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2017-12-13Ignore log files that appear in root dir with "spack -d install ..." (#6670)Scott Wittenburg1-0/+2
2017-12-12new packages: biopieces and dependencies (#6478)Audrey Thoma47-13/+1784
This also adds the tcl, tk, and libx11 dependencies to ruby. All other changes are new packages.
2017-12-12laghos: inject CXX (#6664)Christoph Junghans1-0/+1
2017-12-12swfft: inject CC/CXX (#6666)Christoph Junghans1-0/+11
2017-12-12xsdk: update xsdk@develop to use sundials, plasma, magma (#6649)Satish Balay1-1/+6
Also update xsdk@0.3.0 to use a fixed version of magma
2017-12-11Add new package minisign (#6644)nshtg1-0/+36
A dead simple tool to sign files and verify signatures. See https://jedisct1.github.io/minisign
2017-12-11libsodium: Update to 1.0.15 (#6643)nshtg1-0/+1
2017-12-11git: Update to 2.15.1 (#6642)nshtg1-0/+5
2017-12-11openssl: Update to 1.0.2n (#6641)nshtg1-1/+2
From 07.12.2017, fixes CVE-2017-3737
2017-12-11Py h5py update (#6635)Brian Van Essen1-0/+2
2017-12-11add -d option for edit command (#6416)becker331-3/+21
* add -d option for edit command and improve suffix extrapolation from '.py' to use glob
2017-12-11intel-parallel-studio: restrict patch to versions > 2016 (#6523)健美猫1-4/+5
Fixes #6522 Patch psxevars.sh and psxevars.csh only when year > 2016. pxevars.csh does not exist for versions before 2017. psxevars.sh does not appear to require this patch for versions before 2017.
2017-12-11Simplified "Environment-Modules" section in getting started guide. (#6410)Massimiliano Culpo1-58/+21
Fixes #2440 The "Getting started" guide should be short and sweet. This commit simplifies the "Environment-Modules" section pruning: - outdated / wrong suggestions as noted in #2440 - uncommon setups that are better treated in a reference guide
2017-12-11bazel: include SPACK_DEBUG_LOG_ID in environment (#6562)Johann Klähn2-2/+12
Fixes #6521. Bazel's build system filters environment variables, including those set by Spack for use by its compiler wrapper. This updates the patch to include the SPACK_DEBUG_LOG_ID variable added in #5837.
2017-12-10disable plasma in xsdk 0.3.0 (#6621)Satish Balay1-1/+0
2017-12-10Fix reference to self.versions in neovim package (#6639)Adam J. Stewart1-1/+1
2017-12-08updates to conduit and ascent packages (new PR) (#6584)Cyrus Harrison3-30/+76
* optional path to use spacks py-site-pkgs, install host-cfg for provenance * add more comments and address review requests * only use st-pkgs-dir when +python * ascent does not need doxygen * capture mpiexec if it exists * added missing import * flake8 fix * default adios variant to False * ascent develop now reqs conduit master * optional path to use spacks py-site-pkgs, install host-cfg for provenance * add more comments and address review requests * only use st-pkgs-dir when +python * ascent does not need doxygen * capture mpiexec if it exists * added missing import * flake8 fix * default adios variant to False * ascent develop now reqs conduit master * conduit: use hdf5 1.8 for wider output compat
2017-12-08Relax restriction on lua version. (#5886)Chris Green1-1/+1
2017-12-08Add NekCEM package to spack (#6509)Thilina Rathnayake1-0/+90
2017-12-08Update the Nekbone package (#6508)Thilina Rathnayake1-21/+36
2017-12-08add restriction to py-setuptools dependency on py-flake8 (#6589)healther1-1/+1
2017-12-08Perl-statistics-descriptive: Create new package (#6588)Eric1-0/+34
2017-12-08Fix AstroPy: Missing Markupsafe (#6630)Axel Huebl1-0/+1
`py-markupsafe` was missing during `spack install` as a build error.
2017-12-08Add: Py-Plotly (#6628)Axel Huebl4-0/+42
* Add: Py-Plotly The requirements of py-plotlit are rather strict fixed to specific versions, so I did not add an "upper versions" `:` to the constrains. See https://github.com/plotly/plotly.py/blob/master/requirements.txt * Py-Requests, Py-Six, Py-Pytz: Older Versions Add two older versions of requests, pytz and six for plotly.
2017-12-08Fix in download url for package libaio (#6616)Paschalis Korosoglou1-1/+1
2017-12-08Update zsh to 5.4.2 (#6609)nshtg1-1/+2
2017-12-08r-tidycensus: Create new package. (#6595)lingnanyuan1-0/+53
2017-12-08r-rgdal: Create new package. (#6593)lingnanyuan1-0/+47
2017-12-08r-tigris: Create new package. (#6591)lingnanyuan1-0/+48
2017-12-08Update openSSL to 1.0.2m/1.1.0g (#6596)nshtg1-2/+4
2017-12-08Update openSSH to 7.6p1 (#6598)nshtg1-1/+2
2017-12-08Update tmux to 2.6 (#6597)nshtg1-1/+2
2017-12-08Updated hash for v1.0 tag of Laghos (#6626)Tzanio Kolev1-1/+1
2017-12-08Package 'openjpeg': set INSTALL_NAME_DIR on MacOS for old versions. (#6603)Sergey Kosukhin2-0/+18
2017-12-08r-rhtslib: added build dependency on autoconf (#6627)Paschalis Korosoglou1-0/+1
2017-12-08py-cogent: Create new package (#6624)Eric1-0/+37
2017-12-08dealii: update boost dependency (#6586)Denis Davydov2-22/+57
(i) blacklst 1.65.0 due to issues on Ubuntu with gcc 5.4.0 (ii) add a patch for 1.65.1 to fix serialization (iii) simplify boost's depends_on()
2017-12-08py-htseq: Create new package. (#6623)lingnanyuan1-0/+42
2017-12-08Candle benchmarks update (#6619)Brian Van Essen1-0/+1
Added a dependency on HDF5 support for the CANDLE benchmarks.
2017-12-08Adding openssl dependency to xrootd. Closes #6601 (#6618)Benedikt Riedel1-0/+1
2017-12-08Update vim to 8.0.1376 (#6599)nshtg1-1/+2
2017-12-08subread: Add version 1.6.0 (#6615)Eric1-0/+1
2017-12-08qrupdate: fix blas/lapack and compilation of macOS (#6614)Denis Davydov1-2/+27
2017-12-08py-reportlab: Create new package (#6612)Eric1-0/+35
2017-12-08Update fish to 2.7.0 (#6608)nshtg1-3/+4
2017-12-08bedtools2: Add version 2.27.0 (#6606)Eric1-0/+1
2017-12-08Provide a patch to allow hdf5@1.10.1 to build with intel/18.0.1. (#6583)Kelly (KT) Thompson2-0/+22
This is known issue. See: https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951.
2017-12-08Update for 'eccodes'. (#6604)Sergey Kosukhin5-22/+97
2017-12-08Update for 'grib-api'. (#6605)Sergey Kosukhin5-25/+181
2017-12-08Update openfast package to explicity pass MPI implementation during cmake ↵Jon Rood1-0/+3
configure. (#6590)