# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack.package import *


class RQuantro(RPackage):
    """A test for when to use quantile normalization.

       A data-driven test for the assumptions of quantile normalization using
       raw data such as objects that inherit eSets (e.g. ExpressionSet,
       MethylSet). Group level information about each sample (such as Tumor /
       Normal status) must also be provided because the test assesses if there
       are global differences in the distributions between the user-defined
       groups."""

    bioc = "quantro"

    version('1.30.0', commit='e756c439cdc5a6fb4d7879aff56a8368475513b5')
    version('1.28.0', commit='109e7452a349f273e10d2ffb79d5624260b67dd5')
    version('1.24.0', commit='c7c0180292156a01722d91b353da44324e72d68f')
    version('1.18.0', commit='f6553c2296289eed31e4b2f32a082e990bdb8359')
    version('1.16.0', commit='cfc2e853bdc3cc90fd35e153fe243892d50d61c6')
    version('1.14.0', commit='2d43264b2a95ae8ca51a69d7768fe43b9f1b77bb')
    version('1.12.0', commit='1cfcc73875cf4ecc2618e5e45fda89bd075a5d12')
    version('1.10.0', commit='111337c0aba052aa49c3d2e2d3042794b28858c9')

    depends_on('r@3.1.3:', type=('build', 'run'))
    depends_on('r@4.0:', type=('build', 'run'), when='@1.24.0:')
    depends_on('r-biobase', type=('build', 'run'))
    depends_on('r-minfi', type=('build', 'run'))
    depends_on('r-doparallel', type=('build', 'run'))
    depends_on('r-foreach', type=('build', 'run'))
    depends_on('r-iterators', type=('build', 'run'))
    depends_on('r-ggplot2', type=('build', 'run'))
    depends_on('r-rcolorbrewer', type=('build', 'run'))