L and -Wl,-rpath to compile-only command lines ("cc mode" or
"-c") causes clang (if not also other compilers) to emit warnings that
confuse configure systems.
- Clang will print warnings about unused command-line arguments.
- This fix ensures that -L and -Wl,-rpath are not added if the compile
line is just building an object file with -c
- This also cleans up the cc script in several places.
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Spack currently prepends include paths, library paths, and rpaths to the
compile line. This causes problems when a header or library in the package
has the same name as one exported by one of its dependencies. The
*dependency's* header will be preferred over the package's, which is not
what most builds expect. This also breaks some of our production codes.
This restores the original cc behavior (from *very* early Spack) of parsing
compiler arguments out by type (`-L`, `-I`, `-Wl,-rpath`) and reconstituting
the full command at the end.
`<includes> <other_args> <library dirs> <rpaths>`
This differs from the original behavior in one significant way, though: it
*appends* the library arguments so that dependency libraries do not shadow
those in the build.
This is safe because semantics aren't affected by *interleaving* `-I`, `-L`,
and `-Wl,-rpath` arguments with others, only with each other (so the order of
two `-L` args affects the search path, but we search for all libraries on the
command line using the same search path).
We preserve the following:
1. Any system directory in the paths will be listed last.
2. The root package's include/library/RPATH flags come before flags of the
same type for any dependency.
3. Order will be preserved within flags passed by the build (except system
paths, which are moved to be last)
4. Flags for dependencies will appear between the root flags and the system
flags, and the flags for any dependency will come before those for *its*
dependencies (this is for completeness -- we already guarantee this in
`build_environment.py`)
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