This PR ensures that environment activation sets all environment variables set by the equivalent `module load` operations, except that the spec prefixes are "rebased" to the view associated with the environment.
Currently, Spack blindly adds paths relative to the environment view root to the user environment on activation. Issue #12731 points out ways in which this behavior is insufficient.
This PR changes that behavior to use the `setup_run_environment` logic for each package to augment the prefix inspections (as in Spack's modulefile generation logic) to ensure that all necessary variables are set to make use of the packages in the environment.
See #12731 for details on the previous problems in behavior.
This PR also updates the `ViewDescriptor` object in `spack.environment` to have a `__contains__` method. This allows for checks like `if spec in self.default_view`. The `__contains__` operator for `ViewDescriptor` objects checks whether the spec satisfies the filters of the View descriptor, not whether the spec is already linked into the underlying `FilesystemView` object.
Boost iostream autodetects the compression libraries libzstd and
liblzma outside of the Spack environment.
This commit disables mentioned libraries. In the future if the
Spack zstd/lzma packages were added as dependencies of the Spack
Boost package, additional work could be done to build Boost with
the Spack-built versions of these libraries.
For some reason, newer versions of qt fail to build because they cannot
find certain system libraries such as libatomic and libdl.
Leaving the qmake compiler set to gcc seems to fix the problem.
Fixes#13221
* DataSpaces: 1.8.0
Add a newer release of DataSpaces for ADIOS2.
Also add missing `-fPIC` flags since this is a static library.
* ADIOS2: Dataspaces, libffi, libfabric
Add missing dependencies to ADIOS2. Without explicit control,
those dependencies might get picked up from the system environment
and will cause unstable builds.
* Hide transitive SST dependencies
* ADIOS2: Simplify SST CMake Flags
As proposed by Chuck
* Methods setting the environment now do it separately for build and run
Before this commit the `*_environment` methods were setting
modifications to both the build-time and run-time environment
simultaneously. This might cause issues as the two environments
inherently rely on different preconditions:
1. The build-time environment is set before building a package, thus
the package prefix doesn't exist and can't be inspected
2. The run-time environment instead is set assuming the target package
has been already installed
Here we split each of these functions into two: one setting the
build-time environment, one the run-time.
We also adopt a fallback strategy that inspects for old methods and
executes them as before, but prints a deprecation warning to tty. This
permits to port packages to use the new methods in a distributed way,
rather than having to modify all the packages at once.
* Added a test that fails if any package uses the old API
Marked the test xfail for now as we have a lot of packages in that
state.
* Added a test to check that a package modified by a PR is up to date
This test can be used any time we deprecate a method call to ensure
that during the first modification of the package we update also
the deprecated calls.
* Updated documentation
From Python docs:
--
'surrogateescape' will represent any incorrect bytes as code points in
the Unicode Private Use Area ranging from U+DC80 to U+DCFF. These
private code points will then be turned back into the same bytes when
the surrogateescape error handler is used when writing data. This is
useful for processing files in an unknown encoding.
--
This will allow us to process files with unknown encodings.
To accommodate the case of self-extracting bash scripts, filter_file
can now stop filtering text input if a certain marker is found. The
marker must be passed at call time via the "stop_at" function argument.
At that point the file will be reopened in binary mode and copied
verbatim.
* use "surrogateescape" error handling to ignore unknown chars
* permit to stop filtering if a marker is found
* add unit tests for non-ASCII and mixed text/binary files
Provide up to date specs for build options
Remove non-production versions
Format using autopep8 and flake8
Separate cmake options in adios2 2.4.0 version
Keep default as True as much as possible
Support for Python 2 and 3 for adios2 versions <= 2.4.0
Starting v2.5.0 only Python 3 is supported
Addressing review suggestions
* Add new ACTS releases
* Update ACTS dependency requirements
* We can actually be more specific here
* The material plugin is gone as of ACTS v0.10.0
* Add 0.10.4 release
* Remove material mapping plugin
It was merged into core as of 0.10.x, and given ACTS' youth it is unlikely to have actual users at this point in time.
* Minor clean-up of package information.
* Add variants, fix dependencies, and add conflicts for compilers that do not support C++17.
* Correct dependency type for CMake.
- Add a test that verifies checksums on all packages
- Also add an attribute to packages that indicates whether they need a
manual download or not, and add an exception in the tests for these
packages until we can verify them.
Some packages had incorrect checksums because they needed to be
downloaded from a new place or the package needed tweaking somehow.
These packages to sha256 and the new checksums have been verified by
fetching over https.
These packages have either been retired or are no longer retrievable from
any site we can find. They also aren't needed by other packages, so we're
removing them from Spack.
- allinea-reports: is now arm performance reports
- globus-toolkit: retired, globus is now a paid service.
- uberftp: used globus-toolkit, github site is retired.
- mpiblast: site is dead; no longer fetchable.
- py-mxnet: site and github are gone
- soap2, soapindel, soapsnp: site is gone, unfetchable
- arlecore: could not verify md5 securely
We'd like to use a consistent checksum scheme everywhere so that we can:
a) incorporate archive checksums into our specs and have a
consistent hashing algorithm across all specs.
b) index mirrors with a consistent type of checksum, and not one that
is dependent on how spack packages are written.
- [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
* py-line-profiler: add 2.1.2, re-run cython if needed
See rkern/line_profiler#166.
* Update var/spack/repos/builtin/packages/py-line-profiler/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Addition of 1.1.3 and 1.1.4
* Addition of conditional enum-34 installation.
* Update var/spack/repos/builtin/packages/py-maestrowf/package.py
Addition of versioning for pyyaml.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Addition of enum34 back to older versions 1.1.3 and below.
* adjust building of OpenFOAM 1806 and earlier
- spack now unpacks into spack-src, but earlier OpenFOAM versions
still expect particular directory names (eg, OpenFOAM-v1806).
Resolve by creating a symlink during patching.
* replace openfoam 1806 patch with URL version
* fujitsu-mpi: commit new package
* Add homepage.
* * Modified the MPI commands to a simple form.
* Unnecessary processing has been deleted.
* Add conflict for all compilers except the Fujitsu compiler.
* Fix typo.
* Delete versions.
* Delete conditions for specifying the Fujitsu compiler.
* fftw: grouped precisions in a single variant
* fftw: simd options are now based on target features and not on variants
* fftw: simplified computing the selected precisions
* fix ipykernel dependency, newer versions are python3-only
* Update var/spack/repos/builtin/packages/py-ipykernel/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-ipykernel/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
Dotkit is being used only at a few sites and has been deprecated on new
machines. This commit removes all the code that provide support for the
generation of dotkit module files.
A new validator named "deprecatedProperties" has been added to the
jsonschema validators. It permits to prompt a warning message or exit
with an error if a property that has been marked as deprecated is
encountered.
* Removed references to dotkit in the docs
* Removed references to dotkit in setup-env-test.sh
* Added a unit test for the 'deprecatedProperties' schema validator
* libint: switch to 2-stage build for 2.6.0+
* libint: add tune and fortran variants
* cp2k: add support for libint >= 2.0
* cp2k: use pkg-config for linking libxc
* github releases are not released versions, but from-source
releases
* they lack the mimification of the JS/CSS components and as
such require node-js and npm, this conflicts with python@3:
* this commit
* drops the from-source dependencies on node-js and npm and
* updates the checksums to the correct sha256 hashes of the
pypi releases. The pypi-tarballs are different
* ZFP: CMake Package
ZFP is primarily build via CMake, which will have all install logic
and configuration files generated.
The 0.5.0 release did not support this yet, so we toss it.
