# Copyright 2013-2020 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 import *


class RLumi(RPackage):
    """The lumi package provides an integrated solution for the Illumina
    microarray data analysis. It includes functions of Illumina BeadStudio
    (GenomeStudio) data input, quality control, BeadArray-specific variance
    stabilization, normalization and gene annotation at the probe level. It
    also includes the functions of processing Illumina methylation microarrays,
    especially Illumina Infinium methylation microarrays."""

    homepage = "https://bioconductor.org/packages/release/bioc/html/lumi.html"
    git      = "https://git.bioconductor.org/packages/lumi"

    version('2.38.0', commit='321d480d44ce9a0c02ce5af1bddc1f549abdea59')

    depends_on('r@2.10:', type=('build', 'run'))
    depends_on('r-biobase@2.5.5:', type=('build', 'run'))
    depends_on('r-affy@1.23.4:', type=('build', 'run'))
    depends_on('r-methylumi@2.3.2:', type=('build', 'run'))
    depends_on('r-genomicfeatures', type=('build', 'run'))
    depends_on('r-genomicranges', type=('build', 'run'))
    depends_on('r-annotate', type=('build', 'run'))
    depends_on('r-lattice', type=('build', 'run'))
    depends_on('r-mgcv@1.4-0:', type=('build', 'run'))
    depends_on('r-nleqslv', type=('build', 'run'))
    depends_on('r-kernsmooth', type=('build', 'run'))
    depends_on('r-preprocesscore', type=('build', 'run'))
    depends_on('r-rsqlite', type=('build', 'run'))
    depends_on('r-dbi', type=('build', 'run'))
    depends_on('r-annotationdbi', type=('build', 'run'))
    depends_on('r-mass', type=('build', 'run'))