# 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 RPhyloseq(RPackage):
    """Handling and analysis of high-throughput microbiome census data.

    phyloseq provides a set of classes and tools to facilitate the import,
    storage, analysis, and graphical display of microbiome census data."""

    bioc = "phyloseq"

    license("LiLiQ-R-1.1")

    version("1.44.0", commit="03b74f7d7aa866f5f9a84c7368da57b7a168967e")
    version("1.42.0", commit="de6be71fe9902bdfe7791163acb7b67d238424dc")
    version("1.40.0", commit="20bb27d5e6e0d4368978a15671b829990b1f4568")
    version("1.38.0", commit="1e2409a6ed3c23e308275098c2dc9fdba9d5e5f6")
    version("1.34.0", commit="cbed93ead5528fe9024d646c597dab9fc95952d3")
    version("1.28.0", commit="a86ed1e0a650fdf80bee5a0a5a82aaa5a276178d")
    version("1.26.1", commit="a084072bc9e057b90adfbd59e27db2a1ecee151c")
    version("1.24.2", commit="829992f88c79de48bb8749678624e2bbd3b66645")
    version("1.22.3", commit="c695323f2963636d16acda9f05a583bd58e31344")
    version("1.20.0", commit="107d1d5e3437a6e33982c06a548d3cc91df2a7e0")

    depends_on("r@3.3.0:", type=("build", "run"))
    depends_on("r@3.4.0:", type=("build", "run"), when="@1.22.3")
    depends_on("r-ade4@1.7-4:", type=("build", "run"))
    depends_on("r-ape@3.4:", type=("build", "run"))
    depends_on("r-ape@5.0:", type=("build", "run"), when="@1.22.3:")
    depends_on("r-biobase", type=("build", "run"))
    depends_on("r-biobase@2.36.2:", type=("build", "run"), when="@1.22.3:")
    depends_on("r-biocgenerics@0.18.0:", type=("build", "run"))
    depends_on("r-biocgenerics@0.22.0:", type=("build", "run"), when="@1.22.3:")
    depends_on("r-biomformat@1.0.0:", type=("build", "run"))
    depends_on("r-biostrings@2.40.0:", type=("build", "run"))
    depends_on("r-cluster@2.0.4:", type=("build", "run"))
    depends_on("r-data-table@1.9.6:", type=("build", "run"))
    depends_on("r-data-table@1.10.4:", type=("build", "run"), when="@1.22.3:")
    depends_on("r-foreach@1.4.3:", type=("build", "run"))
    depends_on("r-ggplot2@2.1.0:", type=("build", "run"))
    depends_on("r-igraph@1.0.1:", type=("build", "run"))
    depends_on("r-multtest@2.28.0:", type=("build", "run"))
    depends_on("r-plyr@1.8.3:", type=("build", "run"))
    depends_on("r-reshape2@1.4.1:", type=("build", "run"))
    depends_on("r-scales@0.4.0:", type=("build", "run"))
    depends_on("r-vegan@2.3.5:", type=("build", "run"))
    depends_on("r-vegan@2.4:", type=("build", "run"), when="@1.22.3:")
    depends_on("r-vegan@2.5:", type=("build", "run"), when="@1.24.2:")