* Patch ADIOS1: ZFP 0.5.1+ support
* ZFP: Expose all CMake variants
* new package: py-python-ldap
* fix dependency types
* improvements
* Update var/spack/repos/builtin/packages/py-python-ldap/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-python-ldap/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add openldap dependency
* go-md2man: disable module-mode
* Update var/spack/repos/builtin/packages/go-md2man/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add singularity 3.4.1
Signed-off-by: ArangoGutierrez <eduardo@sylabs.io>
* revert some changes
Signed-off-by: ArangoGutierrez <eduardo@sylabs.io>
* add maintainers list to pkg singularity
Add @alalazo and me to the Singularity maintainers list
* Update var/spack/repos/builtin/packages/singularity/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/singularity/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/singularity/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
7bcb306 updated setup_environment in the GCC package to examine the
bin/ directory to find alternatively-named instances of CC, but this
failed to account for when GCC was being installed and failed when
it attempted to list the not-yet-existing installation prefix. This
commit updates the logic to skip this search if the bin/ directory
doesn't exist.
* libaio: fixed a condition that checks whether we are running on OS X
* libaio: simplified package by adding an explicit conflict for darwin
* libaio: added information to the docstring
* fio: added version 3.16, added conflict when using libaio, docstring
* lvm2: conflict due to libaio dep, improved docstring, simpler install
* mariadb: conflict due to libaio dep, improved docstring, version 10.4.7
* mariadb: the dependency on libaio is now conditional, removed conflict
* mariadb: fixed a typo in previous commit
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* libaio: turned into a MakefilePackage
Unlike the compiler binary name search logic, the `setup_environment` in
GCC's package assumes the compiler names are *exactly* `gcc`, `g++`,
etc. In many external installations (Homebrew, Macports) the
installation includes only *suffixed* versions such as `gcc-9`.
This patch uses the GCC compiler search suffixes to actually locate the
correct filenames for the installed compilers, allowing the
Spack-generated module file to have useful definitions of CC, CXX, etc.
It also allows for the possibility that the user's external installation
of GCC is compiled without Fortran support, in which case the `FC`
environment variables are not defined.
* The perl-uri-escape package duplicates perl-uri
The Perl URI::Escape module is in the Perl URI package so the Spack
perl-uri-escape package is a duplicate of the perl-uri package. This PR
does the following:
- replace `depends_on('perl-uri-escape')` with `depends_on('perl-uri')`
in packages that dependend on perl-uri-escape
- add the version from perl-uri-escape to perl-uri
- remove the unneeded dependency from perl-uri
- remove the perl-uri-escape package
* Reinstated perl-test-needs dependency
Put the perl-test-needs dependency for perl-uri back in but set it to
type='test'.
* For tests to succeed the type must be ('build', 'test')
Now that Spack injects microarchitecture specific optimizations for
the selected target, packages should avoid adding flags that could
step over those.
This PR adds interproscan-4.8, which has a completely different build
system than version 5. Note that this builds for running on a host as
opposed to a queue system. I am fairly certain that a queue system can
be configured later.
This PR also adds a patch for intrproscan-5 to build when the user
building the packages has a large GID by setting posix mode for tar.
* llvm: fixed issues with syntax and formatting
* use spec.architecture.target.family
* use spec.target instead of spec.architecture.target
* mesa: use == instead of __contains__
A function added to this package ran as part of importing it and
printed a warning for most Spack invocations, this removes the
warning message.
Also:
* Use compilers directly instead of Spack compiler wrappers (since
references to the compiler are embedded in text and binary files
of the installation)
* Add 'cross' variant for setting CROSS environment variable for
build
* Set UPCXX_INSTALL for generated module files
* Set UPCXX_GASNET_CONDUIT/UPCXX_NETWORK in generated module files
on Cray systems
* Also set UPCXX_NETWORK in build environment for Cray systems
The following dependencies were added:
+ depends_on('perl-exporter-tiny', type=('build', 'run'))
+ depends_on('perl-list-moreutils-xs', type=('build', 'run'))
Seamless translation from 'target=<generic>' to either
- target.family == <generic> (in methods)
- 'target=<generic>:' (in directives)
Also updated docs to show ranges in directives.
Fixes#12829
This adds a variant to the util-linux package that controls whether it
builds its own libuuid. Variant defaults to True. It enables other
packages to choose to get libuuid from the libuuid package instead.
This also changes the cryptsetup package to build util-linux with
~libuuid (so it uses an explicitly-Spack-built instance of libuuid
instead).
- add missing perl dependency
- only filter Makefile if referred to dependency is in the spec
- rewrite the shebang line of scripts to use spack perl
- remove tabix dependency as tabix and bgzip are part of htslib
* cuda: New version 10.1.243
Adds CUDA 10.1.243. The installer command-line arguments have slightly
changed, hence in the install method the version needs to be inspected
in order to give the correct arguments for the new installer.
* cuda: Combine common command-line arguments
The CUDA 10.1+ installer has slightly different command-line arguments
than previous versions. Keep the common parts together and only split
where they are different.
* Make flake8 happy
* update py-bokeh: new version & dependencies
* Revert "update py-bokeh: new version & dependencies"
This reverts commit 5e191a0b20a89f09630b4d223a28b19db715603f.
* update py-bokeh: new version & dependencies
* trigger travis-ci
* adjust python dependency-type to br
* update py-bokeh: new version & dependencies
* Revert "update py-bokeh: new version & dependencies"
This reverts commit 5e191a0b20a89f09630b4d223a28b19db715603f.
* new package: py-fsspec: add package.py
* trigger travis-ci
* adjust python dependency-type to br
* CGNS: Add setting of RPATH on Darwin
This should go in the CGNS CMakeLists.txt, but it isn't there yet and won't be in previous versions, so best to handle it here.
If building on darwin/MacOSX, need to set the RPATH so applications can find shared library correctly.
* Restrict MACOSX_RPATH setting
This has now been added to the CGNS distribution, so the setting of `CMAKE_MACOSX_RPATH` should be restricted to current and previous releases and not upcoming releases.
* new package: py-configojb
* add version 4.7.2
* improve dependencies
* fix url for versions > 5.0.0
* Update var/spack/repos/builtin/packages/py-configobj/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-configobj/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* use format to create url strings
* fix typo
* improve style
* Update var/spack/repos/builtin/packages/py-configobj/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* py-gpaw: Fixing missing numpy include path, adding newer version of py-gpaw and fixing a bug with libxc.c in older py-gpaw
* py-gpaw: Fix Python and ASE version dependencies
- GPAW 19.8.1 requires Python 3.x, add dependency on python@3.5:
- GPAW releases are associated with a corresponding ASE release, add
matching ASE version dependencies.
* py-gpaw: Enable the scalapack variant by default
GPAW installation instructions say scalapack is optional but "highly
recommended". Thus enable it by default.
* add new cutadapt release 2.5, and adjust dependencies conditional on version
* use https, not ssh, for git url
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* update py-xopen (add 0.8.2 checksum)
* refine version specific dependencies
add py-bz2file, which needs to be created
* create py-bz2file
* Revert "refine version specific dependencies"
This reverts commit 70649da98851fefb2f936ca99a012fe6bef07b70.
* Revert "update py-xopen (add 0.8.2 checksum)"
This reverts commit 7400f44caa6e98419eb4bc3107704b91e8a2018b.
* update py-xopen (add 0.8.2 checksum)
* refine version specific dependencies
add py-bz2file, which needs to be created
* py-bz2file needed when built with python 2.7
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* space after comma
- Fix trailing whitespace missed by the bug described in #12755.
- Fix other style issues that have crept in over time (this can happen
when flake8 adds new checks with new versions)
There are problems with libunwind for arm and trying to use it with mesa.
