* Update digest for vim@8.0 tarball.
The digest appears to have changed.
The new digest value matches the value in their
[MD5SUMS](ftp://ftp.vim.org/pub/vim/unix/MD5SUMS)
file.
* Change ftp.vim.org -> github.com/vim/vim/archive
Vim seems to do weekly releases, but the name of the tarball on
ftp.vim.org doesn't change so we have to regularly play 'update the
digest' (aka Internet whack-a-mole).
This commit changes the url so that we are now downloading particular
versions from the Vim project's github archive.
I didn't walk back through of time to get all of the versions that
used to be explicit. I grabbed the final `7.4` and the current `8.0`
releases. If people need more we can add them.
* Add package for fastqc
This tool is a java mess. Their Way To Do It is to just copy the entire
tree into it's final resting place, make the perl script at the top
level executable and take it from there.
Yuck.
This package assumes that `set_executable` actually sets all the user
bits. If that change doesn't go in, then something equivalent needs to
be done.
* Use chmod to make fastqc executable
I haven't gotten any feedback on changing set-executable, so switch to
using chmod (from the cuda package).
* Flake8 cleanup
* Install files neatly, don't just copy top level of dir
Rather than blindly copying everything in the distribution, carefully
put the necessary bits into reasonable places. Neatness counts, etc...
This requires patching the `fastqc` perl script, so this commit adds a
patch file.
* Additional pep8 cleanup
* Let dependency handle adding jdk to PATH
* Flake8 cleanup
* Ensure that java is on PATH
I thought that the run dependency on the jdk would put
java on my PATH, but it does not appear to work.
For now, do it by hand.
* Customization for make targets in build and test phases for AutotoolsPackage
* Updated Blitz++ to use customized make build and test targets
* Removed flake8 error
* Removed make test customization, added make install customization, need to figure out issues with multiple make targets
* Changed build_targets and install_targets to normal attributes
* py-markdown: Add new package for python-markdown.
* py-markdown: Added restrictions on Python version.
* py-markdown: Removed upper-limit on compatible Python versions.
* py-markdown: Reinstated upper bound on Python version. Also fixed small formatting error.
* MakefilePackage: changed build_args and install_args for consistency with #2464
openblas: derives from MakefilePackage
* MakefilePackage: changed default edit behavior
* Add python cdo support
* Correct pypi url
* Corrected a blanck space that was failing CI
* Corrected url that was failing CI
* Following @alalazo indications, Write this line wrapping it around 80 chars to pass Travis
* Added cdo package depency
* Added support for xSDKTrilinos package
* Updated xsdktrilinos/package.py for PR review
* Added trilinos version # reqs to xsdktrilinos
* xsdktrilinos now uses CMakePackage
* Cleaned up xsdktrilinos/package.py
* Removed unused cxxflags from xsdktrilinos
* Removed unused sys import from xsdktrilinos
* clang: do xcode mockup iff requested by a package
* add a note
* add pkg to setup_custom_environment() and decide whether or not to use mockup XCode there based on the package
Supports installing both a "known version" of PETSc/PFlotran that works and
the develop/master branches of both packages
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: 4 hour
* update flux dependencies and package
* refinements from @adamjstewart
* fix flux document generation
The docbook-xsl package has been added, and correctly configures catalog
files to generate documentation correctly with asciidoc.
* Update emacs: current release, use our x11 bits
Add checksum for 25.1 release.
Rework the X support:
- use Spack's X11 bits
- add ability to specify an X toolkit (gtk or athena, default is gtk).
- change toolkit names to align with Emacs' configure usage.
* PEP8 cleanups.
* glib dependency should not be type=build
I'd like to blame that on a typo, but it's a few too many characters
for that to be viable. I'm not sure what I was thinking.
* Pass X variant down: emacs->pango->cairo
* X variants default to False, warn on bad toolkit
Change the X variants for emacs, pango and cairo to default to False.
Check that the toolkit is a valid choice and give a reasonable error if
not.
* Fix flake8 issue, reword warning text
* gtkplus needs to use +X variant for pango to work
In order for a useful variant of pango to be built into the spec I
needed to make the dependency on gtkplus explicitly specify it's X
variant. The X variant is the default, but that wasn't enough to make
it happy. Since it's happiness is the most imporant thing in the
world, this change! :)
yaml-cpp has a boost dependency, and according to [yaml-cpp
page](https://github.com/jbeder/yaml-cpp):
yaml-cpp 0.5.3 has been released! This is a bug fix release. It also
will be the last release that uses Boost; futures releases will require
C++11 instead.
See #2059 for background.
I'm unable to install `lmod` because lua-luafilesystem fails.
The luarocks install bits attempt to do a shallow clone of the luafilesystem
sources and the default git on my CentOS 7 test box (`git version 1.8.3.1`)
fails.
This adds a build dependency that ensures that a relatively modern git is
available.
* Update texlive digest value
While the discussion in #2494 progresses, this changes fixes the digest
values so that builds succeeed.
