* bowtie: new versions and %gcc@8.0.0: fix
Bowtie development shifted from Sourceforge to GitHub.
This commit adds several versions from GitHub, using the archive
tarballs. Note that the URL for 1.2.2 tarball is actually an '_p1'
tag....
It leaves the old 1.2 release download info in place.
Versions 1.2.0 and newer come from GitHub (I'm unsure if the 1.2 and
1.2.0 are equivalent).
Include a fix that enables %gcc@8.0.0: from:
https://github.com/BenLangmead/bowtie/issues/87
But, v1.2.2 has trouble with "newer" gcc's, so it only adds v1.2.2 for
%gcc@6.0.0:.
Feel free to tighten this. I know that:
- 1.2 -> 1.2.2 work with %gcc@5.5.0;
- 1.2 -> 1.2.1.1 work with %gcc@8.2.0; and
- 1.2.2 fails with %gcc@8.2.0
* Tighten to `conflicts('%gcc@8:', when='@1.2.2')`
* Point 1.2.2 and 1.2.2_p1 at the 1.2.2_p1 tarball
* Update package.py
Doxygen has migrated from a private SVN to GitHub. This PR updates the URLs and adds versioned commit hashes from GitHub. It also includes version 1.8.15 as the latest option.
* Update package.py
This enforces conventions that allow for correct handling of
multi-valued variants where specifying no value is an option,
and adds convenience functionality for specifying multi-valued
variants with conflicting sets of values. This also adds a notion
of "feature values" for variants, which are those that are understood
by the build system (e.g. those that would appear as configure
options). In more detail:
* Add documentation on variants to the packaging guide
* Forbid usage of '' or None as a possible variant value, in
particular as a default. To indicate choosing no value, the user
must explicitly define an option like 'none'. Without this,
multi-valued variants with default set to None were not parsable
from the command line (Fixes#6314)
* Add "disjoint_sets" function to support the declaration of
multi-valued variants with conflicting sets of options. For example
a variant "foo" with possible values "a", "b", and "c" where "c"
is exclusive of the other values ("foo=a,b" and "foo=c" are
valid but "foo=a,c" is not).
* Add "any_combination_of" function to support the declaration of
multi-valued variants where it is valid to choose none of the
values. This automatically defines "none" as an option (exclusive
with all other choices); this value does not appear when iterating
over the variant's values, for example in "with_or_without" (which
constructs autotools option strings from variant values).
* The "disjoint_sets" and "any_combination_of" methods return an
object which tracks the possible values. It is also possible to
indicate that some of these values do not correspond to options
understood by the package's build system, such that methods like
"with_or_without" will not define options for those values (this
occurs automatically for "none")
* Add documentation for usage of new functions for specifying
multi-valued variants
* PARALLEL-NETCDF: Update new version and location
PnetCDF-1.11.0 is released.
Also, the canonical download area has been changed and they are now using git, so can also provide a develop and master checkout.
One issue is that they changed the name of the tar files, so 1.11.0 needs special handling (and future versions will also).
All checksums at new location match the checksums from the old location.
* Address concerns in review
Added a `url_for_version` function to handle the name change in the tar files at version 1.11.0 and later. Updated description to match current shown on website. Updated `homepage` setting since it has recently moved.
* Address issues in second review
- in many files, regular strings were used in places where raw strings
should've been used.
- convert these to raw strings and get rid of new flake8 errors
* express: new version, use tags and fix gcc@6.0.0:
Express fails to build with gcc@6.0.0:.
The debian project [has a
fix](https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811859) but
they don't seem to have pushed it upstream.
I've opened an issue and a PR in eXpress repo, but eXpress isn't
actively developed, so I'm fixing it here too.
Since the Spack package was created, the eXpress team tagged their
releases. I've updated the package to use the tags.
Version 1.5.1 used to be known as 2015-11-29 (same commit). 1.5.2 is
new(er).
* Make flake8 happ{y,ier}
Apply fix from aspell issue (519) for a pointer dereference bug that
newer versions of gcc won't let slip past.
There hasn't been a release that includes the fix, this applies the
change to the latest release.
There's a missing break in a switch statement that newer gcc's
dislike.
Our #4696 simply disallowed newer gcc's.
This fixes the problem instead.
It's been [PR'ed upstream](https://github.com/agordon/fastx_toolkit/pull/22).
Tested with gcc@5.5.0 and gcc@8.2.0 on CentOS.
The most recent release of bamutil that we support uses an embedded
copy of libStatGen that has several issues that keep it from building
with newer releases of gcc.
They've all been fixed upstream and the latest release of bamutil
would pick them up if/when we support it. The build process has
changed though, plus my team needs *this* version.
This commit backports those fixes.
- cleanup patch.py:
- make patch.py constructors more understandable
- loosen coupling of patch.py with package
- in Package: make package_dir, module, and namespace class properties
- These were previously instance properties and couldn't be called from
directives, e.g. in patch.create()
- make them class properties so that they can be used in class definition
- also add some instance properties to delegate to class properties so
that prior usage on Package objects still works
* Always build glib with iconv
My early PR, #10165, which added a variant to configure glib to use
libiconv and defaulted to false, seems to be causing more trouble than
the knob is worth.
This changes the glib package to always depend on and use libiconv.
* libiconv depends_on is no longer conditional
* First draft for installing Stata 15
I've tested this works on my systems and gives a successful install of STATA 15.
* Flake8 cleanup
* Another Flake8
* Update license header
* Various improvements
A lot of improvements as suggested by @adamjstewart
* flake8 check
* paraview: adding variants to use external packages as internal do not compile
* paraview: add latest paraview version
* catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5
* catalyst: add latest catalyst version
* catalyst: added ParaView_DIR env variable to catalyst module
* add paraview, catalyst patches
- https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2433
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2436
* - Handle updated library paths for catalyst.
Versions 5.4 and old places libraries under a paraview subdirectory.
