%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  SQUIRE
%global packver   1.0.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.0.0
Release:          1%{?dist}%{?buildtag}
Summary:          Statistical Quality-Assured Integrated Response Estimation

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


BuildRequires:    R-devel >= 4.2.0
Requires:         R-core >= 4.2.0
BuildArch:        noarch
BuildRequires:    R-stats 
Requires:         R-stats 

%description
Implements statistically validated biological parameter optimization that
combines automated parameter type detection with rigorous statistical
quality assurance. Unlike conventional optimizers that fit parameters to
any data, 'SQUIRE' first validates whether statistically significant
biological effects exist before proceeding with parameter estimation. Uses
trust region methods from Conn et al. (2000)
<doi:10.1137/S1052623497325107>, ANOVA-based validation following Fisher
(1925) <doi:10.1007/978-1-4612-4380-9_6>, and effect size calculations per
Cohen (1988, ISBN:0805802835). Automatically distinguishes rate-based,
positive-constrained, and unconstrained variables, applying
geometry-appropriate optimization methods while preventing over-fitting to
noise through built-in statistical validation, effect size assessment, and
data quality requirements. Designed for complex biological and
environmental models including germination studies, dose-response curves,
and survival analysis. Enhanced successor to the 'GALAHAD' optimization
framework with integrated statistical gatekeeping. Developed at the
Minnesota Center for Prion Research and Outreach at the University of
Minnesota.

%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}