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2020-06-12bazel: patch to allow py-tensorflow (and likely other bazel packages) to ↵Andrew W Elble3-0/+27
build. (#17013) bazel uses gcc's -MF option to write dependencies to a file. Post-compilation, bazel reads this file and makes some determinations. "Since gcc is given only relative paths on the command line, non-system include paths here should never be absolute. If they are, it's probably due to a non-hermetic #include, & we should stop the build with an error." Spack directly injects absolute paths, which appear in this file and cause bazel to fail the build despite the fact that compilation succeeded. This patch disables this failure mode by default, and allows for it to be turned back on by using the '~nodepfail' variant.
2020-06-12New package: FrontFlow Blue (#16901)h-denpo2-0/+175
* New package: FrontFlow Blue Computational Fluid Dynamics Software for aeroacoustics * Modify Package ->MakefilePackage * Update var/spack/repos/builtin/packages/ffb/package.py Co-authored-by: Greg Becker <becker33@llnl.gov> * Update var/spack/repos/builtin/packages/ffb/package.py Co-authored-by: Greg Becker <becker33@llnl.gov> Co-authored-by: Greg Becker <becker33@llnl.gov>
2020-06-12cscope: Link tinfow instead of tinfoJohn Jolly1-1/+1
Whenever attempting to use any ncurses functionality within cscope, a page fault would result within the ncurses library. Program received signal SIGSEGV, Segmentation fault. 0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6 (gdb) bt #0 0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6 #1 0x00007ffff7faa794 in _nc_setupscreen_sp () from .../lib/libncursesw.so.6 #2 0x00007ffff7fa614c in newterm_sp () from .../lib/libncursesw.so.6 #3 0x00007ffff7fa65b9 in newterm () from .../lib/libncursesw.so.6 #4 0x00007ffff7fa2970 in initscr () from .../lib/libncursesw.so.6 #5 0x0000000000403dc2 in main (argc=<optimized out>, argv=0x7fffffffcea8) at main.c:574 This is due to a conflict between libtinfo.so and libtinfow.so. Both are linked into cscope: $ ldd $(which cscope) /bin/bash: .../lib/libtinfo.so.6: no version information available (required by /bin/bash) linux-vdso.so.1 (0x00007fff5dbcb000) libncursesw.so.6 => .../lib/libncursesw.so.6 (0x00007f435cc69000) libtinfo.so.6 => .../lib/libtinfo.so.6 (0x00007f435cc2c000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f435ca29000) libtinfow.so.6 => .../lib/libtinfow.so.6 (0x00007f435c9e8000) /lib64/ld-linux-x86-64.so.2 (0x00007f435cca7000) Specifically linking libtinfow.so instead of libtinfo.so resolves the issue. All instances of '...' above represent the path to the installed ncurses for Spack.
2020-06-12New package: alps (#17023)Sinan2-0/+63
2020-06-12pygpu: fix linking with gpuarray (#17033)Harsh Bhatia2-1/+16
* add build_ext_args to link pygpu with gpuarray * libgpuarray: add version 0.7.6
2020-06-12libtree package: add version 1.2.0, 1.1.4, and 1.1.3 (#17035)Harmen Stoppels1-0/+3
2020-06-12New package: clinfo (#17042)Matthias Diener1-0/+24
2020-06-12Geant4 +Python: fix module load (#17046)Axel Huebl1-0/+1
Adding `extends('python')` makes sure that a ``` spack load -r geant4 +python python -c "import Geant4" ``` find the module.
2020-06-12libffi 3.3: float128 ppc patch (#17043)Axel Huebl2-0/+60
Apply a patch to fix builds on Power7 and 8, wrongly requesting float128 support. Upstream patch: libffi/libffi#561
2020-06-12readline: fix linking to ncursesAdam J. Stewart1-1/+2
2020-06-12New package: antimony (#17061)Robert Blake1-0/+54
2020-06-12hydrogen: add version 1.3.4 (#17066)Brian Van Essen1-0/+1
2020-06-12magics: add version 4.2.4 (#17054)Tom Payerle1-2/+7
* Add version 4.2.4 * Update checksum for 4.1.0 * Version @4: requires python and py-jinja2 to build
2020-06-12gcc: Add 7.5.0Michael Kuhn1-2/+3
2020-06-11New package: py-uncertainties (#16997)Sinan1-0/+26
2020-06-11py-gpy: new package at 1.9.9codeandkey1-0/+22
2020-06-10py-paramz: new package at 0.9.5 (#17026)Justin S1-0/+21
2020-06-10ADIOS 2.6.0: New Options (#17025)Axel Huebl1-1/+4
Control new options/dependencies in ADIOS2 to avoid pick-up of system packages.