Eg, "lib/paraview-5.4", they are now placed directly under "lib"
- Minor code style cleanup
* Handle update library and python paths for ParaView-5.5
* catalyst: added ParaView_DIR path to spack_env
* BUG: applied the patch to the extracted catalyst source files
* paraview: added missing self to a member variable
* paraview: added Paraview_DIR to env
* catalyst: added osmesa variant
* of-catalyst: added new package
* add (FOAM,WM)_PROJECT_DIR also to spack_env environment
* depends on first openfoam release supporting catalyst
* openfoam-com: added missing env variables to module generation
* openfoam: fixed flake8 errors
* of-catalyst: added full variant and openfoam version dependency
* paraview: adding variants to use external packages as internal do not compile
* catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5
* catalyst: added ParaView_DIR env variable to catalyst module
* add paraview, catalyst patches
- https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2433
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2436
* - Handle updated library paths for catalyst.
Versions 5.4 and old places libraries under a paraview subdirectory.
Eg, "lib/paraview-5.4", they are now placed directly under "lib"
- Minor code style cleanup
* Handle update library and python paths for ParaView-5.5
* catalyst: added ParaView_DIR path to spack_env
* BUG: applied the patch to the extracted catalyst source files
* of-catalyst: added new package
* add (FOAM,WM)_PROJECT_DIR also to spack_env environment
* depends on first openfoam release supporting catalyst
* paraview: added missing self to a member variable
* openfoam-com: added missing env variables to module generation
* openfoam: fixed flake8 errors
* paraview: added Paraview_DIR to env
* catalyst: added osmesa variant
* of-catalyst: added full variant and openfoam version dependency
* paraview-catalyst: use always external expat and netcdf
* of-catalyst: reformatted package description
* paraview-catalyst: removed duplicated function
* catalyst: fixed flake8 error
* of-catalyst: fixed license header
* of-catalyst: minor changes
* of-catalyst: renamed gitrepo with git
* of-catalyst: removed useless gitrepo parameter
* Added a package for the MDAnalysis toolkit.
* Added python packages for breathe and m2r. Updated versions and URL
for the sphinx package.
* Fixed flake8 error
* Updated package requirements based on feedback.
* Updated with requirements from the setup.py
* Switched it back to pypi.
* py-pynio: new package
* Major re-working to add some of the optional dependencies, and make it conform to the approach described in the pynio setup.py comments. Much of it turned out to be too complicated, and I have added some notes in comments to explain this to future adventurers.
* Added variants for the hdf5 and gdal dependencies, which do seem to be genuinely optional. Also added absolute dependencies for jpeg and zlib, which setup.py says it wants, but were being found as the os-installed versions.
* Added descriptions for the new variants, and moved them to above the dependencies
Enable explicitly building glib with or without libiconv.
Heads up: if you build with ~iconv but there is something else in the
spec that includes libiconv then glib will *still* automagically
discover it and the build will fail.
* add the tfel package
* fix the tfel package
* fix the tfel package
* fix the tfel package
* Taking Adam J. Steward' remarks into account
* fixes trailing white spaces
* Update description
* Update dependencies following @adamjstewart adices
* Style fixes
* Style fixes
* Add java optional support
* add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice)
* flake8 fixes
* Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL)
* Style fixes
* Style fixes
* Fix test on python version
* Follow @adamjstewart advices: code is much cleaner and readable
* Small fix
* Small fix
* Add comment
* Small fix in cmake option
* try again (trying to overcome Travis CI unstable build process)
* CGNS: Allow use of git branch versions
Add ability to use git `master` and `develop` branches of the CGNS library. The `seacas` package sometimes needs to use the `master` or `develop` branch due to some new changes to the parallel I/O implementation in CGNS which has not yet been released.
* CGNS: Reorder to put newest version on top
Based on review comments, place newest version (develop) first in list.
* dyninst: patch to build dyninst with older gcc
Add 'v9.3.2-auto.patch'. This patch changes some 'auto t: type' usage
to the older but equivalent 'type.begin()'. This allows building
dyninst 9.3.2 with gcc 4.4 which doesn't support the newer syntax.
This patch is harmless with newer gcc.
* Fix typo in patch. (My bad for sloppy cut-and-paste.)
* Restrict the patch to gcc 4.7 and earlier. gcc 4.8 supports the newer
usage and thus doesn't need the patch.
* proper include & linking of libarchive
* due to linux headers, mfu can't build on mac
* hard code deps in configure line
rather than relying on pkg-config
* +xattr during config
* must also link the lib
* find mfu.h
* long lines
* Add thread count variant
Atlas automatically configures itself and optimizes to run with a fixed number of threads. This can be overridden during compile by setting a flag and atlas will tune itself to use the specified number, rather than all system CPUs.
Default value is the existing logic, autoconfigure.
* Fix Linting
* Another lint for longline
* Added rocksdb package
* Fixes based on @tristan0x and @pramodk comments
* Cleanup
* A couple minor fixes based on @adamjstewart 's advice
* Fixed flake8 errors
- previous removal of FOAM_EXT_LIBBIN (ThirdParty) from the environment
during the build could lead to the system scotch library being found
instead of the spack installation.
Avoid this largely cosmetic change to the setting in favour of
improved build robustness. These modifications will be largely
superfluous in the 1812 release anyhow.
- Split the patching algorithm into 'regular' and '@:1806' since the
next versions of openfoam will again need fewer patches.
- Add hook into foamCreateManpage to be used where available
* SEACAS: Add preliminary support for seacas package
* Eliminate leftover from package I copied from.
* And remove another stray line
Sorry, thought I had checked this better...
* SEACAS: Shorten long lines; fixup indentation
* SEACAS: Remove unused os import
* Add PLASMA version 18.11.0 and Lua variant (#9689)
* Add PLASMA 18.11.1 with optional Lua and test for headers
* New versions for a few python modules (#9969)
* py-jupyter-console: Add version 5.2.0
* py-jupyter-core: add version 4.4.0
* py-lxml: add version 4.2.5
* py-zmq: add version 17.1.2
* py-terminado: add version 0.8.1
* py-pexpect: add version 4.6.0
* py-pytables: add version 3.4.4
* SEACAS: Default to mpi on
* SEACAS: Modify to reduce variants
Instead of using an `allpkgs` or explicitly specifying each individual subset,
changed to minimize variants:
* By default, the exodus and IOSS libraries are built and a few
executables directly related to the IOSS library.
