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2019-02-07petsc@xsdk-0.2.0: fix sowing dependency (#10535)Satish Balay1-0/+1
2019-02-07xsdk@develop fixes (#10521)Satish Balay2-4/+9
* xsdk@develop: switch trilinos from @master to @develop * xsdk@develop: dtk - fix trilinos dependency on dtk. - dkt-3.0 should be used with trilinos-12.4* - dtk/master should be used with trilinos@develop
2019-02-07orthofiller: new package at 1.1.4 (#10373)Justin Stanley1-0/+38
2019-02-07fixed checksum (#10393)Gregory Lee1-1/+1
2019-02-07new package: perl logger simple (#10509)Levi Baber1-0/+17
2019-02-07perl-file-homedir: new package (#10533)Levi Baber1-0/+17
2019-02-07py-biopython: new version (#10532)Levi Baber1-0/+2
2019-02-07cmake: add version 3.13.4 (#10538)Matthias Diener1-0/+1
2019-02-06phrap-crossmatch-swat: new package at 1.090518 (#10529)Justin Stanley1-0/+25
2019-02-06mafft package: add version 7.407 (#10488)Owen Solberg1-0/+1
2019-02-06jdk package: add version 1.8.0_202 (#10536)Matthias Diener1-0/+2
2019-02-06New package: perl-object-insideout (#10508)Levi Baber1-0/+20
2019-02-06fmt package: fix cmake arguments (#10500)Matthias Wolf1-1/+1
2019-02-06py-black: add new packageStephen Herbein1-0/+29
2019-02-06py-toml: add latest version and update checksums to sha256Stephen Herbein1-1/+2
A version >= 0.9.4 required for py-black. Added latest, which is 0.10.0. Manually verified that the .tar.gz for v0.9.3 used to generate the sha256 matched the previous md5.
2019-02-06curl package: add version 7.63.0 (#10516)Matthias Diener1-0/+1
2019-02-06py-multiqc: add version 1.7 (#10520)Douglas Duckworth1-4/+5
Added sha256 for py-multiqc as well as require py-matplotlib < v 3.0
2019-02-06genemark et package: add version 4.38 (#10519)Levi Baber1-1/+9
Also add heu_dir to bin/
2019-02-06Paraview package: update PYTHONPATH for dependents (#10501)Jon Rood1-2/+7
Add vtkmodules directory to PYTHONPATH in Paraview for Trilinos
2019-02-06Add Python 3.7.2 updated (#10531)Daniel Topa1-1/+6
Also add versions 3.7.1, 3.6.8, 3.6.7, 3.6.6. Does NOT alter preferred version (2.7.15). Supplants PR 10491 "Add Python 3.7.2" (https://github.com/spack/spack/pull/10491). Verification builds on LANL Darwin: **Intel Xeon** [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.7.2-d3p7vg6w2r563cpmwsmbgjbsiqc4j4fq [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.7.1-ibom6qj2z64egyaqz5htkwp5tr362il6 [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.8-rkifc3c7mjgdglw27upiap767ut4wpkz [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.7-meuesn43twttt756exyzqgdhohjgipjq [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.6-qwnwme7otyuoqqudcglfmfy75t5npywl **Arm** [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.7.2-qj27kzs4ttdqudm3hsi3pt57kv7lshco [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.7.1-io5eneirgvpegy3tosvp6wq5ndf7yjis [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.8-ej3vnvta2hbtrh7p5hokfqkuewxeqgsa [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.7-l3qnue72ewppn2wxza3w6l62l7ijlque [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.6-b55pdoqsr5bie4k5djd4vokm3nywhm45 **Power9** [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.7.2-cicayvl7ki4tswoqlljsmcetwqcnoh3x [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.7.1-7vej3zvnvyj2jvz5lnxhnts3ok2fcxbp [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.8-xijljmdanyrybcx2rv65qshycmbrfv6c [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.7-vqdhzg7c3xxxregqmzxsqqfzxt2hajvq [+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.6-jf4bnsdwk3qjhtmvjjhblnrcz5dztfdq 2019-02-05 Signed-off-by: Daniel Topa <dantopa@lanl.gov> Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-02-06Update CLAW package with version 1.2.1 (#10528)Valentin Clement (バレンタイン クレメン)1-0/+1
2019-02-06perl-yaml: new package (#10514)Levi Baber1-0/+17
2019-02-06wordnet: new package (#10526)simo-tuomisto1-0/+33
2019-02-06xsdk: enable slepc in deal.ii (used to be a concretization error) (#10218)Denis Davydov1-2/+2
2019-02-05New package: PMDK (#10453)Phil Carns2-0/+75
2019-02-05r-wgcna: new package at 1.64-1 (#10392)Justin Stanley1-0/+31
2019-02-05MPark: Variant v1.4.0 (#10512)Axel Huebl1-1/+2
Add the latest release of Michael Park's C++ Variant lib.