2020-06-10adios2: fix to build on Fujitsu MPI and Fujitsu compiler (#17034)Toyohisa Kameyama1-0/+16
2020-06-09add gaussian-view (#16890)asmaahassan901-0/+41
2020-06-09teach spack how to build pmix from git (#16973)Rob Latham1-3/+29
* teach spack how to build pmix from git * add variant for new REST feature * reorder package to match guidance
2020-06-09Add new package: wcs (#16958)Robert Blake2-1/+37
* Adding a package for wcs. * Turning on sbml for wcs. * The cpp flag needs to be available for wcs. * Wcs needs SBML to properly define the namespace. * Flake8 fixes. * Fixing the help string with the description. * Changing cpp to use the new variant syntax. * Fixing flake8 errors. * Forgot to delete one last fixme comment. * Spack "develop" needs to link to repo "devel" Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Robert Blake <rob.c.blake.3@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-09libffi: add patch for building with clang on power (#16855)Joseph Ciurej2-0/+26
* libffi: add patch for building with '%clang target=power*' * libffi: fix version of clang/power patch
2020-06-09Add new package: py-workload-automationdarmac1-0/+38
2020-06-09New package: py-pygelf (#17004)victorusu1-0/+22
2020-06-09jansson: add versions 2.10 to 2.13.1 (#17011)Rob Latham1-0/+5
2020-06-09[util-linux] disabling systemd (#17008)Jen Herting1-0/+1
If systemd support is enabled, install will attempt to modify files in system systemd directories.
2020-06-09Set the BOOST_ROOT environment variable when library is loaded (#16818)Nathan1-0/+3
* Adding BOOST_ROOT env variable * Update var/spack/repos/builtin/packages/boost/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-09suite-sparse: build libraries without running demos (#17007)Massimiliano Culpo1-1/+1
fixes #16638
2020-06-08Update miniconda3@4.8.2 (#17003)oracleLee1-0/+1
* Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py
2020-06-08Cray: fix Blue Waters support and user-built MPIs on Cray (#16593)Adam J. Stewart2-6/+12
* Cray: fix Blue Waters support * pkg-config env vars needed on Blue Waters * cray platform: fix support for user-build MPI on cray machines * reintroduce cray environment cleaning behind cnl version guard * cray platform: fix support for user-build MPI on cray machines Co-authored-by: Gregory <becker33@llnl.gov>
2020-06-08HELICS: add version 2.5.1 (#17014)Ryan Mast1-0/+1
2020-06-08rt-tests: fix build error (#16998)darmac1-2/+4
This is a makefile package and needs to invoke make.
2020-06-08Add new package: py-devlib (#16982)darmac1-0/+34
* Add new package: py-devlib * Update var/spack/repos/builtin/packages/py-devlib/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * add depends Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-08Add Package HSF-CMakeTools (#16951)vvolkl1-0/+26
* [hsf-cmaketools] add package * fix formatting * Apply suggestions from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * [hsf-cmaketools] remove cmake_prefix_path which is set already by spack Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-08R: url-version custom, release 4 (#16962)Amjad Kotobi1-1/+9
* R: url-version custom, release 4 * r: pcre condition
2020-06-08Add py-storm@0.23 and update URL (#16991)iarspider1-2/+6
* Add py-storm@0.23 and update URL * Update package.py
2020-06-08ltr-retriever: new package at v2.8.7 (#16832)Justin S1-0/+45
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-08view remove: directly check whether specs own files before removing from ↵Greg Becker1-0/+28
view (#16955) Bugfix for hardlinks and copies
2020-06-08hpcviewer, ibm-java: updates versions (#16987)Mark W. Krentel2-0/+8
hpcviewer: added v2020.05. ibm-java: added v8.0.6.10.
2020-06-08py-ipykernel: added v5.1.1 (#16988)iarspider1-0/+1
2020-06-07boost: Don't use pre-compiled headers for Fujitsu compiler (#16914)Toyohisa Kameyama1-1/+1
* boost: Dopn't use pre compile header. * move %fj.
2020-06-07rose: Add build dependencies for flex and bison (#16981)John Jolly1-0/+2
2020-06-07py-gast: add version 0.3.3 (#16945)Sinan1-0/+2
* py-gast: add version 0.3.3 * add python version constraints Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-06-06Add rpy2@3.0.4 (#16924)iarspider1-5/+12
* Add rpy2@3.0.4 * Style fixes * Update package.py * Proper Python version requirement
2020-06-06ffr: fix mpi programs to use mpi compiler wrapper. (#16948)Toyohisa Kameyama1-3/+12
2020-06-06[prmon] add package (#16949)vvolkl1-0/+27
2020-06-06mongo-c-driver: Add 1.16.2 (#16956)Michael Kuhn2-10/+116
This also updates libbson to the corresponding version and adds a few missing older versions.
2020-06-06added CTRE package (#16964)Matthieu Dorier1-0/+25
2020-06-06gcc: Fix error 'size of array is negative' (#16969)John Jolly4-3/+183
gcc 9.3.0 and glibc 2.31 (found in the base install of Ubuntu 20.04) cause the gcc package to error during build with the error: "size of array 'assertion_failed__####' is negative" Previous to this fix, the error was resolved for v8.1.0 <= gcc <= v9.2.0 via two patches. This fix backports those patches for v5.3.0 <= gcc <= v7.4.0 Potentially these patches need to be backported to versions of gcc before v5.3.0, but other compile issues need to be resolved for earlier versions of gcc first. Fixes #16968
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