* variant `common` defaults to True and builds the "common" seacas
applications. This is based on my definition, so there may be
could be some discussion on what belongs here.
* variant `legacy` defaults to True and builds the remainder of the
seacas applications. These are still used, but mainly in more
esoteric areas. Might be better to default to False, but I wanted
default to just build everything which is what other SEACAS builds
always do...
Removed the `kokkos` variants for now as I need to do some more
thinking on how best to support this. Not often used currently,
so shouldn't be an issue.
Cleaned up other issues raised by Adam and found by me.
* SEACAS: Address flake8 issues
* SEACAS: Clean up variant package logic
Fixed package variant logic.
Consolidated some other variant handling logic
Other minor refactors for hopefully better readability
* SEACAS: Fix flake8 error
Missing whitespace around operator fixed.
* GDL: python integration fixes
* renamed python-related variants to follow the convention
* building the Python module requires patches currently targetting 0.9.8 othwerwise asking for the Python module *only* builds the Pyhton module
* building the python module also requires patching the vendored (with the GDL) antlr to be built as a shared library
* Typo
Co-Authored-By: rmsds <ricardo.d.silva@gmail.com>
* Rename embed-python variant to embed_python
* zoltan: only add gussed MPI libs if no MPI wrappers are used
- if MPI-wrappers are used for compilation, we can assume that
linking works without manually specifying MPI libs
(guessing may result in wrong libs, cf. #8979)
- thus, only guess the NPI libs and add them explicitly if no
MPI-wrappers are used
- use llnl.util.filesystem.find_libraries instead of a locally
defined routine to guess the MPI libs if needed
(cf. #8979)
* zoltan: rely on MPI-wrappers to know the required MPI libs
The sys_ustat.h.patch to file sanitizer_platform_limits_posix.cc from
PR #10046 does not apply cleanly to gcc 4.8 or 4.9 (or earlier).
GCC up to 4.8.x either don't have libsanitizer or else don't include
ustat.h in sanitizer_platform_limits_posix.cc.
GCC 4.9.x includes ustat.h, but needs a slightly different patch.
The patch applies to GCC 5.x up to 6.4, and 7.x up to 7.3 and also
8.1.0.
The patch is already included in the tar files for gcc 6.5.0, 7.4.0
and 8.2.0.
* flux-sched: fix compilation errors
configure was being run twice becuase the staging symlinks were
confusing autotools
mirror flux-core in building in a subdirectory to avoid other common
compilation problems, like the one in PR #3543
* flux-core: update dependencies
munge is no longer a dependency
provide hints for lua version so that `spack install flux-core` works
"out-of-the-box". Currently, when no explicity version is provided, the
concretizer attempts to use lua@5.3, which is invalid. Closes#10000
* Added a package for the MDAnalysis toolkit.
* Added Ninja as the generator for LBANN, Hydrogen, and Aluminum. Also
fixed a bug in how the Conduit variant is included in LBANN. Added
new versions for Hydrogen and LBANN.
* Updated lbann package so that the CMAKE parameters are set when the
variant is on and off.
Fix the install of the single header amalgate in catch2.
The public API for catch < 2.3.0 was "#include <catch.hpp>".
For 2.3.0+ it is "#include <catch2/catch.hpp>"
* Spades: Add version 3.13.0
In version 3.13.0 the CmakeLists.txt dir is at a different location than
in other versions. Versions up to 3.12.0 are located in "src" whereas
3.13.0 is a level deeper at "assemblers/src".
* Remove git and add new version hash
* Add mising QE releases.
* Update QE dependencies and conflicts.
* QE 6.3 install method requires a patch to work properly.
* include QE git develop branch
* QE HDF5 needs Fortran support. HDF5 versions prior to 1.8.16 leads to QE runtime errors.
* Number of MKL related conflicts for QE.
* Flake8 fixes for QE for hdf5 lines.
* Pass in all compilers properly to QE configure
* Fixed external BLAS/LAPACK linkage in QE.
* Library search was problematic in QE.
* Add section headings to QE package.
* External FFTW compatible libraries properly detected in QE.
* Flake8 fixes for QE
* QE configure defaults to False for ELPA, thus Spack package should as well.
* QE depends on FFTW3 provider instead of FFTW explictly.
* Primary QE repo is gitlab.com, not github.com. Github mirror lags behind gitlab site.
* Support both 6.3-backports branch and develop branch in QE.
* QE patch needed for proper MKL detection. MKL_ROOT is detected and preferred, still falls back to finding first MKL installation in /opt/intel.
* Use FFTW-API provider versioned interface for specify QE FFT dependency.
* QE FFTW conflicts no longer need thanks to FFTW-API provider versioned interface.
* Flake8 3.6.0 fix in support of https://github.com/spack/spack/pull/9853
* Fix QE conflict with ilp64 variant in support of https://github.com/spack/spack/pull/9853
* Remove custom url_for_version for QE package and use builtin url instead. In support of https://github.com/spack/spack/pull/9853
* Use FFTW builtin flags for QE instead of custom Python code. In support of https://github.com/spack/spack/pull/9853
* Fix typo in QE package comments. In support of https://github.com/spack/spack/pull/9853
* Future proof QE package patches in anticipation of QE >= 6.3.1. In support of https://github.com/spack/spack/pull/9853
* Adding version 2.0.12 of numactl.
* Adding new versions of hwloc.
* Adding NVML variant to hwloc.
* Adding gl variant to hwloc.
* Updating hwloc numactl dependency and gl dependency.
* Using gl virtual package in hwloc.
Clang 8.0 now supports openmp 4.5 and many commerical compilers also support
openmp >= 4.0. This commit removes the openmp version guard and rely on CMake
to throw errors out when openmp version requirement is not satisified.
It also add options for precision control.
* CGNS: Add option for 64-bit integers
Added the `int64` variant which will build the library using 64-bit integers for certain values. This gives the capability to have models with more than 2 billion cells and/or nodes.