See for example:
https://github.com/grate-driver/mesa/issues/6
disabling use of libunwind for arm, allows the package to be built
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
- Use of symbol testing macro requires explicit include()
- CMake policies are not version-portable and the support has to queried
based on CMake version
* libpeas@1.22.0: new package
* libpeas: note more build dependencies
Build and link dependencies were obtained through a combination of
examining the `config.log` file from `configure` and looking at the
pkg-config files of `libpeas`.
* libpeas: add search path for GIR/typelib files
* Use spec.architecture.target insted of platform.
* remove default in simd variant value.
simd variant change to archtecture independent values.
* Add check simd values.
* rewrite check simd values.
* * flake8
* change aarch64 to arm (neon support only 32 bit arm.)
* py-ase: New version 3.18
Add ASE version 3.18. ASE 3.18 has dropped support for python 2.x,
hence add a dependency on python@3.5: for it.
* Add more ASE dependencies
Address review comments, add dependencies on py-scipy, py-matplotlib,
py-flask, and also add type=('build', 'run') dependency specifiers.
While debugging this package on our Cray machine, tmux was throwing an
error involving the ncurses headers. Tmux would look for headers in
system locations rather than where spack installed ncurses. Tested only
on a Cray.
* Install the newest version of ncbi-rmblastn
Version ncbi-rmblastn 2.2.28 coonfiguration fails for gcc compiler on ubuntu 16.04 due to some compatibility issues that requires manual intervention to keep the installation going. However you still stumble upon other issues while compiling it.
Using Intel compiler passes the configuration step but fails for the compilation process as well.
Here I'm using the latest version and patch, and the recommended configuration option as mention in http://www.repeatmasker.org/RMBlast.html
* uploading ncbi-blast patch
The mariadb-5.5 series can not be compiled with gcc-9.1.0 and above. Add
a conflicts statement to reflect that.
The error is due to -Werror=address-of-packed-member, a warning that is
new in gcc-9.
* Update R CRAN packages
This PR update R CRAN packages. It also ensures that spack built
packages that correspond to R recommended packages are specified in the
dependency list. This is needed for #12015.
* Add more updates to packages
* Updated dependencies of CRAN R packages
Also, use cloud.r-project.org rather than cran.r-project.org to use
automatic redirection to mirrors. This minimizes the load on the cran
server.
* Update to latest versions of CRAN R packages
* Fix flake8 issues
Some blank lines at the end of a coupple of package files crept in.
* Adjust r-animation dependencies
The r-magick package depends on image-magick, so r-animation should as
well. Also, add in texlive for LaTeX support.
* New package: r-magick
* Adjust line spaces in r-magick
* Add swftools dependenct to r-animation
* New package: swftools
This is needed bt r-animation
* Add 'when' clause to some package dependencies
- r-animation
- r-coin
- r-dt
- r-openssl
* New package: r-ellipsis
* New package: r-vctrs
* New package: r-zeallot
* New package: r-generics
* New package: r-cardata
* Add r-progress dependency to r-readxl
* New package: r-askpass
* New package: r-openxlsx
* New package: r-rio
* New package: r-sys
* New package: r-zip
* Add more updated packages
These are updates that have happened while working on this PR as well as
catching the ones from the cran.rstudio.com URL that were missed before.
* New package: r-gower
* New package: r-recipes
* New package: r-squarem
* New package: r-libcoin
* New package: r-rcmdcheck
* New package: r-remotes
* New package: r-sessioninfo
* New package: r-xopen
* New package: r-rgexf
* New package: r-rook
* New package: r-later
* New package: r-promises
* New package: r-xfun
* New package: r-urca
* New package: r-ggsignif
* New package: r-polynom
* New package: r-ucminf
* New package: r-ordinal
* New package: r-inum
* New package: r-debugme
* New package: r-fs
* New package: r-shinyfiles
* New package: r-gsa
* New package: r-nmof
* New package: r-dosnow
* New package: r-rann
* New package: r-reticulate
* New package: r-future
* New package: r-globals
* New package: r-listenv
* New package: r-future-apply
* New package: r-rsvd
* New package: r-sctransform
* New package: r-mitools
* Remove a stray FIXME line
* Fix typo in dependency for r-rcmdcheck
* Remove the dependency on r-splines
The r-splines package never existed in spack, but it does not exist on
CRAN either. There is an archive version from 1999 but it does not have
the proper extension format for modern R packages. The latest version
does not depend on r-splines, and apparently previous versions at least
built without it. Also, bump the required R version.
* Fix typo in r-rcpp dependency
* Fix typos in dependencies
- r-diagrammer
- r-janitor
- r-seurat
Also, bump minimum R version for r-rngtools.
* New package: r-clisymbols
* New package: r-fitdistrplus
* New package: r-gbrd
* New package: r-gh
* New package: r-ini
* New package: r-metap
* New package: r-npsurv
* New package: r-rdpack
* New package: r-snakecase
* New package: r-tinytex
* New package: r-usethis
* Make recommended changes
Made the changes that were recommended in the initial review.
- change cran.rstudio.com to cloud.r-project.org
- change R-project to r-project
- for packages with no listed homepage use the canonical link to the
package page
- for packages with a dependency constraint on R itself, specify the
dependency type
- add `list_url` where missing from package
* New package: r-hdf5r
This is needed for some older versions of r-seurat.
* Set R versions in packages
If the R version is specified in the DESCRIPTION file then set it in the
respective spack package.py file.
* Update var/spack/repos/builtin/packages/r-aer/package.py
Change dependency version of r-car.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Set constraint of mlbench dependency of r-adabag
* Set constraint on r-rcpp dependency of r-ape
* Removed "suggested" r-testthat from r-bibtex
* Update var/spack/repos/builtin/packages/r-bindrcpp/package.py
Fix dependency spec of r-bindr in r-bindrcpp.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/r-blob/package.py
Add r-vctrs version constraint.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Remove r-base64enc dependency from r-callr
* Update var/spack/repos/builtin/packages/r-car/package.py
Set constraint on r-cardata dependency.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Remove unneeded dependencies from r-clipr
* Add gmake dependency to r-construct
* Set the proper homepage for r-crayon
* Add r-jsonlite as a dependency for r-crul
The jsonlite package moved from "suggests" to "imports" with 0.8.4.
* Remove accidental colon after package name
* Add version constraint to r-fpc dependency in r-dendextend
* Additional constraints for R version with r-digest
* Add r-jsonlite dependency for latest verion of r-dt
* Add r-htmltools dependency in r-dygraphs package
* Removed unneeded dependencies from r-fnn
* Remove unneeded dependencies from r-formatr
* Add version constraint for r-mvtnorm dependency in r-fpc
* Added gmake dependency to r-fs
* Add r-globals dependency in r-future-apply
* Add perl dependency to r-gdata
* Add openssl dependency for r-ggally
* Removed unneeded dependencies from r-globaloptions
* Update r-haven
- Add version constraint on r-forcats
- Add gmake build dependency
* Fixed gmake dependency
Gmake is a build only dependency.
* Apply suggestions from code review
Apply a batch of suggestions from Adam Stewart.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Remove unneeded dependencies from r-hoardr
* Fix r-htmlwidgets homepage
* Add gmake build dependency to r-httpuv
* Remove unneeded dependency from r-log4r
* Remove unneeded dependency from r-maldiquant
* Add gmake build dependency to r-minqa
* Remove unneeded dependency from r-mlbench
* Set constraint on R6 dependenvy of r-pbdzmq
* Set constraints on r-callr dependency of r-pkgbuild
* Remove unneeded dependency from r-nloptr
* Remove unneeded dependencies from r-pkgmaker
* Set R version constraint for r-raster
* Set version constraint on rcpp for r-rcppprorgess
* Added gmake build dependency
* Remove unneeded dependencies from r-rematch
* Remove unneeded dependency from r-plogr
* Add gmake build dependency for r-rcurl
* Apply suggestions from code review
Bring in more suggestions from Adam Stewart.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Remove cnpy dependency from r-rcppcnpy
The r-rcppcnpy package has its own modified copy of the cnpy source and
will build from that internal source. The cnpy dependency is therefore
unnecessary.
