This is my first cut at a package to support nextflow. It's also my
first package. It works, but has issues. I'm going to submit a pull
request and get some coaching on how to deal with it.
One issue particular: if I install, then uninstall, then try to install
again (which uses the cached copy of the "distribution file"), it
explodes.
WIP: I started trying to build gtkplus@3.20, but this package has many more
dependencies than v2 and it requires newer versions of existing packages. This
commit provides updates for 5 packages that are required by GTK+3. This is not
the complete set of changes required for GTK+3.
atk - move default version from 2.14 -> 2.20.
glib - move default version from 2.42 -> 2.49
- v2.49 requires pcre+utf as a new dependency.
pcre - if variant +utf is selected, add '--enable-unicode-properties' to the
configure options.
libepoxy - new package to spack
- manages OpenGL function pointers.
pango - move default version from 1.36 -> 1.40
Add a package for [tree](http://mama.indstate.edu/users/ice/tree/).
It has a Makefile that hardcodes a prefix and some CFLAGS. Used
filter_file to:
- set the make variable *prefix* to `prefix`; and
- comment out their CFLAGS, just use ours....
It installs, runs on CentOS7, and uninstalls cleanly.
With the addition of dependency types and with `py-setuptools` set as
type='build' there are more packages that need to have `py-setuptools`
added as a dependency.
This PR adds that dependency for the following packages:
- py-h5py
- py-networkx
- py-pytables
- py-scikit-image
This PR adds the `nolink` dependency type to r- package dependencies.
This is needed due to the new dependency types in Spack. A couple of
packages were updated with new versions as well.
This commit introduces a mechanism to insure that R package dependencies
are built with the Spack compiler wrapper. A copy of Makeconf is made
before `filter_compilers` is called. This is then pointed to by the
R_MAKEVARS_SITE environment variable set up in
`setup_dependent_environment`. With this the normal compilers are used
outside of spack and the spack wrapper compilers are used inside of
spack.
This commit also standardizes on the `join_path` call. It also sets the
commented build command to reflect what is actually used with the newer
string formatting.
A while ago I was asked to convert packages to all lowercase. That was
done but some dependencies did not get converted in the specification.
This commit fixes that as well as a couple of urls that need to be made
explicit and a missing dependency on jdk.
- OpenSSL no longer checks remote versions on the openssl site.
- Spack is used on systems that aren't connected to the internet, and
this check is probably in the wrong place and affects too many
commands. We can work on figuring out a better, more configurable
place to put a check like this.
Lmod's configure script goes to the trouble of finding
tclsh. This change uses that info to rewrite the #! lines
in the tcl scripts so that they call the tclsh that the
configure script discovered.
It needs to massage the existing shebang lines into something
that the sed statement in the makefile can manipulate and
it needs to add the path_to_tclsh info into the set of sed
statements.
Checked with versions 6.4.1 and 6.3.7 (the checksum for 6.0.1 is
incorrect, a fix for another time).
The lmod package needs a tclsh. Up until now it just assumed
that one was available on the system.
This change adds a depends_on('tcl') to the lmod package.
The tcl package installs a tclsh script with an embedded version
number (e.g. tclsh8.6) but the lmod configuration looks for tclsh.
This change extends the tcl package to symlink tclshX.Y to tclsh in
the tcl package bin directory.
- Redid the code for setting the itac symlink for the cluster edition.
- Removed the *PATH variables for MPI to avoid a conflict with other MPI
environment modules.
- Added missing test for `+all` when checking variants.
Set up the environment for the Intel compilers and tools. This commit
does the following:
- Unset variables that were incorrect from the auto guess prefix
inspections.
- Add a RemovePath environment_modifications_formats for dotkit.
- Set the module environment variables appropriate for the different
variants.
- Change the component logic so that the '+all' variant works. It was
getting split by letter and leaving COMPONENTS empty.
- Added a variant checking function.
- Added NONRPM_DB_DIR to the silent.cfg so that the product database
goes to the installation directory.
- With the product database in prefix the code to remove the product
database file from the home directory is no longer needed and was
removed.
- Reformat the 'tools' variant description.
There are probably more variables needed for the '+tools' for the
'professional' product version but I do not have access to that.
* upstream/develop: (126 commits)
Fix indent/flake8 error.
openexr : Add new package
Set environment variables
Added gnu packages datamash, parallel, and screen
added package as argument to setup_platform_environment
ilmbase : Add new IlmBase package
Documented linker default
fixed flake errors
removed commented-out code
Set default link type to dynamic on cray. Includes hooks for platform-based environment changes
fixed flake errors
fixed flake errors
Improved cray_xc detection bug fix
Improved cray_xc detection
remove FIXMEs
Ensure that per-4.4.1 NetCDF doesn't use HDF5 1.10
Re-ignore licenses directory
Add "default" configuration scope.
Draft CDO
Make frontend OS on Cray machines a proper linux distro.
...
