%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  drugsens
%global packver   0.1.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.1.0
Release:          1%{?dist}%{?buildtag}
Summary:          Automated Analysis of 'QuPath' Output Data and Metadata Extraction

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
Requires:         R-core >= 4.2
BuildArch:        noarch
BuildRequires:    R-CRAN-testthat >= 3.0.0
BuildRequires:    R-CRAN-dplyr 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-CRAN-ggpubr 
BuildRequires:    R-CRAN-knitr 
BuildRequires:    R-CRAN-roxygen2 
BuildRequires:    R-stats 
BuildRequires:    R-CRAN-stringr 
BuildRequires:    R-CRAN-tidyr 
BuildRequires:    R-CRAN-tidyselect 
BuildRequires:    R-utils 
Requires:         R-CRAN-testthat >= 3.0.0
Requires:         R-CRAN-dplyr 
Requires:         R-CRAN-ggplot2 
Requires:         R-CRAN-ggpubr 
Requires:         R-CRAN-knitr 
Requires:         R-CRAN-roxygen2 
Requires:         R-stats 
Requires:         R-CRAN-stringr 
Requires:         R-CRAN-tidyr 
Requires:         R-CRAN-tidyselect 
Requires:         R-utils 

%description
A comprehensive toolkit for analyzing microscopy data output from 'QuPath'
software. Provides functionality for automated data processing, metadata
extraction, and statistical analysis of imaging results. The methodology
implemented in this package is based on Labrosse et al. (2024)
<doi:10.1016/j.xpro.2024.103274> "Protocol for quantifying drug
sensitivity in 3D patient-derived ovarian cancer models", which describes
the complete workflow for drug sensitivity analysis in patient-derived
cancer models.

%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}