* Add comment to reconcile dependencies
The CRAN site lists Perl, Getopt::Long as a dependency. The Spack Perl
will have the Getopt::Long package installed so just depend on Perl.
* Add dependency on udunits2 with newer versions of r-units
* Set additional proj constraint for r-sf
Support for PROJ6 was added in r-sf-0.7-4.
* New package: pandoc
This package installs the pandoc and pandoc-citeproc binaries in order
to satisfy dependencies on pandoc until the Haskell framework is in
Spack.
* Add pandoc dependency to r-bookdown
* Add comment about MPI in r-ergm
* Add pandoc dependency for r-reprex
* Add proj constraints to r-rgdal dependencies
Support for PROJ6 was added in version 1.4-2.
* Modifications to r-rgl
- Rearranged the dependencies to be more consistent with other packages
- put the type last on the depends_on lines to be consistent with other
packages
- Added version constraints for some dependencies
- Added pandoc build dependency
* Be more accurate with rjsonio constraint for r-rgooglemaps
* Remove unneeded dependencies from r-rhmmer
* Tweak constraints for r-rjava
- Set java version constraint
- add gmake build dependency
* Add pandoc dependency to r-markdown
* Remove unneeded dependencies from r-rrcov
* Tweak r-rstan package
- remove duplicate specifications
- remove unneeded when conditions
- add version constraints
- arrange to follow order on CRAN page more closely
- add gmake build dependency
- add pandoc build dependency
* Add pandoc build dependency for r-rstantools
* Remove unneeded dependency from r-runit
* Remove unneeded dependencies from r-selectr
* Remove example R code from description
The example would module loading to break, at least in the case of Lmod
using TCL module files. It could be during the TCL to Lua conversion but
the module fails due to interpreting ipart of the example as a command.
* Update r-seurat
New version of r-seurat with new dependencies.
* New package: r-dqrng
* New package: r-leiden
* New package: r-rcppannoy
* New package: r-rcppparallel
* New package: r-rspectra
* New package: r-sitmo
* New package: r-uwot
* Remove unneeded dependency from r-snow
* Remove unneeded dependency from r-sourcetools
* Added pandoc build dependency for r-stanheaders
* Remove unneeded dependencies from r-taxizedb
* Remove unneeded dependencies from r-tclust
* Add dependency constraints for r-threejs
The following are needed for version 0.2.2:
- r-matrix
- r-jsonlite
* Remove unneeded dependencies from r-vfs
* Remove unneeded dependencies from r-vgam
* Remove unneeded dependency from r-xlconnectjars
* Remove unneeded dependency from r-xlsxjars
* Remove unneeded dependency from r-xnomial
* Remove ~mpi from fftw dependency of swftools
* Apply suggestions from code review
Add latest round of suggestions from Adam Stewart.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Fix rjsonio spec for r-rgooglemaps
The r-rjsonio spec is a when conditional.
* Rename 3 R.* packages
- r-utils --> r-r-utils (R.utils)
- r-oo --> r-r-oo (R.oo)
- r-methodss3 --> r-r-methodss3 (R.methodsS3)
Also, renamed dependencies in packages that depend on these three.
* Loosen version constraint on mariadb for r-rmysql
Make the mariadb constraint on mariadb-5.5 rather than the more
specific, and limiting, mariadb-5.5.56. This will allow an external
mariadb, such as mariadb-5.5.60 on CentOS-7.5 to be used. It also allows
for r-rmysql to be built against newer versions of the mariadb-5.5
series that might be added to spack.
* Convert to Autotools package
* dyninst and papi are now optional (off by default)
* limit dyninst version to < 10 (see
https://github.com/bsc-performance-tools/extrae/issues/30)
* Add numactl dependency
* Enable parallel installs for 3.7 and later
* Set EXTRAE_HOME in module files and for dependent package installs
* Generalize cxx11 support flag (previously it was using a specific
syntax and this updates it to use the cxx11 support flag for the
compiler in use).
* The install for kaldi was copying library symlinks but not the
actual library files, this makes sure to copy the libraries
* All libraries are installed to 'prefix.lib' (the original
library directory structure is no longer maintained)
* The install step for executables did not account for the different
dynamic library suffix on MacOS
e891cc4 updated the cairo package to make gobject support optional
and disabled it by default. gtkplus requires gobject support so this
explicitly enables +gobject on the cairo dependency of gtkplus.
Change the depends_on type from default (build + link) to just 'link'
for binutils and a few other packages. We don't use the binutils
utilities (only libs). On cori at NERSC (Cray), this was breaking the
build by covering up the system ld.
* Only apply issue-87.patch for versions before 1.2.3
* 1.2.3 builds fine with gcc@8:, but 1.2.2 and 1.2.2_p1 both fail
(with or without the patch) so the conflict is updated to exclude
only these two versions.
* Make mpi, scipy, petsc4py, and nlopt support optional
* Later versions depend on python@3.5:
* Versions before 0.4.1 must build with MPI: add a conflict for
@:0.4.1~mpi
Before this commit, CMake would still attempt to detect OpenMP, even
if RAJA were being installed with `spack install raja~openmp`, because
the option `ENABLE_OPENMP` is set to "On" by default. This commit
explicitly disables OpenMP when the Spack install spec contains
'~openmp`, ensuring that CMake does not attempt to detect and link
with OpenMP.
* esmf: add patch when building with intel for 7.0.x
* esmf: set Makefile variables required to propagate CXX/F90 flags
* ncl: add ymake patch for @6.4.0:
* ncl: add pixman, bzip2, freetype dependencies
* Add version 6.3.2 (which does not require patches like 6.1.5)
* Add +python variant to build Python bindings
* Option to build shared libraries does not exist for newer
versions including 6.3.2
* Update 'libs' property (library names are different for newer
versions)
* Add support to detect and build with MKL as blas provider
SEACAS is now using versions instead of just relying on always
installing master. There are now tagged versions.
The most recent version is the first that can be used with a
non-patched develop version of the CGNS package; previously, seacas
required that the CGNS library have some internally-developed patch
applied, but this is no longer needed.
Also, added support for adios2 package with the adios2 variant.
This currently defaults to off.
This variant (off by default) adds support for the kdreg option in
the GNI provider. It is disabled by default in order to avoid
potential runtime conflicts with the cray-mpich library. Only one
library at a time can use this feature.
This patch allows the libfabric package to work correctly out of
the box on systems like Cori at NERSC (since it's CLE7 update).
Otherwise the spack build may autodetect kdreg headers on the system
and enable this problematic feature.
* nlohmann-json: 3.7.0
The version 3.6.0 fix compile issues with GCC 9.0.
* nlohmann-json: proper test handling
tests are controlled via `spack install --test root|all ...`
instead of a variant.
This adds a special package type to Spack which is used to aggregate
a set of packages that a user might commonly install together; it
does not include any source code itself and does not require a
download URL like other Spack packages. It may include an 'install'
method to generate scripts, and Spack will run post-install hooks
(including module generation).
* Add new BundlePackage type
* Update the Xsdk package to be a BundlePackage and remove the
'install' method (previously it had a noop install method)
* "spack create --template" now takes "bundle" as an option
* Rename cmd_create_repo fixture to "mock_test_repo" and relocate it
to shared pytest fixtures
* Add unit tests for BundlePackage behavior
* new package: libglvnd
* remove virtual provides from libglvnd
libglvnd does not provide them directly, but
through implementations that depend on it.
