# Copyright 2013-2023 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 RWatermelon(RPackage):
    """Illumina 450 methylation array normalization and metrics.

    15 flavours of betas and three performance metrics, with methods for
    objects produced by methylumi and minfi packages."""

    bioc = "wateRmelon"

    version("2.6.0", commit="a46541ffcc08efebf08ea29cb214a45f51f5cb72")
    version("2.4.0", commit="31c15255511940b8b83d039c42ec89e43ceb0885")
    version("2.2.0", commit="6ec49efe98aef31d0789b31ab048eb46edec762c")
    version("2.0.0", commit="f6a331bdf50e0e5c94009fb67be873d996348ade")
    version("1.34.0", commit="3fa2745535c22068a438747b41b9d793196098d4")
    version("1.30.0", commit="66d7579fe49206d965832288df7937c3d43ed578")

    depends_on("r@2.10:", type=("build", "run"))
    depends_on("r@3.5.0:", type=("build", "run"), when="@2.0.0:")
    depends_on("r-biobase", type=("build", "run"))
    depends_on("r-limma", type=("build", "run"))
    depends_on("r-matrixstats", type=("build", "run"))
    depends_on("r-methylumi", type=("build", "run"))
    depends_on("r-lumi", type=("build", "run"))
    depends_on("r-roc", type=("build", "run"))
    depends_on("r-illuminahumanmethylation450kanno-ilmn12-hg19", type=("build", "run"))
    depends_on("r-illuminaio", type=("build", "run"))