| Age | Commit message (Collapse) | Author | Files | Lines |
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* Touch up string expansion.
I'm chasing this:
```
$ (module purge; spack install perl %gcc/5.4.0)
==> Error: No installed spec matches the hash: '%s'
```
There's something deeper going on, but the error message isn't helpful.
After this change it tells me this:
```
$ (module purge; spack install perl %gcc/5.4.0)
==> Error: No installed spec matches the hash: '5.4.0'
```
Which is weird because `5.4.0` is not a hash... Whatever is going on here, the error message needs to be fixed.
* Flake8 whitespace
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* trilinos: add DTK external package
* Making +dtk and ~tpetra conflict
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* fix parser
* Removed xfails
* cleaned up debug print statements
* make use of these changes in gcc
* Added comment explaining unreachable line, line left for added protection
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* Add latest version of CONVERGE
* Flake8 fixes
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* cairo: ensure that X support is disabled for variant "~X"
* cairo: explicitly enable X support for +X variant
* cairo: prefer "variant in spec" over spec.satisfies(variant)
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* Trailing whitespace cleanup
* Handcraft an install process for mummer (grumble)
Mummer punts on an installation step, they just build in and run from
the same directory.
Mummer also has various hardcoded paths built into it that allow it to
find other executables that it needs as well as its Perl library.
This updates the package to deal with this approach.
It patches the Makefile and scripts/Makefile so that the correct info
is fed to sed when it munges the perl scripts.
The install step is now finer grained and puts things where mummer
relatively wants to find them.
* Add perl dependency
* perl should be build/run dependency
* Fix whitespace
* Delete stray u at top of file
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* new package virtualgl, depends on mesa-glu but NOT on mesa, so added a variant to mesa-glu
* add comment on mesa variant of mesa-glu
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Two changes:
- It seems that Illumina version numbers are dotted and that the
dashed version in the 2.18... filename is an anomaly (based on the
names for 2.17.1.14 and 2.19.0). `url_for_version` does the right
thing for 2.18. It will need to be fixed when support for 2.19 is
added. 2.17 is no longer generally available so it gets a pass.
- Add version and hash for 2.17.1.14.
2.17.1.14 is no longer distributed. If you have a copy of the
source tarball, you can drop it into a local mirror w/ the name
mirror/bcl2fastq2/bcl2fastq2-2.17.1.14.zip and go from there.
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* magics: use filter_file to avoid using system python in all versions
* magics: add eccodes variant to switch between eccodes and grib-api
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* Add mpi support to R
* Add multiple precision math routines to R
* Add packages for r-ergm and it's dependents
* Fixed depends-on types
* Correct flake8 errors
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* plumed: fixed compilation on rhel6 with mvapich2 and gcc@5.4.0 (#77)
* plumed: prevent parallel compilation, as it breaks for the newest version
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* flex: create variant +lex that creates symlinks for lex and libl.{a,so}
* flex: enable variant +lex by default
* flex: use dso_suffix for portability; replace repetitive code with a loop
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ncview has to be compiled using the same compiler as netcdf.
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* adding mpifileutils
* mpifileutils: add +lustre variant
* mpifileutils: add variant for xattr
* mpifileutils: update to AutotoolsPackage
* mpifileutils: simplify and eliminate redundant make
* mpifileutils: drop unnecessary comments
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I need boost@1.54.0 for bcl2fastq2. I tested bcl2fastq2 using the
system compiler (gcc@4.8.5). My full build uses a spack-build
gcc@5.4.0.
boost@1.54.0 won't build. I found the answer
[here](https://github.com/hashdist/hashstack/issues/802) with the
details in [this upstream/boost
ticket](https://svn.boost.org/trac/boost/ticket/10125).
I've confirmed that these combo's build:
boost version| compiler
------------ | ------------------
boost@1.54.0 | gcc@4.8.5 (system)
boost@1.54.0 | gcc@5.4.0 (Spack)
boost@1.64.0 | gcc@5.5.0 (system)
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* Add mpi support to R
* Add multiple precision math routines to R
* Updated the URL to match the version
* Remove duplicate packages
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bcl2fastq2 needs this older version.
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added new md5
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* added openmpi support to meme
* openmpi is a link dependency which leverages r_path
* openmpi support now the default - meme does not have configure argument for mpi - if it's found then it's used
* added serial option and set mpi to not be default
* modified meme
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* Add the gnupg package and missing dependencies. Update versions of existing dependencies.
* this ended up in the wrong repo
* put versions back, remove uneeded function
* OK ;)
* autopep8
* typo on npth line
* whitespace
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* Add a new package for Open Babel
* Add post-installation tests, stolen from the fine folks at Homebrew
* Add patch to fix Python 3.6 support
* Add a more complete patch to get Python 3.6 support working
* Add patch to convert tabs to spaces in test script
testpdbformat.py contains mixed tabs and spaces
causing the unit tests to fail. With this patch,
all tests pass with flying colors.
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* benchmark: New package
* benchmark: Remove empty function
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* Add v1.1.26 and make crypto a variant
I need 1.1.26 for bcl2fastq2.
I also need to build it without crypto support.
* Initial support for bcl2fastq2
* Clean up commentary, messages, names
No substantial changes intended, just cleanup.
* fix flake8 and extra import
* The masked grammarian strikes again...
* Be normal (messages don't end in periods)
* When +crypto, add --with-crypto
Add `--with-crypto` to configure args when user hasn't explicitly set
`~crypto`.
* self.spec.satisfies is unsatisfying, in is in instead
See #4135, self.spec.satisfies has issues. @adamjstewart suggests
simply using in.
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* Move doc dependencies to requirements.txt for readthedocs
* Move sphinx to doc requirements.
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