* fix flake8 errors
* libglvnd: fix style/remove unecessary variants
* remove older libglvnd version
* explicitly enable all libglvnd stubs
* libglvnd: conflict with non-linux platform
* Choose a specific commit as a version (before, the only version was
the master branch)
* Add CMake patch which allows for building the version added here
(this replaces the existing patches for percept in Spack)
* Update trilinos dependency
Also update dependencies to build latest py-deeptools versions and
add a patch to run tests:
* Replace pypi URL with github URL to download tests
* Update dependency versions of py-pysam, py-matplotlib
* Add new py-deeptoolsintervals package as a dependency
* Add py-plotly and py-nose dependencies
* Patch setup.py to collect and run tests
UnifyCR has been renamed to UnifyFS. Renaming the Spack package is
the last step in this process.
This renames the package and changes any UnifyCRs to UnifyFS within
the package.
* Overhaul PyTorch package
* Flake8
* Distributed requires MPI, NCCL not specified correctly
* Binary was being specified incorrectly
* Run tests at install time
* Disable GLOO in addition to GLOO_IBVERBS
* Add option to disable QTDesigner plugin for qwt
Qt designer shouldn't be necessary to build downstream GUI code.
Currently `qwt^qt~tools` fails to build:
(darwin clang@10.0.1)
```
compiling qwt_designer_plugin.cpp
compiling qwt_designer_plotdialog.cpp
moc qwt_designer_plugin.h
moc qwt_designer_plotdialog.h
rcc qwt_designer_plugin.qrc
qwt_designer_plugin.h:23: Error: Undefined interface
make[1]: *** [moc/moc_qwt_designer_plugin.cpp] Error 1
make[1]: *** Waiting for unfinished jobs....
qwt_designer_plugin.cpp:17:10: fatal error: 'QDesignerFormEditorInterface' file not found
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make[1]: *** [obj/qwt_designer_plugin.o] Error 1
make: *** [sub-designer-make_default-ordered] Error 2
```
* Update VTK for newer VisIt and compiler versions
Several changes/enhancements to VTK package
---
Add version 8.1.0 (default version for VisIt 3.x)
---
Tweak VTK options for version 8 and VisIt:
- only add mpi4py version option when mpi4py is enabled
- Require object factory for downstream packages
- Remove OpenGL preference for VTK 8
---
Combine +python3 into +python
The spec for using python3 should just be `+python^python@3:`.
---
Remove unused VTK cmake argument on newer version
---
Patch for Python 3 fails on VTK 6.1 (needed for VisIt 2.x):
```
==> Patch /rnsdhpc/code/spack/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch failed.
==> Error: ProcessError: Command exited with status 1:
'/usr/bin/patch' '-s' '-p' '1' '-i' '/rnsdhpc/code/spack/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch' '-d' '.'
```
and as it happens, VisIt 2.13 is incompatible with Python 3 anyway.
---
Fix compiler error:
As spack's configuration warning says, double-quotes can cause trouble:
```
==> [2019-07-29-11:47:55.269653] Warning: Quotes in command arguments can confuse scripts like configure.
The following arguments may cause problems when executed:
-DVTK_REQUIRED_OBJCXX_FLAGS=""
Quotes aren't needed because spack doesn't use a shell.
Consider removing them
```
They were being added to the compile line, causing clang to think it was
asked to compile an empty file:
```
cd /private/var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/s3j/spack-stage/spack-stage-3nk9bwe_/spack-build/Rendering/OpenGL && /rnsdhpc/code/spack/lib/spack/env/clang/clang++ -DVTK_IN_VTK -DvtkRenderingOpenGL_EXPORTS -F/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks -DGLX_GLXEXT_LEGACY -O2 -g -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -fPIC -fvisibility=hidden -fvisibility-inlines-hidden "" -o CMakeFiles/vtkRenderingOpenGL.dir/vtkCocoaGLView.mm.o -c /rnsdhpc/code/spack/var/spack/stage/vtk-6.1.0-b2mj276iz77fadisv2me365qe27t3gxt/spack-src/Rendering/OpenGL/vtkCocoaGLView.mm
clang: error: no input files
make[2]: *** [Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/vtkCocoaGLView.mm.o] Error 1
```
* Modernize/PEP-8 visit package statements
* Add new VisIt version and patches for building on Mac
- VisIt's cmake assumes a 'vtk(tiff|jpeg|png)' *library* target exported by
VTK, but VTK 8.1.x on my configuration seems to have these as header-only
targets with library dependencies.
- Explicitly add QT path to visit configure: Without this, somehow
`${VISIT_QT_DIR}` was being set to empty, so that the build failed with
`missing /bin/moc`.
- VisIt assumes that if it isn't being built statically, QWT has been built as
a mac Framework. QWT actually is built as a framework based on whether QT
itself is.
Error message:
```
-- Looking for QWT
CMake Error at CMake/SetUpThirdParty.cmake:131 (MESSAGE):
Include Directory for QWT (/rnsdhpc/code/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/qwt-6.1.3-bmfxirweplzhjoiil4rw632evkyteuwk/lib/qwt.framework/Versions/Current/Headers) does not exist.
Call Stack (most recent call first):
CMake/FindQwt.cmake:57 (SET_UP_THIRD_PARTY)
CMakeLists.txt:1251 (INCLUDE)
```
* ADIOS 2.4.0: Add new Deps
Version 2.4.0 of ADIOS2 added new dependencies that are not
yet listed as `depends_on` and/or disabled otherwise. Add them
now to avoid picking them up from system paths, e.g. `libpng`.
* ADIOS2: Variant Defaults Change
* Python: False by default
* ADIOS1: only used prior to 2.3.0
* UnifyCR: update dependencies and build options
This adds some specifics about dependencies and conflicts and adds
additional build options and variants. UnifyCR now also has limited
fortran support.
* Remove debug statements condition on Spack debug
Change debug print statements to now be turned on when the -g cflag
is found in the flags the user sets.
* add new package: py-python-magic
* tidy up
* Update var/spack/repos/builtin/packages/py-python-magic/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add master and dependencies
* remove gcc and make
* add variants, make doc and ch-grow dependencies optional
* capitalize description sentence
* move dependencies and variants below version block
* fix typos
* gromacs: fix simd detection for pre 2018 versions
* pre 2018 the cmake file was named differently
* fixed up post 2018 patch file which was non pretty
* Trim patch
* Create package.py
* applied reviewer suggestions
* Update package.py
* remove CamelCase from variant names
* add comment on why fetching package via git
* found typo in variant to cmake-argumentlist translation
* rename variants to ~nonuma ~nompi to be in sync with cmake-args, refine mpi@3-dependency definition
* Revert "rename variants to ~nonuma ~nompi to be in sync with cmake-args, refine mpi@3-dependency definition"
This reverts commit 58e8cf7d93c5665f0b4b50228946857734716cef.
* remove version-preference
* add checksum for singularity release 3.3.0
* update singularity doc URL
URL at the lbl.gov domain has message saying:
"This website is going away soon! Update your bookmarks!"
* add note about build log file for post-install step
* provide links to both 2.x and 3.x security docs
* remove whitespace. Passing flake8 confirmed locally this time :)
* add TODO comment for fakeroot support
The previous version does not properly install the required cmake
configuration files for blaze-lib, so find_package does not work
correctly.
This patch converts the blaze-lib package to use CMakePackage,
adds the required cmake dependency, and removes the install()
member function, which is not working correctly and is no longer
needed.
In a review of a previous pull request (
https://github.com/spack/spack/pull/10713 ) it was mentioned that the
proper way to figure out the target architecture is via
spec.architecture.target. This patch fixes this for the openblas
package.
