A flexible package manager that supports multiple versions, configurations, platforms, and compilers.
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Justin S 1b24dfb8ba Replace git-based Bioconductor R packages (#12005)
* Replace git-based Bioconductor R packages

The current collection of bioconductor packages tend to have scattered
dependencies and missing versions. This commit replaces git-based
packages with tool-generated Spack package recipes with correct
dependencies and descriptions in place.

* Fix some broken package names, add periods to title docstrings

* r-clue: new package at 0.3-57

* r-genomeinfodbdata: add 1.2.1

* r-gofuncr: new package at 1.4.0

* r-pfam-db: add 3.8.2

* Add missed package r-genelendatabase

* update r-goseq package

* update r-glimma package

* update r-rots package

* r-org-hs-eg-db: add 3.8.2

* r-vgam: fix incorrect R version

* r-rnaseqmap: new package at 2.42.0

* r-rhdf5lib: new package at 1.6.0

* r-scrime: new package at 1.3.5

* r-delayedmatrixstats: new package at 1.6.0

* r-hdf5array: new package at 1.12.1

* r-biocfilecache: new package at 1.8.0

* r-ctc: add new versions, dependencies

* r-genemeta: new package at 1.56.0

* r-scrime: fix flake8

* r-ensembldb: add missing dependencies

* Added missing dependencies to packages with certain DESCRIPTIONS

* r-mapplots: new package at 1.5.1

* r-beachmat: new package at 2.0.0

* r-beeswarm: new package at 0.2.3

* r-biocneighbors: new package at 1.2.0

* r-biocsingular: new package at 1.0.0

* r-ecp: new package at 3.1.1

* r-enrichplot: new package at 1.4.0

* r-europepmc: new package at 0.3

* r-ggbeeswarm: new package at 0.6.0

* r-ggplotify: new package at 0.0.3

* r-ggraph: new package at 1.0.2

* r-gridgraphics: new package at 0.4-1

* r-rcppannoy: new package at 0.0.12

* r-rcpphnsw: new package at 0.1.0

* r-rsvd: new package at 1.0.1

* r-scater: new package at 1.12.2

* r-singlecellexperiment: new package at 1.6.0

* r-tximport: new package at 1.12.3

* r-upsetr: new package at 1.4.0

* r-vioplot: new package at 0.3.2

* r-readr: add 1.3.1

* r-matrixstats: add 0.54.0

* r-ecp: flake8 fix

* r-biocmanager: new package at 1.30.4

* update bioconductor packages requiring BiocManager, new versions

* r-lambda-r: add 1.2.3

* r-vegan: add 2.5-5

* r-cner, r-rcppannoy, r-reportingtools, r-rsvd: add missing newlines at EOF

* r-chemometrics: flake8 fixes

* r-vgam: flake8 fixes

* CRAN packages: use cloud.r-project.org

* Use DESCRIPTION for R version constraints over bioconductor releases

* Update missed packages ABAData, acde, affydata

* Update remaining missed packages

* bio: Drop 'when' clause from first checksummed versions

* bio: improve package description generation logic

* r-genomeinfodbdata: use explicit sha256 sums

* r-pfam-db: update dependencies, add 3.10.0

* update r-org-hs-eg-db

* r-dirichletmultinomial: re-add gsl

* r-polyclip: new package at 1.10-0

* r-farver: new package at 1.1.0

* r-tweenr: new package at 1.0.1

* r-ggforce: new package at 0.3.1

* r-ggforce: remove redundant dep

* r-ggraph: add missing deps

* r-rcpphnsw: remove redundant depends_on

* r-reportingtools: re-add r-r-utils dep

* r-rhdf5: add gmake dep

* r-rhtslib: add system dependencies

* r-rsamtools: add gmake dep

* r-farver: remove redundant dep

* r-tweenr: remove redundant dep

* r-variantannotation: add gmake dep

* r-rgraphviz: add graphviz dep

* r-vsn: correct r-hexbin constraint

* r-scater: fix obsolete deps

* r-variantannotation: fix gmake dep type

* r-scater: tighten R version constraints

* r-rsamtools: fix gmake dep type

* r-rhtslib: fix gmake dep type

* r-rhtslib: use xz over lzma

* r-rhdf5: fix gmake dep type

* r-farver: replace with newer recipe for 2.0.1

* r-mzr: remove old dependency

* r-reportingtools: remove builtin dependency

* r-mzr: add gmake dep

* r-rhtslib: make system libraries link deps

* r-genomeinfodbdata: fix R version constraints

* r-geoquery: remove old deps from new versions

* r-genomicfeatures: tighten r-rmysql dep

* r-ensembldb: tighten r-annotationhub dep

* r-complexheatmap: fix r-dendextend dep

* r-cner: fix utils dep name

* r-clusterprofiler: fix r-gosemsim version req

* r-biostrings: fix r-iranges version reqs

* r-rhdf5lib: add gmake dep

* r-oligoclasses: fix r-biocinstaller dep range

* r-organismdbi: fix r-biocinstaller dep range

* r-hdf5array: add gmake dep

* r-gtrellis: tighten r-circlize version req

* r-gostats: fix r-graph version req

* r-glimma: fix old dependency ranges

* r-biostrings: syntax fix

* r-organismdbi: syntax fix

* r-dose: fix r-igraph dep

* r-dose: fix r-scales, r-rvcheck deps

* r-affy: fix r-biocinstaller dep

* r-ampliqueso: fix homepage

* r-aneufinder: fix r-biocgenerics dep

* r-beachmat: fix changed deps

* r-biocneighbors: fix old R constraint

* r-biocmanager: rewrite recipe for 1.30.10

