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fixes #7239
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Fixes issue #7449
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* augustus: 3.3 package hash changed
* augustus: bamtools libraries now seem to be in lib64
* augustus: fix lib problem with older bamtools
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This re-adds the option to create and install unsigned tarballs, now
with the -u option (--unsigned) rather than the -y option.
This also changes the "keys" command, replacing the -y/--yes-to-all
option with the -t/--trust option (which has the same effect but is
more-clearly named).
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Fixes #7130
shutil.move expects a source path like "/x/y/" to be a directory and
fails if "/x/y" is a symlink. This invokes realpath on the source
path to avoid the issue.
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Also added missing deps for libpcap: bison and flex
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Fixes #7356
In some cases OperatingSystem (e.g. LinuxDistro) was getting
instantiated with a version that contains dashes. This breaks because
the concretizer later converts this value to a string and re-parses
it, and the '-' character is used to separate architecture components.
This adds a guard in the initializer to convert '-' to '_'.
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There are two additional releases moved to bintray.
Change to bintray for 1.64 and 1.65 as well since SF downloads are
too instable.
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This is needed when using system lua on RHEL and clones where lua
is installed in /usr/lib64. Note that the path entry for lua in
packages.yaml should specify the major/minor version of lua (since
this is used to calculate the lua lib directory)
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* json-c: Update to 0.13.1
0.12.1 does not compile with GCC 7.
* json-c: Add patch to make 0.12.1 build with gcc 7
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updated hoomd-blue to latest tagged release in repo. This version also supports newer gcc6 compilers, so added constraint for older version to avoid breaking existing installs.
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+ Newer versions of zoltan2 are doing test compiles that link to parmetis. If
these checks don't find `metis.h`, the check fails.
+ This small tweak ensures that the zoltan2 configure step can find `metis.h`
that is provided by spack.
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Generalized ExaSP2 Install to use glob due to changes in naming
convention between previous release and current development branch
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CudaPackage is always used as a mixin. As such it should inherit from
PackageBase, and not Package.
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Fixes #7237
Fixes #6404
Fixes #6418
Fixes #6369
Identify when binary relocation fails to remove all instances of the
source prefix (and report an error to the user unless they specify
-a to allow the old root to appear). This check occurs at two stages:
during "bincache create" all instances of the root are replaced with
a special placeholder string ("@@@@..."), and a failure occurs if the
root is detected at this point; when the binary package is extracted
there is a second check. This addresses #7237 and #6418.
This is intended to be compatible with previously-created binary
packages.
This also adds:
* Better error messages for "spack install --use-cache" (#6404)
* Faster relocation on Mac OS (using a single call to
install_name_tool for all files rather than a call for each file)
* Clean up when "buildcache create" fails (addresses #6369)
* Explicit error message when the spack instance extracting the binary
package uses a different install layout than the spack instance that
created the binary package (since this is currently not supported)
* Remove the option to create unsigned binary packages with -y
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For hdf5 `1.8.10` and some compilers, the hdf5 build system adds the
'-ansi' flag. hdf5 1.8.10 is not actually ansi compliant so this
adds a patch to modify the places where it violates ansi
compatibility (which ends up being a few comments).
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Add PnMPI, a dynamic MPI tool infrastructure that builds on top of the
PMPI interface.
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Add versions released after 3.5.0 (3.4.3, 3.5.1, and 3.6.x)
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SOSflow depends on MPI and pkg-config, but neither of these
dependencies are currently in the spack package, so this commit adds
them.
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