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2020-04-18autotools: set FORCE_UNSAFE_CONFIGURE to 1 in autotools.py (#16132)Diego Magdaleno1-0/+15
This commit sets the `FORCE_UNSAFE_CONFIGURE` environment variable to 1 in autotools builds. We see a lot of builds popping up and complaining about `FORCE_UNSAFE_CONFIGURE`. This behavior is not actually part of `autoconf` per se. It comes from this patch to `mknod.m4`, which is used by a lot of autoconf builds: * https://lists.gnu.org/archive/html/bug-gnulib/2010-07/msg00282.html Which originated from this problem that someone had on AIX: * https://lists.gnu.org/archive/html/bug-gnulib/2010-07/msg00279.html The gist of the problem seems to be that they want to check whether `mknod` can do something as root, but instead of checking whether they're running as root and using `su` or something to test this, they just made it harder to run `configure` as root. This seems very ad hoc and this is one of many checks that are run as root in `configure`. Many of them run before this check, so it's not clear that the `FORCE_UNSAFE_CONFIGURE` thing is even preventing bad things from happening. So: 1. This only happens in `autotools` builds, so we should go ahead and put it into `autotools.py` instead of in the global build environment, and 2. The variable does too little and provides a false sense of security in the first place, so we'll just disable it and avoid the nuisance. If we really feel strongly about this we can put some warnings in Spack about running as root, but at the top level, not in the middle of an already running script like `configure`.
2020-04-18votca-*: add v1.6 (#16139)Christoph Junghans5-9/+18
2020-04-17remove files accidentally committed with 0.14.0 (#16138)Todd Gamblin3-11712/+0
2020-04-17DDD bugfix (#16095)Daryl W. Grunau1-0/+5
* DDD: apply extended-prompt patch * DDD: apply extended-prompt patch * use the upstream patch Co-authored-by: Daryl W. Grunau <dwg@lanl.gov>
2020-04-17py-cutadapt: add version 2.9 (#16135)Levi Baber1-0/+1
2020-04-17MPFR: fix patch checksum, add dependencies (#15783)Adam J. Stewart1-6/+14
* MPFR: fix patch checksum, add dependencies * Update checksum again
2020-04-17AutotoolsPackage: add aclocal for all build deps (#15784)Adam J. Stewart1-5/+5
2020-04-17OpenMPI: add +cxx variant (#15477)Adam J. Stewart1-10/+18
* OpenMPI: add +cxx variant * C++ support will be removed in 5.0.X release
2020-04-17Language-specific PIC flags (#15474)Adam J. Stewart62-160/+415
* Language-specific PIC flags * Add tests for every compiler flag * Fix bad rebase * pic_flag -> cxx_pic_flag
2020-04-17charliecloud: fix url (#16133)Jordan Ogas1-1/+1
2020-04-17LLVM libomptarget fixes (#16104)Nichols A. Romero1-5/+10
* Throw an error at spack install invocation instead of most of the way through the build process when cuda_arch is unspecified. * Clean-up of CMake booleans. No actual change. * Use CMake variables for hwloc and libelf installation directories and avoid injecting extra flags into CMAKE_CXX_FLAGS * Conflict should only exist for +cuda variant.
2020-04-17coreutils: add variant for g prefixTodd Gamblin1-1/+4
- [x] Add a `gprefix` variant to coreutils, so that the 'g' prefix on binaries is optional. - [x] Make un-prefixed binaries the default again
2020-04-17NCCL: add new version (#16130)Adam J. Stewart1-1/+4
2020-04-17oneDNN: add new version (#16129)Adam J. Stewart1-1/+2
2020-04-17singularity: new variants to enable non-suid and non-network builds (#16088)Andrew W Elble1-23/+32
Defaults are left as they are currently
2020-04-17New package: Biopandas python package (#16066)ilbiondo1-0/+24
* Biopandas python package * Update var/spack/repos/builtin/packages/py-biopandas/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-biopandas/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * remove scipy dependency Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-17magma: added v2.5.3 (#16097)Stan Tomov1-1/+2
Also updated maintainer list
2020-04-17py-gcovr: added new package at v4.2 (#16100)Michael Kuhn1-0/+23
2020-04-17open-iscsi: added new package at v2.1.1 (#16113)darmac1-0/+32
2020-04-17aespipe: added new package at v2.4f (#16114)darmac1-0/+22
2020-04-17sz: run "make clean" after configure (#15759)Kai Germaschewski1-0/+3
At least the v2.0.2.0 tar ball contains compiled object files etc, which cause the build to fail on other architectures (ppc64le in particular), so this patch adds a `make clean` after configuring first.
