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2018-11-26Feature/gatk (#9872)Miles Perry1-6/+4
* added 3.8-1 version * fixed flake8 stuff
2018-11-26Uncomment dependencies previously disallowed by concretizer (#9942)Adam J. Stewart14-63/+22
2018-11-24Package/py scikit learn (#9843)Sinan1-3/+8
* add v0.20 specific dependency versions, also add cython and py-test as dependencies * make flake8 happy * make cython a build-only dependency
2018-11-24py-pygresql: new package (#9922)Neil Flood1-0/+19
* py-pygresql: new package * Added dependency on py-setuptools, as the build will use it if present
2018-11-24py-psycopg2: new package (#9926)Neil Flood1-0/+18
* py-psycopg2: new package * Added dependency on py-setuptools, as the build will use it if present
2018-11-24p4est: fix a typo (#9932)Denis Davydov1-1/+1
2018-11-24mc: add version 4.8.21 (#9943)Matthias Diener1-0/+1
2018-11-24intel-parallel-studio: add missing updates to 2019.1 (#9941)Matthias Diener2-0/+3
2018-11-24py-geopandas: New package. (#9919)Neil Flood5-0/+116
* py-geopandas: New package, including packages for its dependencies * Trailing whitespace removed, etc * One more trailing whitespace * Removed some extraneous dependencies. No idea why I thought I needed them, but it now builds fine without them. * Added a variant +plotting, to include the dependencies required for plotting, as these are large-ish if not being used. * Added explicit dependency on py-matplotlib
2018-11-24cmake: add version 3.13.0 (#9940)Matthias Diener1-0/+1
2018-11-24r-geor: new package, and a couple of its dependencies (#9920)Neil Flood4-0/+85
* r-geor: new package, and a couple of its dependencies * Update to new copyright header * Include the list_url for the R package archive dir * Added explicit version ranges on dependencies, as per the relevant CRAN pages * Correct dependency types in r-splancs.
2018-11-23new version 18.1 for py-pip (#9938)Andreas Baumbach1-0/+1
Change-Id: Ie462e802049dd6150767dc555fb5708999e081ec
2018-11-23r-compositions: new package, including its dependencies (#9921)Neil Flood3-0/+61
* r-compositions: new package, including its dependencies * Include the list_url for the R package archive dir * Added explicit version ranges on dependencies, as per the relevant CRAN pages
2018-11-22libspatialite: new package (#9923)Neil Flood2-0/+37
2018-11-22munge: update versions and url format to reflect switch to .xz format… (#9916)Nicholas Labello1-2/+3
* munge: update versions and url format to reflect switch to .xz format in recent releases * package:munge remove unneeded version-specific urls
2018-11-22minced: add version 0.3.2 and fix install paths (#9918)Eric1-2/+4
2018-11-22qca: new package (#9924)Neil Flood1-0/+25
2018-11-22qjson: new package (#9925)Neil Flood1-0/+18
2018-11-22p4est: apply patches to 2.0 only (#9928)Denis Davydov1-2/+4
2018-11-22multitime: new package (#9929)Michael Kuhn1-0/+18
2018-11-22flecsale: add missing dependencies and fix flecsi runtime model (#9774)Michael Kuhn1-1/+6
2018-11-21Add MPICH version 3.3 (#9915)Ken Raffenetti1-0/+1
2018-11-21dyninst: overhaul package.py to CMakePackage (#9871)Mark W. Krentel2-69/+91
Drop versions 8.1.x. These were > 5 years old, no other spack package uses them, and they used autotools. Packages 'stat' and 'mitos' still use 8.2.1, so we keep that. Switch class Dyninst to CMakePackage. Clean up how the versions depend on various packages. For example, Dyninst used libelf up to 9.2, and then elfutils starting with 9.3. This makes things easier going forward. Add variant 'openmp' (default True) to enable openmp support for ParseAPI. This was added in 10.0.0. Add variant 'static' (default False) to also build static libraries. This goes back to 9.1.0. Disable cotire for the 9.3.x versions. Cotire has no real use in a one-time build and can break parallel builds with both static and shared libs.