Signed-off-by: Janne Blomqvist <janne.blomqvist@aalto.fi>
Not sure what happened between #5321 and now but the CC=CXX fix now
prevents py-matplotlib from building with the Intel compiler. I verified
with versions of py-matplotlib from 2.0.2 to 3.0.2 and intel-17.0.4 and
19.0.4 that py-matplotlib successfully builds with the Intel compiler
without that code.
* Add preCICE xSDK support
* Cleanup generation of cmake arguments
* Generalize numpy include
* Fix python spec
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Fix numpy spec
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* hunspell: write autoreconf method to triage error
This commit fixes the error described in GitHub issue
`AutotoolsPackage` class attempts to call `libtoolize`, which doesn't
exist on macOS systems that externally install `libtool` in Spack via
Homebrew -- Homebrew installzes GNU libtoolize as `glibtoolize`.
The fix is to call `autoreconf` only, and GitHub pull request #12344
makes this change in
AutotoolsPackage (https://github.com/spack/spack/pull/12344). However,
while waiting for that pull request to be merged, overriding the
`autoreconf` method achieves the same result for a self-contained
fix. This self-contained fix is necessary to fix a dependency bug in
the `hunspell` package.
* hunspell: add missing gettext dependency
* hunspell: add version 1.7.0
* add new package cromwell
* fix flake8 errors, add cromwell-womtool package
* change name of cromwell to cromwell-server
* renamed cromwell-server to just cromwell
* update description to what is in the project docs
* fixing format call for python2.6 compatibility
* Add comment that 1.0.1 versions are no longer supported
* Add comment that 1.0.2 versions are only supported up to
December 2019
* Add versions 1.0.2s, 1.0.2r, and 1.0.2p
* Add versions 1.1.0k, 1.1.0j, and 1.1.0i
* Add version 1.1.1c
* Add comment that 1.1.0 versions are only supported up to
September 2019
Resolves#11932.
Move the PIC flags from CFLAGS on the configure line to the spack
compiler wrapper for ncurses. The problem with the configure line for
autotools is that specifying CFLAGS sets the entire flags, thus
deleting the flags that configure would add itself.
By default, if CFLAGS is unspecified, then configure picks a sensible
default of `-g -O2`. But adding `-fPIC` erases these and it ends up
building unoptimized.
* Add patch to detect newer versions of MacOS and to fix a typo in
configure.ac (AM_LIBTOOLSFLAGS should be AM_LIBTOOLFLAGS)
* Remove variant declarations for unsupported languages
* Add support for quartz on MacOS
* Add optional X Window support
* Specifically build against qt@4 when building QT support
* Point to appropriate C++ standard libraries when building with
Clang on MacOS
* Disable parallel build (for all platforms)
* Increase verbosity of configure script by adding
--disable-silent-rules
* Add numpy 1.17.0
* Overhaul numpy package
* Flake8 fixes
* Undefined reference fix
* HeaderList and LibraryList need an arg
* veclibfort has no headers
* Add patch for older versions of py-numpy
* Remove py-meep hack from py-numpy package
* libflame: always add max arg hack flag
* Fix build with GCC 4.8
* Compiler flags come from self.compiler
* Only apply -std=c99 to cflags
* Try to fix libflame package
* Fix ATLAS build on macOS
* --force-clang flag added in 3.10.3
When building with GCC, c-blosc requires the -std=gnu99 flag.
Before this patch, the build would only add -std=gnu99 for GCC when
building on specific architectures; this adds -std=gnu99 in all cases
when using GCC.
When loading `openpmd-api` as a lib to build outside of
spack or to build depending spack packages, the "CMake-PUBLIC"
header-only library MPark.Variant must be available. Also,
the `*Config.cmake` package must be able to find dependent
libs if used.
* new package: py-backports-tempfile
* Update var/spack/repos/builtin/packages/py-backports-tempfile/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* remove rc version
* fix single quote
* add new version, add sha256 sums
* Update var/spack/repos/builtin/packages/py-apipkg/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add python dependencies
* new package: py-usgs
* Update var/spack/repos/builtin/packages/py-usgs/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-usgs/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* new package: py-requests-futures
* Update var/spack/repos/builtin/packages/py-requests-futures/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* minimap2: remove py-mappy dependency and build on ARM
py-mappy: Change URL and new version.
* merge py-mappy to minimap2.
* 1. add type in depends_on.
2. remove unneeded which.
* Incorporate as a patch upstream commit 0c20dbf059 (diff-acb9169b4ccbac494ced5140d285a015) resolving problems with `-Wno-...` options not being understood by GCC.
* Incorporate as a patch upstream PR https://github.com/ericniebler/range-v3/pull/1202 fixing upstream issue https://github.com/ericniebler/range-v3/issues/1196.
* Compile tests only if we actually want to run them.
* Optionally compile documentation with a `+doc` variant.
* Add `+examples` and `+perf` variants to avoid unnecessary compilation of components usually not required for install.
* Add conditional build-only dependency on Boost when appropriate.
* Install docs, examples and performance tests if built (not part of upstream build instructions).
* Add @chissg as a maintainer.
- Update c-blosc to 1.17.0
- Add patch to build test_forksafe for versions 1.15.0 through 1.17.0
when compiled with the Intel compiler.
- Remove code that turned off building the test with the Intel compiler
1. xmmintrrin.h is included x86 only.
2. Add makefiles for non-x86 hosts.
3. mpicc in Makefiles is replaced spacks mpi compile command.
4. variant check is rewite with satisfies.
* Geant4 data packages: Set the install path name explicitly.
* Use the correct directory name for g4photonevaporation,g4radioactivedecay,g4realsurface
* Add versions 8.0.16, 5.7.26, and 5.6.44
* Update boost dependency for versions 8.0.16, 8.0.15, and 8.0.14
* Update dtrace script when building for versions before 8 as is done
for the glib package
* Set perl as a build dependency for versions before 8
* cxxstd=17 conflicts with version 8 when server code is built
(~client_only)
* Add -Wno-deprecated-declarations for cxxstd > 11
* Add -Wno-error=register for cxxstd > 14
This updates the Spack QT package to enable building qt version 4 on
MacOS.
This includes the following changes to the qt package:
* add version 4.8.7
* add option to build with or without shared libs
* add options to disable tools, ssl, sql, and freetype support
* add qt4-tools patch when building qt@4+tools
* add option to build as a framework (only available on MacOS)
* replace qt4-el-capitan patch with qt4-mac patch (which includes the
edits from qt4-el-capitan)
* apply qt4-pcre-include-conflict.patch only for version 4.8.6
(rather than all 4.x versions)
* apply qt4-gcc-and-webkit.patch for 4.x versions before 4.8.7 and
create a separate qt4-gcc-and-webkit-487.patch for version 4.8.7
* update patch function for qt@4 on MacOS to update configure
variables relevant to Spack (e.g. PREFIX)
* add option to build freetype with Spack, as a vendored dependency
of QT, or not at all (default is to build with Spack)
This includes the following edits outside of the qt package:
* Update MacOS version utility function to return all parts of the
Mac version (rather than just the first two)
* gettext package: implement "libs"
* python package: add gettext as a dependency
Fixes#12007.
The Cray cc wrappers don't handle the -s flag (strip) cleanly, It's
not essential to strip the binary, so just remove the flag on Cray.
Note: the default build on Cray is for the back end and the unzip
binary won't run on the front end. To build for FE, use something
like arch=cray-fe-x86_64.
* Add +shared variant, which builds shared library in addition to the
static library.
* Install libraries even when specifying the header-only option
(header-only is just about installing an additional folder).
* An additional make call is not required to build generator
executables (they are built by default).
* Streamlined help-line of each variant.