2020-04-17asdcplib: added new package at v2.10.35 (#16118)darmac1-0/+23
2020-04-17libtree: added v1.1.2 (#16119)Harmen Stoppels1-0/+1
2020-04-16SourceForge: Mirror Mixin (#16112)Axel Huebl39-68/+162
* SourceForge: Mirror Mixin Add a mixing class for direct `CNAME`s to sourceforge mirrors. Since the main gateway servers are often down, this could reduce timeouts and fetch errors for sourceforge.net hosted software. * SourceForge: unspectacular mirror replacement add mirrors to all sourceforge packages with trivial download logic. tested fetch of latest version of each of these packages with various mirrors before committing. * SourceForge: xz the author homepage is chronocially overrun and this is the offical upload with many mirrors.
2020-04-16bugfix: fix emacs support on macOS (#16110)Todd Gamblin1-1/+1
- fix missing self.spec
2020-04-16macOS: Fix emacs Linking (#16106)Axel Huebl2-1/+9
* macOS: Fix emacs Linking Fix linking issue of emacs on macOS (clang and gcc). Applies the same work-around as conda-forge: https://github.com/conda-forge/emacs-feedstock/blob/b051f6c928d8b99fed3fabd9a8d67be993f94494/recipe/build.sh Homebrew avoids this by linking against the system ncurses lib: https://github.com/Homebrew/homebrew-core/blob/master/Formula/emacs.rb * ncurses: fix outdated variant comment this comment was build on the assumption that gnutls triggers a termlib dependency in emacs. that's not the case, ncurses itself depends on termlib when build with this feature.
2020-04-16libpng: github downloadAxel Huebl1-5/+4
libpng still has its sourceforge page but is actively been developed on github. since the sourceforge urls are too often down (as seen in my nightly CI/CD tests), just switch the download source to GitHub instead.
2020-04-16macos: use DYLD_FALLBACK_LIBRARY_PATH instead of DYLD_LIBRARY_PATHTodd Gamblin5-10/+14
`DYLD_LIBRARY_PATH` can frequently break builtin macOS software when pointed at Spack libraries. This is because it takes *higher* precedence than the default library search paths, which are used by system software. `DYLD_FALLBACK_LIBRARY_PATH`, on the other hand, takes lower precedence. At first glance, this might seem bad, because the software installed by Spack in an environment needs to find *its* libraries, and it should not use the defaults. However, Spack's isntallations are always `RPATH`'d, so they do not have this problem. `DYLD_FALLBACK_LIBRARY_PATH` is thus useful for things built in an environment that need to use Spack's libraries, that don't set *their* RPATHs correctly for whatever reason. We now prefer it to `DYLD_LIBRARY_PATH` in modules and in environments because it helps a little bit, and it is much less intrusive.
2020-04-16darwin: cut DYLD_LIBRARY_PATH from default modulesGeoffrey Malcolm Oxberry1-2/+0
This commit removes the DYLD_LIBRARY_PATH variable from the default modules.yaml for darwin. The rationale behind deleting this environment variable is that paths in this environment variable take precedence over the default locations of libraries (usually the install path of the library), which can lead to linking errors in some circumstances. For example, executables intended to link with Apple's system BLAS and LAPACK will instead link to a spack-installed implementation (e.g., OpenBLAS), causing runtime errors. These errors are resolved by instead relying on paths set in DYLD_FALLBACK_LIBRARY_PATH, which is lower in precedence than default locations of libraries.