2019-02-04mercury package: add 'udreg' variant (#10415)Phil Carns1-0/+10
Faster and/or more robust in some cases on Cray platforms
2019-02-04New package: perl-hash-merge (#10506)Levi Baber1-0/+18
2019-02-04New package: perl-clone-choose (#10507)Levi Baber1-0/+16
2019-02-04votca*: add v1.5 (#10495)Christoph Junghans4-10/+15
* votca-tools: add v1.5 * votca-csg: add v1.5 * votca-xtp: add v1.5 * votca-ctp: add v1.5
2019-02-04augustus: fix bam2wig auxprog build (#10362)Justin Stanley1-5/+35
* augustus: fix bam2wig auxprog build * augustus: few more changes to make new versions work
2019-02-04tar: add version 1.31 (#10485)Matthias Diener1-0/+1
2019-02-04Catch2: v2.6.0 (#10490)Axel Huebl1-0/+1
Add the latest Catch2 release.
2019-02-01New package: py-alembic (#10436)wspear1-0/+17
2019-02-01New package: py-prometheus-client (#10440)wspear1-0/+17
2019-02-01plumed package: add versions 2.4.4 and 2.5.0 (#10496)Nicholas Labello1-1/+3
2019-02-01dyninst: add patch to work with new boost (#10454)Mark W. Krentel2-0/+35
Add tribool.patch to add explicit casts from tribool to bool in two places. Boost, starting with version 1.69, turned on explicit conversions for tribool, which breaks the build for dyninst. This is merged into the current dyninst develop and is expected to be part of the next release, so the version range uses the current release as an upper bound.
2019-02-01New package: py-async-generator (#10439)wspear1-0/+18
2019-01-31gatk package: new versions, updated helper script (#10459)zschulte1-44/+76
Closes #10168 * Add versions 4.1.0.0 and 4.0.12.0 * Replace md5 checksums with sha256 * Logic to generate a helper script for versions earlier than 4 was not running. This corrects the branch which controls whether this script is generated. * Constrain Java dependency to version 8 (GATK does not work with Java 11) * Avoid adding scripts that have dependencies not handled by Spack such as gcloud and google-chrome. These scripts are good candidates for later extensions.
2019-01-31py-pybigwig: fix build with python3, add numpy variant (#10444)Ricardo Silva2-2/+23
* added patch to correctly pick up non-system curl when building with Python 3 * added numpy variant * add version 0.3.12 * update checksums to sha256
2019-01-31New package: openjdk (#9861)snehring1-0/+98
Closes #2622 This retrieves and installs the binary of Oracle's OpenJDK (an open-source JDK implementation). The logic is largely based on the Spack JDK package (Oracle's closed-source JDK implementation). For now this is only supports Linux. If the download could be customized based on OS (for the same version), binaries are also available for MacOS and Windows.
2019-01-30git-lfs: add version 2.6.1, update build system (#10405)Matthias Diener1-13/+6
Build system was changed to use a Makefile. Therefore older versions (which don't support this) are removed. The new build system also supports testing by default.
2019-01-30fftw: fix include error for 2.x versions (#10039)Tom Payerle1-6/+15
Fixes #7372 Added patch method which renames config.h in the fftw subdir of the source tree. fftw 2.1.5 appears to ship with a copy of this file with all defines commented out. This gets read by the #include directives instead of the version in the build directory with the correct defines. As a result, many C preprocessor macros left undefined, including F77_FUNC_ which causes the bulk of fttwf77.c to be skipped due to an #ifdef, so fftw_reverse_int_array et al not included in library. Fixes #7372 Also fixed some inconsistencies with the handling of quad and long_double in specs between the configure method and the build, check, and install methods.
2019-01-30HDF5: Add develop Version (#10382)Axel Huebl1-0/+13
2019-01-30Mercury package: update libfabric dependency on Cray (#10408)Phil Carns1-1/+0
The Mercury package previously depended on libfabric@develop on Cray platforms in order to pick up a fix for the GNI provider that was only available in git. This is no longer needed now that the libfabric package is at 1.7.0.
2019-01-30r-pkgmaker: add 0.27, new dependencies (#10419)Justin Stanley1-0/+14
2019-01-30gobject-introspection: add 1.56.1 and fix download (#10462)Michael Kuhn1-0/+5
Define url_for_version, since Spack's default substitution is not sufficient
2019-01-30go: fix directory structure issue for 1.11.5 (#10484)Matthias Diener1-2/+9
2019-01-30cmake: Fix linker errors on Darwin when using external dependencies (#10467)Chuck Atkins2-0/+33
Adds upstream patch for a missing framework. This is anticipated to be fixed by CMake 3.13.4 so is only applied up to version 3.13.3
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2024-11-08 03:50:47 +0000