* Add warning that texlive is not repeatably installable
* Update OpenMPI to the AutotoolsPackage
* Add Java support to OpenMPI
* Fix missing commas
* Be more specific about what versions support what flags
* Revert description for thread_multiple variant
* py-rtree: Added package
* py-rtree = RTree (spatial indexing) data structure for Python
* libspatialindex = Underlying C library wrapped by py-rtree
* Flake8 and Copyright issues.
* Fix Python syntax error.
* Fixed dependency type error.
* Added new version, based on updates requested in upstream PR
* 1. Change cmake to build dependency.
2. Updated to CMakePackage
* Update go to 1.7.4 and 1.6.4 to fix security issues
The go team recently rolled out two releases to address security
issues. Details available on the [go release
site](https://golang.org/doc/devel/release.html).
This commit updates our explicitly supported versions.
It also includes a comment about two CentOS requirements (enable
user_namespace and ensure that the static c library is installed) that
are required for the pacakges to pass their tests.
* Flake8 cleanup
* Make X11 font install dir the font search default
We install the X11 fonts into `/share/fonts` beneath the font-util
installation prefix, but that directory is not one of the places that
the font subsystem searches.
This commit makes the fontconfig package depend on the font-util
package, and then it makes
```python
spec['font-util'].prefix + "/share/fonts"
```
be the fontconfig default font location.
Before this change, plots drawn by R have bounding boxes where font
glyphs should be. After this change fonts appear as expected.
* Enrich description string (trigger new CI run)
Improve the docstring for the package.
Also interested in the side effect of triggering another CI run
to see if the recent flake8 fix lets this PR run clean.
* Flake8 cleanups
* Update R&friends to use our X11 libs
Add `depends_on()`'s for R, Cairo, and Tk so that they use the Spack X
bits.
* Conditionalize X stuff on variant
Another step towards hooking up the X stuff.
There's still discussion happening on the issue, but this is better
than the 'everything must build with X' state that it was in.
- Added 'dap' and 'cdmremote' variants
This is based on work in #2324 with the following motivation:
Turn off DAP support by deafult. DAP requires curl, which has issues
with circular dependencies. For 95% of NetCDF users that do not need
DAP, turning it off avoides this rats nest of problems.
- Added 'parallel-netcdf' variant
To support work with parallel-netcdf
- Added 'shared' and 'static' build separation
* Update go-bootstrap package
The last C based Go src tree was the 1.4 series. For a while they
were cutting new releases so that people could bootstrap from a C only
system. Now they're recommending that you either use the release-1.4
branch or that you use a date-stamped tarball that they'll produce on
an as-needed basis.
There are several issues that keep 1.4.2 from building on a CentOS 7
system.
I've switched to the date based tarball.
The cgo bits were also mis-behaving, but they're not needed for the
bootstrapping task so I've set an environment variable that disables
them.
Details [on the install-from-source
page](https://golang.org/doc/install/source#go14) and these issues:
- https://github.com/golang/go/issues/17545
- https://github.com/golang/go/issues/16352.
* Update go package
Switched from pulling from the git repository to using the source
tarballs and added digest values.
Added support for 1.7.3, continued supporting 1.6.2, including patches
for a couple of problems (details in
[17545](https://github.com/golang/go/issues/17545) and
[17986](https://github.com/golang/go/issues/17986).
Dropped support for 1.5.4 and 1.4.2 because they no longer pass their
tests and the patches above to not apply.
* Updating SuperLU package file with ability to build version 4.3 (before they added cmake) with external blas or internal blas, and added capability to build the latest version 5.2.1 (with cmake) with internal blas.
* Updating SuperLU package file with suggested changes, i.e. reorganizing installation methods based on version, adding cmake dependency when necessary, removing any use of internal blas, and also adding fpic variant.
* Fixing flake8 failures.
* Update flex package url's and versions
The old sourceforge page for flex is now defunct. While version 2.6.0
still downloads fine, later versions are no longer hosted there.
Development continues on github. I've adjusted urls to point to this
new location.
In addition, from 2.6.0 onwards, a new naming scheme for releases seems
to have been adopted. I've created a url_for_version function to sort
this out.
* Change flex to an AutotoolsPackage
Also move the url_for_version function to the end of the package
definition.
* Implement the autoreconf function for flex
Adds the IceT compositing library from Sandia/Kitware.
Most default functionality needed for image compositing is
added, OpenGL acceleration for very large displays is disabled.
Downstream usage:
most VTK based software which supports parallel image compositing,
such as VisIt, Paraview and in our use-case
[ISAAC](https://github.com/ComputationalRadiationPhysics/isaac).
* Force the recipe for Lua to use the spack compiler.
I'm not sure how the old recipe worked for anyone. The Lua Makefiles set
`CC=gcc` and for my spack environment the first `gcc` found in my `PATH` is
`$SPACK_ROOT/lib/spack/env/gcc`, which is a directory. This caused the build
to fail. My change drops the `-std=gnu99`, but this option doesn't appear
to be required for a sucessful build.
* Preserve the '-std=gnu99' compile option.
* fix tau installation issue : setup_environment() is
called before install phase when 'Makefile.*' doesn't
exist (causing list index out of range error).
* Added detailed comment suggested by @alalazo