2020-04-16ncurses: forward termlib libs (#16101)Axel Huebl1-1/+5
These libs need to be forwarded, as in ncurses `pkg-config` file.
2020-04-16emacs: libxml2 deps (#16103)Axel Huebl1-0/+1
emacs depends on libxml2.
2020-04-16Bugfix: For spack buildcache check, Handle specs where only the hash is (#15663)Marc Allen1-1/+1
provided (#15662). Prior to this fix, the checked Spec object would not be populated, and concretization would fail. Co-authored-by: Marc Allen <mrcall@amazon.com>
2020-04-16Add ncurses+termlib dependency to mesa (#16038)Glenn Johnson1-0/+2
Mesa links against libtinfo so needs to depend on ncurses. It also needs a little help finding the library directory so an LDFLAGS configure option is added.
2020-04-16New version xrootd-4.11.3 (#16092)Amjad Kotobi1-0/+1
2020-04-16singularity: updated maintainer list (#16093)Carlos Arango Gutierrez1-1/+1
2020-04-16openbabel: fix compilation errors (#16090)athanasio1-0/+6
- Disable maeparser as it is broken with CMake - Added missing dependencies
2020-04-16New package bonniepp added (#16091)Amjad Kotobi1-0/+21
2020-04-16Add new version 1.1.1 (#16087)Harmen Stoppels1-0/+1
2020-04-16New matlab versions (#16086)Antonio Arena1-4/+20
2020-04-16MPark.Variant: GCC 7.3.1 Conflict (#16081)Axel Huebl1-2/+11
* MPark.Variant: GCC 7.3.1 Conflict Due to an ICE in this specific patch-release of GCC, compile errors in downstream packages should be avoided with a clean conflict. * Fix superfluous spaces Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Fix typo Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-16dbcsr: expose all options, check openblas feats (#16034)Tiziano Müller1-7/+60
* dbcsr: expose all options, check openblas feats * dbcsr: use Ninja to build, ensure serialized tests * dbcsr: add myself as maintainer
2020-04-16Add Cubist (#16069)asmaahassan901-0/+32
* Add Cubist * enhance recipe * Not using OS module anymore * remove white space * Fix build shell * make Flake8 happy * use bash shell for build * Convert it To MakefilePackage as per peer-review
2020-04-16HAL: added new package at v2.1 (#16085)ilbiondo1-0/+102
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-04-15Add new package: zookeeper-benchmark (#16067)darmac1-0/+25
* Add new package: zookeeper-benchmark * refine zookeeper version * refine zookeeper version variant * remove unused variant
2020-04-15Neo4j (#16068)darmac1-0/+31
* Update var/spack/repos/builtin/packages/neo4j/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Add new package: neo4j * refine neo4j package * fix flake8 warning Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15update: memsurfer with python3 (#15636)Harsh Bhatia1-17/+19
* update: memsurfer with python3 * flake8 compliance * Update var/spack/repos/builtin/packages/memsurfer/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/memsurfer/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/memsurfer/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * removed build_type preferences at adamjstewart's suggestion * Added build/run dependency on python3.7 as suggested by adam stewart * more flake8 horror! Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15Upgrade MSTK versions (#16079)Rao Garimella1-0/+3
2020-04-15netcdf-cxx4: bugfix (#16080)Carson Woods1-0/+1
* Add new variants * Fix missing config_args variable
2020-04-15Merge branch 'releases/v0.14' into developTodd Gamblin2-1/+16
2020-04-15Make tags case insensitiveMichael Kuhn2-0/+10
Currently, tags are case sensitive, which is unintuitive: ```console $ spack list -t hpc ==> 2 packages. nek5000 nektools $ spack list -t HPC ==> 1 packages. mfem $ spack list -t Hpc ==> 0 packages. ``` This change makes them case insensitive: ```console $ spack list -t hpc ==> 3 packages. mfem nek5000 nektools $ spack list -t HPC ==> 3 packages. mfem nek5000 nektools $ spack list -t Hpc ==> 3 packages. mfem nek5000 nektools ```
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