* Fix Mac platform check for dependency in py-ipython package: 'when'
constraints in Spack directives must be Specs (either a Spec
object or a Spec in string format)
* Fix Mac version check in py-numpy: platform.mac_ver() returns a
3-part string as its first tuple item so the check as written would
never pass; use Spack Version object to simplify check.
* Fix Mac version check in qt package (the check was incorrectly
comparing ints and strings) and use Spack version object to
simplify check.
* Add versions 4.3.0, 4.3.1, and 4.3.2
* The URL format changed after 4.1.4, so this adds a url_for_version
function to choose the URL format based on the version
With this PR, a user can designate older versions of OpenGL as an
external Spack package, and dependents can use that installation
as long as they do not have version requirements.
MacOS currently comes with OpenGL 2.1; there is currently no
'provides' directive in the OpenGL Spack package which specifies a
gl version provided for versions earlier than OpenGL 3.3, so earlier
versions of OpenGL are not considered to provide any version of gl.
This PR records that any version of OpenGL provides 'gl' (which is
sufficient for any package that does not require a specific version
of gl).
* Version 1.3.0 requires python 3.5 or later (no Python 2 support)
* Remove test of scipy.weave import (not available since 1.0)
* Add more-sensitive py-numpy constraints based on py-scipy version
* Replace py-nose dependency with py-pytest
* Add adamjstewart as maintainer
* Rename py-pytorch to py-torch
* Add versions 1.1.0 and 1.0.1
* Define modules to test import of after installation (import_modules)
* py-typing dependency is only needed for older versions of Python
(3.4 or before)
* Newer versions of py-torch depend on newer versions of CUDA
* Add adamjstewart as maintainer
* Remove libuuid dependency for python on Darwin
Python 2.7 includes Carbon, which requires a proprietary typedef defined in
the system `/usr/include/uuid/uuid.h`:
```
In file included from /rnsdhpc/code/spack/var/spack/stage/python-2.7.16-chgwvgls4ezgujsknn27vlmkhwbzpqik/Python-2.7.16/Python/mactoolboxglue.c:27:
In file included from /rnsdhpc/code/spack/var/spack/stage/python-2.7.16-chgwvgls4ezgujsknn27vlmkhwbzpqik/Python-2.7.16/Include/pymactoolbox.h:10:
In file included from /System/Library/Frameworks/Carbon.framework/Headers/Carbon.h:20:
In file included from /System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:23:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
```
Similarly, even with Python 3, having Spack's libuuid in the toolchain
causes matplotlib to fail to build downstream because its `osx` backend
links against Carbon:
```
building 'matplotlib.backends._macosx' extension
/rnsdhpc/code/spack/lib/spack/env/clang/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/local/include -I/usr/X11/include -I/opt/X11/include -I. -I/rnsdhpc/code/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/python-3.7.2-bipx24oyxqxowqc75o5vfih7dljiaohz/include/python3.7m -c src/_macosx.m -o build/temp.macosx-10.14.5-x86_64-3.7/src/_macosx.o
In file included from src/_macosx.m:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Cocoa.framework/Headers/Cocoa.h:12:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/Foundation.h:87:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/NSURLError.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
uuid_string_t ext_jnl_uuid;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/device/device_types.h:89:33: note: 'io_string_t' declared here
typedef char io_string_t[512];
```
MacOS version 10.14.5
Xcode 10.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
* Mark libuuid as conflicting with Darwin due to framework
If Spack's libuuid is included by any other package that tests for or
requires the Cocoa or Carbon frameworks, the build will *fail* becuse it
appears that Apple's libraries require a special version of libuuid and
uuid.h.
```
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Cocoa.framework/Headers/Cocoa.h:12:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/Foundation.h:87:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/NSURLError.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
uuid_string_t ext_jnl_uuid;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/device/device_types.h:89:33: note: 'io_string_t' declared here
typedef char io_string_t[512];
```
* Revert "Mark libuuid as conflicting with Darwin due to framework"
This reverts commit 9a68b75202005fc265abe2033e4ad36312a9a34d.
* Document libuuid exception in python package
* update to kim-api-2.1.1 and openkim-models-2019-07-25
* openkim-models provide needed dependency constraints and settings
* add maintainers and fixup flake8 errors
* font-util: Remove duplicated dependencies.
* font-util: Fix path handling for font resources.
The "join_path" call made no sense but still managed to work somehow most of the times.
If +pthreads is specified, googletest actually gets build without
pthreads support and vice versa.
If pthreads is not available, googletest should detect it itself which
is why "enabling" pthreads in case of ~pthreads does not seem to cause
any error.
Change-Id: I29de8c4a23dc3901124b27a1ead3354949b7e65b
* xsdk: phist has a conflict with gcc version <= gcc-4.9.1 - so add a variant to disable it on older compiler builds
This is triggered by #11677
* fix typo
* Added a new package for LAME and a variant in sox for it.
* Fixed download url for LAME
* libmad: Added new package libmad for mp3 decoding. Changed sox variant from lame to mp3.
* libmad: Added m4 as a requirement
* libmad: Added comment on patch origins
* libmad: Added a list_url for alternate download location
* libmad: Fixing libmad download url
- We don't currently make enough use of the maintainers field on
packages, though we could use it to assign reviews.
- add a command that allows maintainers to be queried
- can ask who is maintaining a package or packages
- can ask what packages users are maintaining
- can list all maintained or unmaintained packages
- add tests for the command
* Add QMCPACK v. 3.8.0
* Remove QE variant conflict for serial QMCPACK installations.
* Add support for QE 6.4.1 converter.
* FindLibxml2QMC patch function only needed prior to QMCPACK 3.8.0
* ioapi: add version 3.2
* ioapi: unwrap version checksum; it's exempt from line length QA
* ioapi: drop overridden build(); it's the same as the default
* cmake: Move cxx11 flags for fujitsu into the flag_handler method
* cmake: sanitization and error checking in flag_handler
* cmake: Fix fujitsu flag check from 'fc' to 'fj'
* openjdk
* Removing preferred from latest and adding a few lines for readability.
* Remove bad whitesapce
* removing formatting changes
* stable url for openjdk 1.8
* remove extra blank line
* actual binary
Add version for 'gpu' and variant for 'cuda'. These are currently available from the 'master-gpu' branch.
* hpctoolkit: add version gpu and variant cuda
* The gcc >= 4.8.x requirement only applies for dyninst >= 10.x.
ibm-java: fix the URL to only use a machine type that ibm-java
supports so that 'spack info' doesn't report a non-existent URL on
platforms that it doesn't support.
* Fix scikit-learn build with Apple clang
* Update compiler unit tests
* Fix unit tests
* Fix OpenMP dep
* recursive=True no longer necessary
* Add myself as a maintainer
* Specify which versions require OpenMP
* Typo fixes
* LLVM-OpenMP is the correct dependency, no OMPT
* Flake8 fix
* Undo Apple Clang OpenMP flag change, split into a separate PR
Later versions of libjpeg-turbo build with CMake; to build with
user-specified cflags, the user must supply these to CMake as
-DCMAKE_C_FLAGS (Spack's typical approach of injecting these flags
into the compiler wrapper invocation is insufficient in this case).
Currently libjpeg-turbo cannot be implemented as a CMakePackage
(and thereby take advantage of the flag_handler implementation it
provides) because not all versions of libjpeg-turbo use CMake, so
this adds a custom implementation of flag_handler and
flags_to_build_system_args to libjpeg-turbo.
* cmake: change c++ spec when building with Fujitsu compiler.
* cmake: define cxxflags using a Fujitsu compiler's method.
* cmake: Add condition of whether to add cxx11 option.
It seems that GitHub's output changed slightly for this patch (one more
letter for both short hashes on the index line), probably due to the
number of objects in the repository.