2018-11-20correct sha for axl v1.1 (#9907)Elsa Gonsiorowski, PhD1-1/+1
2018-11-20package: add asciidoctor gem (#9905)Tom Scogland1-0/+20
* package: add asciidoctor gem Faster, easier to use, less impossible to install correctly implementation of asciidoc. * ritual sacrifice of EOF whitespace to flake8
2018-11-20CP2K related fixes and update (#9308)Tiziano Müller4-91/+205
* openblas: enable parallel builds * cp2k: enable parallel builds * cp2k: fix building on multilib/Suse distros use the actual directory path where files where installed to instead of the default prefix+'/lib' * cp2k: ensure we have a non-header-only libxsmm * openblas: disable max num CPU detection on virtualized build * cp2k: install data and set compiled-in DATA_DIR * cp2k: make libxc an optional dependency (enabled by default) * cp2k: link libint statically * cp2k: declare statically linked library deps as type=build * cp2k: add support for PGI compiler * cp2k: rename smm=none to smm=blas for clarification * cp2k: blacklist unsupported compilers * cp2k: mark wannier90 a build-time dep since statically linked * cp2k: make pexsi and elpa optional * cp2k: add support for v6.1 * libxc: add version 4.2.3 * cp2k: use pkg-config to link properly to libxsmm * cp2k: fix OpenMP support by making it explicit Previously, CP2K accepted threaded ELPA or BLAS, leading to #(CPU) processes being spawned even though no explicit OpenMP was requested. Now the `popt` variant should truly be thread free while the `psmp` variant uses threads also internally. * cp2k: source tarballs moved to GitHub
2018-11-20Package: Mercury (#9903)dorier1-0/+56
* added mercury package * updating mercury package to satisfy flake8 * improved mercury package
2018-11-20Add 2019.1 and 2018.4 version of the Intel performance libraries. (#9899)Jon Rood5-0/+17
* Add 2019.1 and 2018.4 version of the Intel performance libraries. * Fixing typo.
2018-11-19mpifileutils: add v0.8.1 (#9346)Adam Moody1-0/+1
2018-11-19openssl: make 1.1.1 the default version (#9836)Michael Kuhn1-3/+8
* openssl: add 1.0.2p, 1.1.0i and 1.1.1 * openssl: make 1.1.1 the default version
2018-11-19added several new perl modules (#9760)Justin Stanley17-0/+270
2018-11-19circos: new package starting at 0.69-6 (#9761)Justin Stanley1-0/+43
* circos: new package starting at 0.69-6 * circos: add homepage, simplify paths * circos: simplified more paths
2018-11-19gdk-pixbuf: explicitly disable building of gtk-docs (#9882)Sinan1-0/+11
2018-11-19r-rrpp: new package (#9887)Levi Baber1-0/+29
2018-11-19Adding openmpi version 4.0.0 (#9888)Jon Rood1-4/+5
2018-11-19breseq: Add version 0.33.1 (#9889)Eric1-0/+1
2018-11-19package/harfbuzz: disable building of gtk-docs, add new version (#9891)Sinan1-0/+12
2018-11-19r-crosstalk: remove unnecessary constraint (#9892)Levi Baber1-1/+0
2018-11-19r-geomorph: new version (#9890)Levi Baber1-0/+3
* r-geomorph: new version * r-geomorph: min r version
2018-11-19r-diversitree: new package (#9893)Levi Baber1-0/+33
* r-diversitree: new package * r-diversitree: system reqs
2018-11-19r-paleotree: new package (#9895)Levi Baber1-0/+24
2018-11-19package/pango: disable gtk-docs (#9896)Sinan1-0/+9
2018-11-19package/gtkplus: disable gtk-docs (#9897)Sinan1-0/+11
2018-11-19Explicitly set FC= empty for non-fortran builds (#9898)Mark C. Miller1-0/+2
2018-11-19Trimmomatic: Add version 0.38 (#9883)Eric1-0/+1
2018-11-19Adding intel-parallel-studio cluster 2019.1 version (#9884)Jon Rood1-0/+1
2018-11-19Add UCX v1.4.0 (#9881)Daniel Topa1-1/+3