Beginning with CGNS-3.1.0, two new typedef variables have been introduced to support 64-bit mode. The `cglong_t` typedef is always a 64-bit integer, and `cgsize_t` will be either a 32-bit or 64-bit integer depending on how the library was built. Many of the C functions in the MLL have been changed to to use `cgsize_t` instead of `int` in the arguments. These functions include any that may exceed the 2Gb limit of an` int`, e.g. zone dimensions, element data, boundary conditions, and connectivity. In Fortran, all integer data is taken to be `integer*4` for 32-bit and `integer*8` for 64-bit builds.
* EXODUS: Update version and dependencies
Allow pulling master version from git. Note that I hope to have better versioning "soon"
Add requirement to use Netcdf-4.6.1 or later as those versions no longer require changing the `maxdims` or `maxvars` defines in the netcdf.h include file. With these versions, Exodus can use an unmodified NetCDF. These versions of NetCDF are also better than previous versions (code quality, performance, robustness).
It is still possible to run exodusII with previous NetCDF versions, but I don't know how to specify that the dependency where maxdims/maxvars variants are only needed for versions prior to 4.6.0.
I also removed the explicit dependency on HDF5 as that dependency should be applied through the NetCDF dependency.
* Remove white-space on blank line
* Provide a new spackage for py-pint.
Pint is a Python package to define, operate and manipulate physical quantities:
the product of a numerical value and a unit of measurement. It allows arithmetic
operations between them and conversions from and to different
units. https://pint.readthedocs.io/en/latest/
* Switch hash from md5 to sha256.
Add several new versions so that current functionality can be accessed. Current version is now 1.5.13.
Update `url`, `list_url`, and `list_depth` so spack can find available versions
* PNETCDF: Update with current versions
Added latest versions. (1.10.0, 1.9.0, 1.8.1)
* PNETCDF: Revert version change in url
Reverted the change in the url variable version since not required.
* NETCDF: Add new versions and update url
Added the 4.6.2 version which was recently released.
Changed the url to point to the official Unidata site and added option to retrieve master version from git.
* NETCDF: checksum and version updates
Reverted back to use of previous URL. The `https://github.com/Unidata/netcdf-c/archive/v4.6.2.tar.gz` location is newer, but spack does not seem to be able to access all of the versions at that location -- only goes back to 4.5.0. Since several installations are still providing 4.4.0, thought it best to go back to previous url. However, it looks like the naming convention has changed since 4.6.2, so need to provide explicit url for 4.6.2. Probably best to go to a `url_for_version()` scheme if that naming convention stays in place?
This commit allows users to enable openmp, rendering, logging and mpi
in vtkm. Meanwhile, it adds support for cuda architecture selection.
[VTK-m 1.3 Release notes](https://gitlab.kitware.com/vtk/vtk-m/tags/v1.3.0)
Overhaul hpctoolkit to AutotoolsPackage and to build its dependencies
directly from spack instead of using hpctoolkit-externals.
Remove hpctoolkit-externals since it's no longer needed.
* py-jupyter-console: Add version 5.2.0
* py-jupyter-core: add version 4.4.0
* py-lxml: add version 4.2.5
* py-zmq: add version 17.1.2
* py-terminado: add version 0.8.1
* py-pexpect: add version 4.6.0
* py-pytables: add version 3.4.4
Fixes#994473c978d replaced a move with a copy, which cased rmdir to fail (as
it expects an empty directory). This switches to use `shutil.rmtree`
instead.
The latest OpenMPI release, v4.0.0, does not build with many GCC
variants. Since this is our default, a lot of users get hit.
Let's wait for some point releases.
* py-geopandas: New package, including packages for its dependencies
* Trailing whitespace removed, etc
* One more trailing whitespace
* Removed some extraneous dependencies. No idea why I thought I needed them, but it now builds fine without them.
* Added a variant +plotting, to include the dependencies required for plotting, as these are large-ish if not being used.
* Added explicit dependency on py-matplotlib
* r-geor: new package, and a couple of its dependencies
* Update to new copyright header
* Include the list_url for the R package archive dir
* Added explicit version ranges on dependencies, as per the relevant CRAN pages
* Correct dependency types in r-splancs.
* r-compositions: new package, including its dependencies
* Include the list_url for the R package archive dir
* Added explicit version ranges on dependencies, as per the relevant CRAN pages
Drop versions 8.1.x. These were > 5 years old, no other spack package
uses them, and they used autotools. Packages 'stat' and 'mitos' still
use 8.2.1, so we keep that.
Switch class Dyninst to CMakePackage.
Clean up how the versions depend on various packages. For example,
Dyninst used libelf up to 9.2, and then elfutils starting with 9.3.
This makes things easier going forward.
Add variant 'openmp' (default True) to enable openmp support for
ParseAPI. This was added in 10.0.0.
Add variant 'static' (default False) to also build static libraries.
This goes back to 9.1.0.
Disable cotire for the 9.3.x versions. Cotire has no real use in a
one-time build and can break parallel builds with both static and
shared libs.
* package: add asciidoctor gem
Faster, easier to use, less impossible to install correctly
implementation of asciidoc.
* ritual sacrifice of EOF whitespace to flake8
* openblas: enable parallel builds
* cp2k: enable parallel builds
* cp2k: fix building on multilib/Suse distros
use the actual directory path where files where installed to instead of
the default prefix+'/lib'
* cp2k: ensure we have a non-header-only libxsmm
* openblas: disable max num CPU detection on virtualized build
* cp2k: install data and set compiled-in DATA_DIR
* cp2k: make libxc an optional dependency (enabled by default)
* cp2k: link libint statically
* cp2k: declare statically linked library deps as type=build
* cp2k: add support for PGI compiler
* cp2k: rename smm=none to smm=blas for clarification
* cp2k: blacklist unsupported compilers
* cp2k: mark wannier90 a build-time dep since statically linked
* cp2k: make pexsi and elpa optional
* cp2k: add support for v6.1
* libxc: add version 4.2.3
* cp2k: use pkg-config to link properly to libxsmm
* cp2k: fix OpenMP support by making it explicit
Previously, CP2K accepted threaded ELPA or BLAS, leading to #(CPU) processes
being spawned even though no explicit OpenMP was requested. Now the
`popt` variant should truly be thread free while the `psmp` variant uses
threads also internally.
