%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  miLAG
%global packver   1.0.5
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.0.5
Release:          1%{?dist}%{?buildtag}
Summary:          Calculates Microbial Lag Duration (on the Population Level) from Provided Growth Curve Data

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


BuildRequires:    R-devel >= 4.3.0
Requires:         R-core >= 4.3.0
BuildArch:        noarch
BuildRequires:    R-CRAN-ggplot2 >= 3.4.1
BuildRequires:    R-CRAN-testthat >= 3.1.8
BuildRequires:    R-CRAN-minpack.lm >= 1.2.2
BuildRequires:    R-CRAN-dplyr >= 1.0.8
BuildRequires:    R-CRAN-nlsMicrobio >= 0.0.3
Requires:         R-CRAN-ggplot2 >= 3.4.1
Requires:         R-CRAN-testthat >= 3.1.8
Requires:         R-CRAN-minpack.lm >= 1.2.2
Requires:         R-CRAN-dplyr >= 1.0.8
Requires:         R-CRAN-nlsMicrobio >= 0.0.3

%description
Microbial growth is often measured by growth curves i.e. a table of
population sizes and times of measurements. This package allows to use
such growth curve data to determine the duration of "microbial lag phase"
i.e. the time needed for microbes to restart divisions. It implements the
most commonly used methods to calculate the lag duration, these methods
are discussed and described in Opalek et.al. 2022. Citation: Smug, B. J.,
Opalek, M., Necki, M., & Wloch-Salamon, D. (2024). Microbial lag
calculator: A shiny-based application and an R package for calculating the
duration of microbial lag phase. Methods in Ecology and Evolution, 15,
301–307 <doi:10.1111/2041-210X.14269>.

%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}