* Update var/spack/repos/builtin/packages/r-biocinstaller/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/r-oligoclasses/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-27 20:57:15 -06:00
.github Revert "add maintainer review action to main.workflow" (#12316) 2019-08-07 17:23:47 -07:00
bin fetching: S3 upload and download (#11117) 2019-10-22 00:32:04 -07:00
etc/spack/defaults Config option to allow gpg warning suppression (#13743) 2019-11-14 16:22:01 -08:00
lib/spack use semicolons instead of newlines in module/python command (#13904) 2019-11-26 17:09:24 -08:00
share/spack Package Index: Build in Dockerhub (#13810) 2019-11-26 10:11:29 -07:00
var/spack Replace git-based Bioconductor R packages (#12005) 2019-11-27 20:57:15 -06:00
.codecov.yml coverage: restore status updates on PRs (#12032) 2019-07-15 22:45:00 -07:00
.coveragerc coverage: use kcov to get coverage for our cc script 2018-12-29 23:47:29 -08:00
.dockerignore fix multiple issues with the docker images (#9718) 2018-12-20 11:11:55 -08:00
.flake8 flake8: add exceptions for overly pedantic camelcase rules from pep8-naming (#11477) 2019-05-16 09:47:02 +02:00
.flake8_packages flake8: add exceptions for overly pedantic camelcase rules from pep8-naming (#11477) 2019-05-16 09:47:02 +02:00
.gitignore Ignore git *.orig files and emacs backup files 2019-09-18 23:51:27 -07:00
.gitlab-ci.yml fetching: S3 upload and download (#11117) 2019-10-22 00:32:04 -07:00
.mailmap
.readthedocs.yml Updated Sphinx configuration (#11165) 2019-04-11 14:38:52 -07:00
.travis.yml Package Index: Build in Dockerhub (#13810) 2019-11-26 10:11:29 -07:00
CHANGELOG.md Add top-level CHANGELOG.md with release notes. 2019-10-25 23:19:36 -07:00
COPYRIGHT External: add macholib and altgraph needed to relocate Mach-o binaries on Linux (#12909) 2019-09-26 11:48:22 -05:00
LICENSE-APACHE relicense: update COPYRIGHT, LICENSE-*, README, CONTRIBUTING, and NOTICE 2018-10-17 14:42:06 -07:00
LICENSE-MIT copyright: update license headers for 2013-2019 copyright. 2019-01-01 00:44:28 -08:00
NOTICE relicense: update COPYRIGHT, LICENSE-*, README, CONTRIBUTING, and NOTICE 2018-10-17 14:42:06 -07:00
README.md readme: make list of links even tighter. 2019-06-30 23:15:37 -07:00

Spack Spack

Build Status codecov Read the Docs Slack

Spack is a multi-platform package manager that builds and installs multiple versions and configurations of software. It works on Linux, macOS, and many supercomputers. Spack is non-destructive: installing a new version of a package does not break existing installations, so many configurations of the same package can coexist.

Spack offers a simple "spec" syntax that allows users to specify versions and configuration options. Package files are written in pure Python, and specs allow package authors to write a single script for many different builds of the same package. With Spack, you can build your software all the ways you want to.

See the Feature Overview for examples and highlights.

To install spack and your first package, make sure you have Python. Then:

$ git clone https://github.com/spack/spack.git
$ cd spack/bin
$ ./spack install zlib

Documentation

Full documentation is available, or run spack help or spack help --all.

Tutorial

We maintain a hands-on tutorial. It covers basic to advanced usage, packaging, developer features, and large HPC deployments. You can do all of the exercises on your own laptop using a Docker container.

Feel free to use these materials to teach users at your organization about Spack.

Community

Spack is an open source project. Questions, discussion, and contributions are welcome. Contributions can be anything from new packages to bugfixes, documentation, or even new core features.

Resources:

Contributing

Contributing to Spack is relatively easy. Just send us a pull request. When you send your request, make develop the destination branch on the Spack repository.

Your PR must pass Spack's unit tests and documentation tests, and must be PEP 8 compliant. We enforce these guidelines with Travis CI. To run these tests locally, and for helpful tips on git, see our Contribution Guide.

Spack uses a rough approximation of the Git Flow branching model. The develop branch contains the latest contributions, and master is always tagged and points to the latest stable release.

Code of Conduct

Please note that Spack has a Code of Conduct. By participating in the Spack community, you agree to abide by its rules.

Authors

Many thanks go to Spack's contributors.

Spack was created by Todd Gamblin, tgamblin@llnl.gov.

Citing Spack

If you are referencing Spack in a publication, please cite the following paper:

License

Spack is distributed under the terms of both the MIT license and the Apache License (Version 2.0). Users may choose either license, at their option.

All new contributions must be made under both the MIT and Apache-2.0 licenses.

See LICENSE-MIT, LICENSE-APACHE, COPYRIGHT, and NOTICE for details.

SPDX-License-Identifier: (Apache-2.0 OR MIT)

LLNL-CODE-647188