* cp2k: source tarballs moved to GitHub
* Add initial packages for citcoms and dependencies
* Ignore Pythia imports
* Add py-merlin package
* Add GMT package
* Fixes to get GMT working
* Get hc package building
* Get CitcomS 3.2.0 working
* Add fstrack package
* Fix hash
* added develop version in argobots package and added valgrind variant
* made autotools required only for develop version
* corrected style
* Added --disable-valgrind
Added --disable-valgrind to explicitly disable it when +valgrind isn't provided.
Pass cflags to configure so that configure gets the values from the
spack install line.
Disable -Werror so that we don't fail the build over a stray warning.
Libunwind releases are few and far between, so we need access to
recent snapshots from the git repository.
Pass cflags to configure so that make will respect the value from the
spack install line.
glib should not use the globally installed gtk-doc. Otherwise, gtk-doc
can fail with Python errors such as `ImportError: No module named site`.
This is due to the fact that Spack sets `PYTHONHOME`, which can confuse
the global Python installation that is used by gtk-doc.
- Add version 2.1.0
- Now that #9264 has been merged, gplates seems to build fine with newer
versions of gcc (tested with gcc@8)
- When using the ninja generator, gplates can be built in parallel
* Update Dyninst package file for TBB dependency
Dyninst master and 10.0 release
versions require the tbb package. This mod
updates the tbb versions adding the one that
dyninst uses and adds the required spack package
changes to dyninst/package.py.
* Put new version of tbb in proper location, per reviewer comment.
* Only depend on tbb if building the development version.
* Changes for the release of Dyninst 10.0.0
* Introduce FFTW2 and FFT3 providers for Intel-MKL and FFTW Spack packages.
* make fftw default package for fftw-api virtual package
* virtual package test assertion now provides location of default virtual packages.
* Change name of virtual package to fftw-api and used versioned interface.
- `spack.util.environment` is the new home for routines that modify
environment variables.
- This is to make room for `spack.environment` to contain new routines
for dealing with spack environments
* modified tutorial packages
* update hint in hdf5 tutorial file (typo for suggested argument)
* add repo.yaml to tutorial repository
* update tutorial docs to refer user to tutorial package repository
* flake edits
* recommend site scope vs. defaults
* you don't specify the repo's name when adding a repo, just the path
* henson: new package
* henson: change github path to henson-insitu
* henson: make mpi-wrappers=off by default
* henson: remove unsued variable and spaces to make linter happy
* henson: rename version master to develop
* xeus: new package
cppzmq: add version 4.3.0
zeromq: make libsodium optional, on by default
* xeus: add patch so it builds, add new version
nlohmann-json: add more versions
cryptopp: add more versions
* xeus: flake8
* xeus: fix license
* Provide a newer doxygen version.
+ Also provide a patch that allows collaboration diagrams to work properly with
C++ std::shared_ptr<T>. Ref:
6c380ba91a
* Add the setting of CBTF_MPI_IMPLEMENTATION to the cbtf-krell
and openspeeedshop package files, so that the mpi implementation
can be found by the tool. This allows users to not have to
set this manually if only one mpi implementation is specified
in the build.
* Update version ranges for dependencies of cbtf packages
* GCC: constrain version 6, 7, and 8 to build with ISL version at
most 0.18
* GCC version 9 (not yet released) will be compatible with
ISL version 0.20 so future GCC releases are constrained to build
with ISL version at most 0.20
* ISL: Add v0.15, replace all md5 sums with sha256 sums for ISL
versions
* GCC versions before 6 were constrained to build with ISL 0.14
but have been confirmed to work with ISL 0.15
* GCC: Place an upper bound on GCC's mpfr dependency
* packages/phist: add variant 'fortran' to enable/disable building the Fortran bindings
* xsdk: add phist
* packages/xsdk: add a comment reg. updating phist dependency
* packages/phist: +fortran variant is only for versions 1.7:
* packages/phist: update comments
* xsdk: forgot to specify kernel library for phist (picked tpetra, assuming trilinos+tpetra will be installed)
* packages/phist: add variant 'openmp' to allow disabling OpenMP
* phist: fix compile error due to missing -lm
* flake8: fix warnings
* packages/phist: fix cmake flag: XSDK_ENABLE_Fortran (rather than XSDK_BUILD_Fortran)
* packages/phist: allow disabling building the scamac matrix generator (which causes trouble on some systems)
* packages/xsdk: disable scamac within phist because it caused problems for @balay and is not essential for now
* packages/phist: actually disable scamac via cmake if ~scamac
* phist: disable openmp from xsdk
This commit overhauls the libMesh package script in a number of ways:
* We now inherit from AutotoolsPackage.
* libMesh contains about a dozen third-party dependencies that can
only be provided by the copy bundled with libMesh. This patch
enumerates all such bundled dependencies and disables all of them
by default.
* libMesh supports compilation with external installations of boost,
eigen, hdf5, slepc, and tbb; this patch adds all of them to
package.py.
* libMesh will look for a few system executables (xz, bzip, gdb) by
default. This is now disabled.
* libMesh will now used a copy of perl installed by spack instead of
trying to find the system copy.
* Compilation with non-system MPI installations requires an additional
flag (--with-mpi=); this has been added.
The install() function in the miniconda2 & 3 package.py files referenced
self.url, which is hard-coded to 4.3.11. That's not necessary the
version that the user requested, though. Changed the install() function
to reference self.stage.archive_file. Also added a version string for
4.5.11.
Move suite-sparse gcc version constraint from dealii to suite-sparse
package and update it (gcc 4.9 is required as of version 5.2.0 rather
than 5.1.0). The constraint is now expressed as a conflict rather
than a dependency.
* updated visit package
* make hdf5 and silo conflict with ~gui variant
* Changed parallel => mpi and quotes in description
* Corrected +mpi variant in VisIt package
The previous commit introduced a bug (+parallel variant wasn't renamed +mpi), and the +mpi variant wasn't True by default. This is corrected.
arrow: add missing dependency for python build
The Parquet library moved into the Arrow organisation, hence add a
parquet flavor and adapt dependencies.
