%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  mashr
%global packver   0.2.79
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.2.79
Release:          1%{?dist}%{?buildtag}
Summary:          Multivariate Adaptive Shrinkage

License:          BSD_3_clause + file LICENSE
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 3.3.0
Requires:         R-core >= 3.3.0
BuildRequires:    R-CRAN-ashr >= 2.2.22
BuildRequires:    R-CRAN-Rcpp >= 1.0.8
BuildRequires:    R-CRAN-RcppGSL >= 0.3.8
BuildRequires:    R-CRAN-assertthat 
BuildRequires:    R-utils 
BuildRequires:    R-stats 
BuildRequires:    R-CRAN-plyr 
BuildRequires:    R-CRAN-rmeta 
BuildRequires:    R-CRAN-mvtnorm 
BuildRequires:    R-CRAN-abind 
BuildRequires:    R-CRAN-softImpute 
BuildRequires:    R-CRAN-RcppArmadillo 
Requires:         R-CRAN-ashr >= 2.2.22
Requires:         R-CRAN-Rcpp >= 1.0.8
Requires:         R-CRAN-assertthat 
Requires:         R-utils 
Requires:         R-stats 
Requires:         R-CRAN-plyr 
Requires:         R-CRAN-rmeta 
Requires:         R-CRAN-mvtnorm 
Requires:         R-CRAN-abind 
Requires:         R-CRAN-softImpute 

%description
Implements the multivariate adaptive shrinkage (mash) method of Urbut et
al (2019) <DOI:10.1038/s41588-018-0268-8> for estimating and testing large
numbers of effects in many conditions (or many outcomes). Mash takes an
empirical Bayes approach to testing and effect estimation; it estimates
patterns of similarity among conditions, then exploits these patterns to
improve accuracy of the effect estimates. The core linear algebra is
implemented in C++ for fast model fitting and posterior computation.

%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
[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \
  sed -i 's@-g0@@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}