This PR adds the ability to specify the auto-dispatch targets that can
be used by the Intel compilers. The `-ax` flag will be written to the
respective compiler configuration files. This ability is very handy when
wanting to build optimized builds for various architectures. This PR
does not set any optimization flags, however.
The default library search for a package checks the lib/ and lib64/
directories for libraries before the root prefix, in order to save
time when searching for libraries provided by externals (which e.g.
may have '/usr/' as their root).
This moves that logic into the "find_libraries" utility method so
packages implementing their own custom library search logic can
benefit from it.
This also updates packages which appear to be replicating this logic
exactly, replacing it with a single call to "find_libraries".
This PR has several modifications for the r package.
- The tk package is always depended on but this pulls in X11, making the
'X' variant non-functional. This PR sets a dependency of tk on '+X'.
- There is a missing dependency on libxmu when '+X' is set.
- The libraries for R wind up in a non-standard location and are thus
left out of the RPATH settings. This PR adds that directory to RPATH.
- The MKL integer interface for gfortran is not in the BLAS libs. This
PR replaces the intel interface with the gfortran interface if needed.
- Use the `LibraryList` `ld_flags` method for blas as that is more in
line with th R Installation and Administration manual.
Note that this PR depends on PR #11956. This PR closes#8642.
TK can be built with support for libXft and X Screensaver. Both of these
are turned on in the Tk configure script. That means the system
libraries will get picked up if they are on the system and nothing is
specified in the package. Since the default for both of them is 'True' I
set the default value for the variants to 'True'.
* bowtie2: Add version 2.5.3.1 and fix to build on ARM
1. Add version 2.5.3.1.
2. Add simde for ARM.
3. Disable -fopenmp-simd when gcc 4.8.X or before for ARM.
4. Add Makefile option POPCNT_CAPABILITY=0 for ARM.
* flake8.
Fixes#11781
* Rename build log to spack-build-log.txt
* Rename environment variables file to spack-build-env.txt
* The name of the log and env files is now the same during the build
and after the build completes
* Update packages which referred to the build log/env files
* For packages installed before this commit using older names for the
build and env files, search for the older names
* ferret: use libx11 from spack
* ferret: use mpi library with or without fortran support
* ferret: add version 7.2
* ferret: no need to specify ~mpi
* ferret: creating symlinks may fail for external packages; set include/lib paths instead
* use autoreconf to regenerate configure script and config.guess for
newer architectures
* Add perl build dependency for older versions. The required perl
version is constrained because the perl script uses syntax that
is deprecated in older versions
Declare a conflict for TAU versions older than 2.28.1, that they
can't depend on libelf or libdwarf. The user can still install it
by specifying tau@2.24~libelf~libdwarf.
* py-antlr4-python3-runtime: new package
* py-antlr4-python3-runtime: fix for flake8
* py-antlr4-python3-runtime: indent docstring
* py-antlr4-python3-runtime: clarify role of this package vs ANTLR in docstring
* py-antlr4-python3-runtime: remove whitespace at end of line
The py-reportlab package includes binaries for easy_install and pip.
That blocks activation if py-setuptools and/or py-pip are installed.
This PR block the binaries from py-reportlab as easy_install and pip
should be installed with their respective packages.
* py-cf-units: new package
* py-cf-units: download from pypi.io
* py-cf-units: include py-pytest-runner as build dep
* py-cf-units: remove empty build_args function
* py-cf-units: fix for flake8
* py-cf-units: indent docstring
* py-cf-units: remove excess spaces
* py-cf-units: list master branch ahead of numeric versions
* py-cf-units: remove extension keyword from version
If R is provided by the system with a module (i.e. registered in
packages.yaml with a "module" entry) and has no discernible prefix,
this allows turbine to still make use of R.
This PR corrects a problem with the opa-psm2 package. It was
installing headers into <prefix>/usr/include and libraries into
<prefix>/usr/lib instead of <prefix>/include and <prefix>/lib.
The extra level of usr/ subdirectories causes dependent packages
like libfabric to fail to build.
The original packaging, with openfoam as a virtual and with
openfoam-com, openfoam-org and openfoam-extend as
providers, adds an obfuscation layer without any benefit.
- Rename `openfoam-com` to `openfoam`, and remove the
`openfoam` virtual package.
- `parse_anonymous_spec()` is a vestige of the days when Spack didn't
support nameless specs. We don't need it anymore because now we can
write Spec() for a spec that will match anything, and satisfies()
semantics work properly for anonymous specs.
- Delete `parse_anonymous_spec()` and replace its uses with simple calls
to the Spec() constructor.
- make then handling of when='...' specs in directives more consistent.
- clean up Spec.__contains__()
- refactor directives and tests slightly to accommodate the change.
Added a wrapperrpath variant to mpich that defaults to `True`.
Users can set this to `False` (e.g., spack install mpich~wrapperrpath) to
disable the wrapper RPATHs. This makes it easier to replacing an MPICH
installation in a container with an MPICH for the host system,
e.g., Cray MPICH with Shifter on Cori, Intel MPI, MVAPICH2, etc.
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
The version of LLVM used by flang is new enough that CppBackend doesn't exist. Unfortunately, `flang-xxxxxxxx` is seen as < `3.9.0` by the version check.
* add a special case for `flang` versions.
* OpenFOAM: rationalize architecture options
- older versions of OpenFOAM had WM_ARCH_OPTION to choose a 32-bit
build on 64-bit architectures. This is not exactly relevant anymore
and has now been largely removed from OpenFOAM.
- simultaneously the newest version of OpenFOAM has rationalized the
handling of special settings for KNL by rolling these into the
compiler options. We now do the same thing here in spack.
1. Reuse the internal variable arch_option to convey processor-specific
optimizations and add these into the C++OPT=... statement.
2. Drop spack support for configuring a 32-bit build on 64-bit
hardware.
These changes can also be applied to older OpenFOAM versions, and to
various OpenFOAM forks without issue.
* update openfoam versions. New release 1906, patched 1812 version.
ncl does not build with newer versions of gdal (or rather proj). This
also needs a small change to gdal, otherwise we end up with both proj@5
and proj@6 in the spec.
* Remove individual font-* packages and add them as resources of the
font-util package
* Update font-util package to Autotools-based package, and call
autoreconf to regenerate the old configure script
* Add font-adobe-utopia-type1
* fmt: Add cxxstd variant, plus cmake/c++ patches
Spack supported versions of fmt default to C++11 for versions
less than 5, C++14 greater than 5, with fmt implementing
fallbacks to whatever compiler supports.
To give better ABI compatibility and use of newer standards, provide
a `cxxstd` variant defaulting to 11 with 98-17 options. Use cmake_args
to set CMAKE_CXX_STANDARD as appropriate, plus use of `FMT_USE_CPP11`
option for C++98 builds. Use `conflicts` to disable use of certain
standards in versions that don't support, or fail the build, with
those standards.
Add patches to unify use of `CMAKE_CXX_STANDARD` in 3.0 versions,
remove hard-coding of compiler flags in `fmt-config.cmake`, and
prevent use of C++11 features in 4.1.0 when in supported C++98
mode.
Default to not building documents as no dependency on Doxygen is
yet present, and they are not part of the "all" build.
* Use CMake to enforce C++ standard support
Fail configure step if fmt tries to build with a cxxstd variant
not supported by the compiler (or known to CMake).
* fmt: New version 5.3.0
* The py-pytables package depends on hdf5-blosc
* Further modifications to py-pytables package
The 3.2.2 version of py-pytables should still build with internal blosc.
The issue with locking in a multithreaded environment has been
fixed/worked around in version 3.3.
Also, add bzip2 and lzo variants.