* flux: ensure git tags are always available
previous `--unshallow` would only run when `--depth 0` was used. If
1--single-branch` was used, then the `.git/shallow` file would not exist
and `--unshallow` would not work.
add v0.6.0 and update dependencies accordingly
update dependencies to match latest flux versions
adds support for python 3
increases precision of czmq version required for older flux versions
adds new lz4 dependency
* Add stat version 4.0.1
* stat 4.0.1: requires py-xdot
* stat versions at or above 4.0.0 dont require python 2 (it still
requires python but can build with 2 or 3)
* stat versions at or above 4.0.0 dont require py-pygtk and py-enum34
* Replace py-xdot version 0.9.1 with 1.0
* py-xdot: use lib directory vs. lib64 for atk dependency
* Add version 18.9.0 (w/CMake)
* Add version dependent install methods to handle transition from
Make-based package (17.1) to CMake-based package, using the NEST
package as an example
* Remove unnecessary build_targets method for older Make-based
version
* Don't retrieve just the C/Fortran interfaces for netlib-lapack -
blas/lapack libs are now handled the same for all implementations
* Remove netlib-lapack detection patch
* add new version 3.1.0
* add conflict for parmetis without mpi
* strumpack >= 3.1.0 uses -DTPL_ENABLE_<package> instead of
-DSTRUMPACK_USE_<package>
* require cmake at least 3.2
* Added support for the Aluminum library to LBANN and Hydrogen. Also
fixed several bugs in the grouping of dependencies of both packages.
* Updated the conduit package to have the proper dependency on the
python variant.
* Added new versions for NCCL
* Fixed a bug in how Hydrogen set the path for OpenBLAS.
* Added support for conduit in LBANN.
* vtk: add variants for Xdmf IO support, ffmpeg support, and MPI
* vtk: depends on boost when Xdmf support is enabled
* vtk: add backported patch for python3.7
* vtk: New policy only for cmake >= 3.12
* mesa: add py-argparse dependency (for build)
* lz4: use MOREFLAGS instead of LIBS to add -lrt
scalasca actually requires cubew, not the full cube bundle. However,
cubew@4.4 causes the build of previous versions to fail because there is
no cube-config script anymore.
- remove the old LGPL license headers from all files in Spack
- add SPDX headers to all files
- core and most packages are (Apache-2.0 OR MIT)
- a very small number of remaining packages are LGPL-2.1-only
- This is bundled into one commit to make it easy to revert if we do get
consent from peetsv's company to relicense these contributions.
- Revert "dialign-tx adding patch for gcc@5.4.0 (#6413)"
- This reverts commit 09eeb991a2.
- Remove the following LGPL-2.1 packages because we have not gotten
consent to relicense them:
- fast-gbs
- igv
- metasv
- perl-xml-libxml
- py-cnvkit
- py-crossmap
- py-pybedtools
- py-pyfaidx
- py-pyvcf
- py-vmd-python
- r-cghflasso
- r-dismo
- r-proc
- r-spatial
- r-utf8
* omega-h: fix dependencies
1. Remove Gmodel altogether. Omega_h doesn't
actually call Gmodel for anything, it was
more or less just doing additional unit
testing for Gmodel
2. Make Trilinos off by default. Most codes do
not need the ParameterList interface, and
Kokkos through Trilinos is not well explored
in Spack
3. Use modern CMake style to choose the zlib
dependency
getopts.pl is not listed as a Spack dependency of sspace-standard,
so without this change, this package was only working on systems
where getopts.pl was already installed.
* Added conflict in Trilinos for STK when building as shared on Darwin.
* Created shared variant for Nalu and Nalu-Wind to automatically build
Trilinos as static library on Darwin.
* Moved ECP tags from Nalu to Nalu-Wind (the latter is the official
ECP application).
* Remove py-setuptools dependency from py-spyder (fixes#9205)
* Add constraint on transitive qt dependency to build with webkit
extension (required for this package)
* Update pycodestyle dependency constraints
* reordered dependencies (py-zmq, py-chardet) to confirm to the
ordering in setup.py
* superlu-dist: Update package.py for superlu-dist v6.0.0 using CMake
* superlu_dist: Update the header of package.py
* Specify lapack_blas and DCMAKE_INSTALL_LIBDIR
disable support for superlu-dist before v5
current stable releases of PETSc and Trilinos have non-overlapping
requirements on Superlu-dist. For now turn it off by default in
Trilinos, which requires older versions.
* bison: Add missing build dependencies
bison also depends on cmp, which is currently not available in Spack.
* help2man: Add missing build dependency
* m4: Fix build with newer versions of glibc
* openssl: Add missing build dependency
openssl's configure script is actually a Perl script.
* texinfo: Add missing perl dependency
* diffutils: New package
* findutils: Fix build with newer versions of glibc
* mvapich2, mpich: Add missing findutils dependency
* Add option to disable threads for Geant4
* Add option to enable DagMC in MOAB
* Explicitly add OFF flag when threading is disabled
* Fix unintentional enabling of C++14 in Geant4
The following always evaluated to True:
'c++14' or 'c++1y' in spec:
* Push default flag handlers into module scope
* Preserve backwards compatibility of builtin flag handler names
Ensure Spack continues to work for packages using the `Package.env_flags` idiom and equivalent.
* update docs and tests to match
* Update packages to match new syntax
* xerces-c: Add variant for choice of transcoder (gnuiconv, iconv, icu,
macos, windows). It's important to specify a --enable-transcoder
option on the configure line or else xerces may make a different
choice when multiple transcoders are available.
* Pass the compile flags to configure. For cflags and cxxflags, this is
necessary to respect the value from the spack install line.
Otherwise, xerces (and any autotools package) will choose a default
value that overrides the spack compiler wrapper.
* Add xerces version 3.2.2.
