%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  rtpcr
%global packver   2.1.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          2.1.0
Release:          1%{?dist}%{?buildtag}
Summary:          qPCR Data Analysis

License:          GPL-3
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
BuildArch:        noarch
BuildRequires:    R-CRAN-multcomp 
BuildRequires:    R-CRAN-multcompView 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-CRAN-lmerTest 
BuildRequires:    R-CRAN-purrr 
BuildRequires:    R-CRAN-reshape2 
BuildRequires:    R-CRAN-tidyr 
BuildRequires:    R-CRAN-dplyr 
BuildRequires:    R-grid 
BuildRequires:    R-CRAN-emmeans 
Requires:         R-CRAN-multcomp 
Requires:         R-CRAN-multcompView 
Requires:         R-CRAN-ggplot2 
Requires:         R-CRAN-lmerTest 
Requires:         R-CRAN-purrr 
Requires:         R-CRAN-reshape2 
Requires:         R-CRAN-tidyr 
Requires:         R-CRAN-dplyr 
Requires:         R-grid 
Requires:         R-CRAN-emmeans 

%description
Amplification efficiency estimation, statistical analysis, and graphical
representation of quantitative real-time PCR (qPCR) data using one or more
specified reference genes is handled by 'rtpcr' package. By accounting for
amplification efficiency values, 'rtpcr' was developed using a general
calculation method described by Ganger et al. (2017)
<doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019)
<doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl
methods. Based on the experimental conditions, the functions of the
'rtpcr' package use t-test (for experiments with a two-level factor),
analysis of variance (ANOVA), analysis of covariance (ANCOVA) or analysis
of repeated measure data to analyse the relative expression (Delta Delta
Ct method or Delta Ct method). The functions further provide standard
errors and confidence intervals for means, apply statistical mean
comparisons and present significance.

%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}