Verification build dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ spack install ucx % gcc @ 4.8.5 ==> Installing libsigsegv ==> Installing m4 ==> Installing pkgconf ==> Installing ncurses ==> Installing readline ==> Installing gdbm ==> Installing perl ==> Installing autoconf ==> Installing automake ==> Installing libtool ==> Installing numactl ==> Installing zlib ==> Installing openssl ==> Installing diffutils ==> Installing bzip2 ==> Installing xz ==> Installing libxml2 ==> Installing tar ==> Installing gettext ==> Installing help2man ==> Installing bison ==> Installing flex ==> Installing libnl ==> Installing rdma-core ==> Installing ucx ==> Successfully installed ucx Fetch: 1.17s. Build: 40.59s. Total: 41.76s. [+] /scratch/users/dantopa/new-spack/pr.ucx.spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/ucx-1.4.0-ilfonxj2f5my4ur65li3sr7kuvfg3kim dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ spack spec ucx Input spec -------------------------------- ucx Concretized -------------------------------- ucx@1.4.0%gcc@4.8.5 arch=linux-centos7-x86_64 ^numactl@2.0.11%gcc@4.8.5 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-centos7-x86_64 ^autoconf@2.69%gcc@4.8.5 arch=linux-centos7-x86_64 ^m4@1.4.18%gcc@4.8.5 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-centos7-x86_64 ^libsigsegv@2.11%gcc@4.8.5 arch=linux-centos7-x86_64 ^perl@5.26.2%gcc@4.8.5+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-centos7-x86_64 ^gdbm@1.18.1%gcc@4.8.5 arch=linux-centos7-x86_64 ^readline@7.0%gcc@4.8.5 arch=linux-centos7-x86_64 ^ncurses@6.1%gcc@4.8.5~symlinks~termlib arch=linux-centos7-x86_64 ^pkgconf@1.5.4%gcc@4.8.5 arch=linux-centos7-x86_64 ^automake@1.16.1%gcc@4.8.5 arch=linux-centos7-x86_64 ^libtool@2.4.6%gcc@4.8.5 arch=linux-centos7-x86_64 ^rdma-core@20%gcc@4.8.5 build_type=RelWithDebInfo arch=linux-centos7-x86_64 ^cmake@3.12.4%gcc@4.8.5~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-centos7-x86_64 ^openssl@1.0.2o%gcc@4.8.5+systemcerts arch=linux-centos7-x86_64 ^zlib@1.2.11%gcc@4.8.5+optimize+pic+shared arch=linux-centos7-x86_64 ^libnl@3.3.0%gcc@4.8.5 arch=linux-centos7-x86_64 ^bison@3.0.5%gcc@4.8.5 arch=linux-centos7-x86_64 ^diffutils@3.6%gcc@4.8.5 arch=linux-centos7-x86_64 ^help2man@1.47.4%gcc@4.8.5 arch=linux-centos7-x86_64 ^gettext@0.19.8.1%gcc@4.8.5+bzip2+curses+git~libunistring+libxml2 patches=9acdb4e73f67c241b5ef32505c9ddf7cf6884ca8ea661692f21dca28483b04b8 +tar+xz arch=linux-centos7-x86_64 ^bzip2@1.0.6%gcc@4.8.5+shared arch=linux-centos7-x86_64 ^libxml2@2.9.8%gcc@4.8.5~python arch=linux-centos7-x86_64 ^xz@5.2.4%gcc@4.8.5 arch=linux-centos7-x86_64 ^tar@1.30%gcc@4.8.5 arch=linux-centos7-x86_64 ^flex@2.6.3%gcc@4.8.5+lex arch=linux-centos7-x86_64 Environment: dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ echo $HOSTNAME darwin-fe2.lanl.gov dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ grep -i 'model name' /proc/cpuinfo | sort | uniq model name : Intel(R) Xeon(R) CPU E5-2695 v3 @ 2.30GHz dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ lsb_release -d -bash: lsb_release: command not found dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ uname -a Linux darwin-fe2.lanl.gov 4.18.8-1.el7.elrepo.x86_64 #1 SMP Sat Sep 15 10:10:09 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ date Mon Nov 19 10:47:47 MST 2018 dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ pwd /scratch/users/dantopa/new-spack/pr.ucx.spack Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2018-11-19new package: mongo-cxx-driver (#9880)Andrea Negri1-0/+18
* new package: mongo-cxx-driver * fixed url
2018-11-19samtools: make zlib/bzip2 dependencies unconditional (#9866)Eric1-2/+2
2018-11-18libmongoc: updated versions (#9877)Andrea Negri1-2/+8
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