%global __brp_check_rpaths %{nil}
%global packname  omicwas
%global packver   0.8.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.8.0
Release:          1%{?dist}%{?buildtag}
Summary:          Cell-Type-Specific Association Testing in Bulk Omics Experiments

License:          GPL-3
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 3.6.0
Requires:         R-core >= 3.6.0
BuildArch:        noarch
BuildRequires:    R-CRAN-broom 
BuildRequires:    R-CRAN-data.table 
BuildRequires:    R-CRAN-dplyr 
BuildRequires:    R-CRAN-ff 
BuildRequires:    R-CRAN-glmnet 
BuildRequires:    R-CRAN-magrittr 
BuildRequires:    R-CRAN-MASS 
BuildRequires:    R-CRAN-matrixStats 
BuildRequires:    R-parallel 
BuildRequires:    R-CRAN-purrr 
BuildRequires:    R-CRAN-rlang 
BuildRequires:    R-CRAN-tidyr 
Requires:         R-CRAN-broom 
Requires:         R-CRAN-data.table 
Requires:         R-CRAN-dplyr 
Requires:         R-CRAN-ff 
Requires:         R-CRAN-glmnet 
Requires:         R-CRAN-magrittr 
Requires:         R-CRAN-MASS 
Requires:         R-CRAN-matrixStats 
Requires:         R-parallel 
Requires:         R-CRAN-purrr 
Requires:         R-CRAN-rlang 
Requires:         R-CRAN-tidyr 

%description
In bulk epigenome/transcriptome experiments, molecular expression is
measured in a tissue, which is a mixture of multiple types of cells. This
package tests association of a disease/phenotype with a molecular marker
for each cell type. The proportion of cell types in each sample needs to
be given as input. The package is applicable to epigenome-wide association
study (EWAS) and differential gene expression analysis. Takeuchi and Kato
(submitted) "omicwas: cell-type-specific epigenome-wide and transcriptome
association study".

%prep
%setup -q -c -n %{packname}

# fix end of executable files
find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \;
# prevent binary stripping
[ -d %{packname}/src ] && find %{packname}/src -type f -exec \
  sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true
# don't allow local prefix in executable scripts
find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \;

%build

%install

mkdir -p %{buildroot}%{rlibdir}
%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname}
test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
rm -f %{buildroot}%{rlibdir}/R.css
# remove buildroot from installed files
find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \;

%files
%{rlibdir}/%{packname}