* icu4c needs the --enable-rpath configure option on Darwin
* New package: tldd
* https://gitlab.com/miscripts/tldd
* Improvements
* make it prefetchable by specifying a hash based version
* specify the constraints on pstreams versions (from INSTALL)
* Improvements
* Make it a Makefile Package and only overwrite the install_targets
* Remove the URL as there's really no downloadable 'tar ball' version
* Initial commit for new package STRUMPACK, a linear solver library.
* Update to STRUMPACK version 3.0.3.
This adds a check for OpenMP task priority support (since OpenMP 4.5)
* treesub: new package starting at 0.2
* treesub: fix ant build, add exec script
* treesub: use portable octal format
* treesub: add license header
not sure how it even went missing.
The build process of Catalyst requires Python at build time (see line 86) even when the +python variant is not selected.
When the +python variant is selected, Python becomes required at build, link, and run time. There doesn't seem to be any restriction on the version of Python required when +python is not selected.
* Fix: bug in VTK package
Fix for issue 9423 (https://github.com/spack/spack/issues/9423): compilers other than clang don't have the `is_apple` property.
* VTK package: removing trailing whitespace
So flake8 stops complaining.
* Release 2.0 of the ECP Proxy Apps suite
* update laghos version
* make install dir structure consistent across all ecp-proxy-apps
* minor
* update macsio version
* patching p4est to select the proper openmp lib
* For when compiler.openmp_flag isn't supported
* authored by @nrichart, I only tested it
* Adding openmp variant
Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>
Building bazel yielded errors since commit cd9691d. The first commit
fixes the build for older bazel versions, the second commit adds new
versions and ports the patches to these versions.
* petsc: add new versions 3.9.4 and 3.10.0
* petsc:update superlu_dist dependency for version 3.10 [might have to change this later for xsdk]
* slepc: add in new releases 3.9.2 and 3.10.0
* Catch2: 2.3.0+
Add the latest two releases of Catch2.
In 2.3.0+, the include changed to a future-proof
`<catch2/catch.hpp>` path which dependent projects will break upon.
* openPMD-api: Catch2 2.3.0+
openPMD-api just updated to use the new, future-proof Catch2
headers `<catch2/catch.hpp>`.
Adds 'code' to the list of suffixes that are excluded from version
parsing of URLs, such that if a URL contains the string
'cistem-1.0.0-beta-source-code', a version X will substitute in to
produce a URL with cistem-X-source-code ('source' was already excluded).
The 'cistem' package version is updated to make use of this (and fix
a fetching bug with the cistem package). A unit test is added to check
this parsing case.
Turns out that there was a configury problem in libhio
which caused issues building the package on non-cray
systems, aka when using mpicc and friends.
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
This commit adds a patch that prevents the package from hanging. The package would hang because CMakeLists would look for a system MPI. This patch changes the behavior.
* add version 1.3.0
* change build parameters, install process
* mxnet will not compile against spack's nnvm and dmlc so we must use
the distributions provided by the source package.
* also removed 'bin' installation as mxnet is just a shared library.
* improve BLAS linking
* remove unnecessary args
* added variant for python bindings
* r-nloptr: Explicit depends_on(nlopt). Previously there was a hidden dependency, masked by the package's configure script.
* r-nloptr: Change spelling of variables to satisfy pyflake8
* r-nloptr: Break a long line to satisfy pyflake8
* r-nloptr: larger indent on continuation, to satisfy pyflake8
* r-nloptr: another attempt at larger indent on continuation, to satisfy pyflake8
* r-nloptr: now a smaller indent on continuation, to satisfy pyflake8
* r-nloptr: Another attempt at right amount of indent.
* r-nloptr: Another attempt at right amount of indent.
* Use the correct attributes for finding the nlopt includes and libs.
* Lines too long, split into pieces
This patch does not apply cleanly anymore and breaks clang/Mac builds
balay@asterix /home/balay/git-repo/github/trilinos (develop=)
$ patch -Np1 < /home/balay/git-repo/github/spack/var/spack/repos/builtin/packages/trilinos/xlf_tpetra.patch
can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- a/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
|+++ b/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
--------------------------
File to patch:
* Added jdk version, added r-ks and r-multicool packages, made some r packages less conservative in their r version requirement
* flake8 fixes
* fix formatting in jdk version cmd
* Added type=('build', 'run') to some R package dependencies,
added some missing dependencies to r-ks. Thanks Adam.
* fix flake8 error
Due to an internal bug regarding the handling of scalars
(ndim must be 0) in numpy prior to 1.15.0, openPMD-api
will require the latest numpy 1.15+.
Since there is a small regression with datetime pickling in
1.15.0 from the required fix and spack only packages 1.15.1
currently, we depend on 1.15.1 in the recipe.
* add 5 most recent versions and git master branch
* add trilinos, gmodel, throw, examples, optimize, symbols,
and warnings variants
* disable XSDK so that Trilinos dependencies are found.
* added py-pycogent
* flake8 edits
* added type=('build', 'run') to deps, changed py-matplotlib and mpi4py
* changed python min version to 2.6
* fixed cython to py-cython dep
* fixed mpi4py to py-mpi4py
* fixed py-sqlalchemy
* added 1.5.3 version
* fixed version 1.5.3 install
* changed deps names to reflect convention
* added variants
* changed download URL and added SHA256 hash
* fixed deps
* added github url for 1.5.3
* removed unneeded deps
* doesn't require py-setuptools
* fixed url and added py-setuptools specific to version 1.9
* fixed variant names and changed cython to normal dependency instead of variant
* removed cython dep, failed to build when it was present. Changed variant name 'mpi4py' to 'mpi' and changed sqlalchemy variant name to mpi
* fixed dependencies and added py-pymysql dep
* added setup-environment step
* changed download url for 1.5.3 to pypi
* fixed flake8 issue
* updated
* added changes
* Addition of latest maestrowf releases.
* Addition of filelock to dependencies.
* Addition of when clause to depends_on for filelock and tabulate.
* Correction of the tar url.
Update the version numbers and now depend on
the develop version of dyninst because of a
feature in openspeedshop depends on new code
in the dyninst develop tree. Without dyninst
develop, openspeedshop will not build.
