%global __brp_check_rpaths %{nil}
%global packname  QTL.gCIMapping
%global packver   3.4
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          3.4
Release:          1%{?dist}%{?buildtag}
Summary:          QTL Genome-Wide Composite Interval Mapping

License:          GPL (>= 2)
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 3.5.0
Requires:         R-core >= 3.5.0
BuildRequires:    R-CRAN-Rcpp >= 0.12.17
BuildRequires:    R-methods 
BuildRequires:    R-CRAN-openxlsx 
BuildRequires:    R-CRAN-readxl 
BuildRequires:    R-CRAN-lars 
BuildRequires:    R-CRAN-stringr 
BuildRequires:    R-CRAN-data.table 
BuildRequires:    R-CRAN-glmnet 
BuildRequires:    R-CRAN-doParallel 
BuildRequires:    R-CRAN-foreach 
BuildRequires:    R-CRAN-MASS 
BuildRequires:    R-CRAN-qtl 
Requires:         R-CRAN-Rcpp >= 0.12.17
Requires:         R-methods 
Requires:         R-CRAN-openxlsx 
Requires:         R-CRAN-readxl 
Requires:         R-CRAN-lars 
Requires:         R-CRAN-stringr 
Requires:         R-CRAN-data.table 
Requires:         R-CRAN-glmnet 
Requires:         R-CRAN-doParallel 
Requires:         R-CRAN-foreach 
Requires:         R-CRAN-MASS 
Requires:         R-CRAN-qtl 

%description
Conduct multiple quantitative trait loci (QTL) and QTL-by-environment
interaction (QEI) mapping via ordinary or compressed variance component
mixed models with random- or fixed QTL/QEI effects. First, each position
on the genome is detected in order to obtain a negative logarithm P-value
curve against genome position. Then, all the peaks on each effect
(additive or dominant) curve or on each locus curve are viewed as
potential main-effect QTLs and QEIs, all their effects are included in a
multi-locus model, their effects are estimated by both least angle
regression and empirical Bayes (or adaptive lasso) in backcross and F2
populations, and true QTLs and QEIs are identified by likelihood radio
test. See Zhou et al. (2022) <doi:10.1093/bib/bbab596> and Wen et al.
(2018) <doi:10.1093/bib/bby058>.

%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}