* py-matplotlib: Add patch to fix FreeType library detection
Adds patch to add $CPATH to locations searched for FreeType header file
Patch has been upstreamed:
https://github.com/matplotlib/matplotlib/pull/11457
* py-matplotlib: Add patch to fix FreeType library detection
* Make patch only apply to versin 2.2.2 (as already upstreamed)
* Fix flake8 format issue
* py-matplotlib: add range to freetype patch
* py-matplotlib: whitespace
1. I presently get errors of the sort
==> Error: KeyError: 'No spec with name mpi in silo@4.10.2%gcc@8.1.0+fortran+mpi
[...]
$HOME/spack/var/spack/repos/builtin/packages/silo/package.py:84, in configure_args:
81 'FCFLAGS={0}'.format(self.compiler.pic_flag)]
82
83 if '+mpi' in self.spec:
>> 84 config_args.append('CC=%s' % self.spec['mpi'].mpicc)
85 config_args.append('CXX=%s' % self.spec['mpi'].mpicxx)
86 config_args.append('FC=%s' % self.spec['mpi'].mpifc)
without the extra explicit MPI dependency.
2. Silo uses zlib, so we should explicitly depend on it.
Added SUNDIALS 3.1.2 and 4.0.0-dev.1 versions and relevant dependencies
(3.1.2 requires CMake 2.8.12). Updated all versions to use sha256 hashes.
Addressed issue specific to clang compiler on macOS.
* Addition of py-filelock and first page of versions.
* Addition of setup.py patch for setuptools.
* flake8 failure fixes.
* Reduced url declaration to a single line.
* Correction to py-filelock to use distutils.
Consolidate prefix calculation logic for intel packages into the
IntelPackage class.
Add documentation on installing Intel packages with Spack an
(alternatively) adding them as external packages in Spack.
Add variant 'nls' for native language support with default True.
The default inside binutils was always on, but this gives a way of
turning it off, if desired.
Adjust the dependencies. Flex is never used for a one-time build.
Bison and m4 should not be needed, except that prior to rev 2.30, gold
did not include its generated files, so bison is needed when +gold.
Drop configure option --enable-interwork. This option does not exist.
This PR includes the following changes:
* Added JDK 10
* Changed the JDK version numbers according to the consensus reached
in #2284
* Added spec['java'].home and spec['java'].libs, similar to #3367
(JDK and IcedTea)
* Added a check to prevent people from installing JDK on macOS
* Set CLASSPATH for packages depending on Java (JDK and IcedTea)
* Add TODO for extending virtual packages (not currently possible)
* Add TODO for adding Java dependents to views
* Add TODO for packages which extend multiple packages (e.g. Java
and Python)
The Trilinos/stk configuration is pretty Nalu specific right
now (and is acknowledged as such in a comment in package.py), and
this commit enables a module that Nalu will be needing.
* r-goseq: new package
* r-goseq: git not url
* r-goseq: adding packages needed at runtime
* r-goseq: package type
* r-goseq: dep types
* r-goseq: one more
- OpenFOAM-v1806/wmake/scripts/have_kahip must check
$KAHIP_ARCH_PATH instead of $METIS_ARCH_PATH to detect the KAHIB
library
- use a local patch file until the issue is hopefully fixed upstream
* Add latest release 3.0.2
https://www.open-mpi.org/software/ompi/v3.0/:x
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
* 1. Added correct md5 sum for Open MPI v3.1.1 (https://www.open-mpi.org//software/ompi/v3.1/)
2. Made v3.1.1 the default version
3. Added libmpiso versions for v3.1.1 and 3.0.2
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
* Added Open MPI v2.14 to version list; Tested build; Added libmpi.so version
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
* Open MPI 3.1.2 built and tested
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
* libquo: Packaging updates.
This commit accomplishes a few things:
* Changes distribution fetch source
* Removes a deprecated version (1.2.9)
* Changes dependencies based on version type
* Adds a custom autoreconf stage when using the 'develop' version,
omitting this step when building from a distribution
* Reintroduce v1.2.9.
leveldb headers are typically included via <leveldb/c.h>. The migration
to install_tree in 73c978ddd9 caused the
headers to end up in prefix.include, which breaks existing applications.
* Add latest release 3.0.2
https://www.open-mpi.org/software/ompi/v3.0/:x
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
* 1. Added correct md5 sum for Open MPI v3.1.1 (https://www.open-mpi.org//software/ompi/v3.1/)
2. Made v3.1.1 the default version
3. Added libmpiso versions for v3.1.1 and 3.0.2
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
* Added Open MPI v2.14 to version list; Tested build; Added libmpi.so version
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
* QMCPACK now supports QE 6.3. Dropped QE 5.3 due to incompatibilities.
* QMCPACK general clean-up of depends_on.
* Add QMCPACK 3.5.0
* More robust support of MKL detection in QMCPACK.
Fixes#9001#8289 added support for install_tree and copy_tree to merge into an existing
directory structure. However, it did not properly handle relative symlinks and
also removed support for the 'ignore' keyword. Additionally, some of the tests
were overly-strict when checking the permissions on the copied files.
This updates the install_tree/copy_tree methods and their tests:
* copy_tree/install_tree now preserve relative link targets (if the symlink in the
source directory structure is relative, the symlink created in the destination
will be relative)
* Added support for 'ignore' argument back to copy_tree/install_tree (removed
in #8289). It is no longer the object output by shutil.ignore_patterns: you pass a
function that accepts a path relative to the source and returns whether that
path should be copied.
* The openfoam packages (currently the only ones making use of the 'ignore'
argument) are updated for the new API
* When a symlink target is absolute, copy_tree and install_tree now rewrite the
source prefix to be the destination prefix
* copy_tree tests no longer check permissions: copy_tree doesn't enforce
anything about permissions so its tests don't check for that
* install_tree tests no longer check for exact permission matching since it can add
file permissions
* 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.
* 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.
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.
* 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
- 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.
* r-genelendatabase: new package
* r-genelendatabase: git not url
* r-genelendatabase: add runtime deps and fix package type
* r-genelendatabase: dep type
* 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
