%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  ComBatFamQC
%global packver   1.0.6
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.0.6
Release:          1%{?dist}%{?buildtag}
Summary:          Comprehensive Batch Effect Diagnostics and Harmonization

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


BuildRequires:    R-devel >= 4.1.0
Requires:         R-core >= 4.1.0
BuildArch:        noarch
BuildRequires:    R-CRAN-tidyr 
BuildRequires:    R-CRAN-dplyr 
BuildRequires:    R-CRAN-magrittr 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-CRAN-DT 
BuildRequires:    R-CRAN-shiny 
BuildRequires:    R-CRAN-car 
BuildRequires:    R-CRAN-broom 
BuildRequires:    R-CRAN-pbkrtest 
BuildRequires:    R-parallel 
BuildRequires:    R-CRAN-Rtsne 
BuildRequires:    R-CRAN-MDMR 
BuildRequires:    R-CRAN-gamlss 
BuildRequires:    R-CRAN-lme4 
BuildRequires:    R-CRAN-mgcv 
BuildRequires:    R-CRAN-bslib 
BuildRequires:    R-CRAN-shinydashboard 
BuildRequires:    R-methods 
BuildRequires:    R-CRAN-gamlss.dist 
BuildRequires:    R-CRAN-invgamma 
BuildRequires:    R-CRAN-openxlsx 
Requires:         R-CRAN-tidyr 
Requires:         R-CRAN-dplyr 
Requires:         R-CRAN-magrittr 
Requires:         R-CRAN-ggplot2 
Requires:         R-CRAN-DT 
Requires:         R-CRAN-shiny 
Requires:         R-CRAN-car 
Requires:         R-CRAN-broom 
Requires:         R-CRAN-pbkrtest 
Requires:         R-parallel 
Requires:         R-CRAN-Rtsne 
Requires:         R-CRAN-MDMR 
Requires:         R-CRAN-gamlss 
Requires:         R-CRAN-lme4 
Requires:         R-CRAN-mgcv 
Requires:         R-CRAN-bslib 
Requires:         R-CRAN-shinydashboard 
Requires:         R-methods 
Requires:         R-CRAN-gamlss.dist 
Requires:         R-CRAN-invgamma 
Requires:         R-CRAN-openxlsx 

%description
Provides a comprehensive framework for batch effect diagnostics,
harmonization, and post-harmonization downstream analysis. Features
include interactive visualization tools, robust statistical tests, and a
range of harmonization techniques. Additionally, 'ComBatFamQC' enables the
creation of life-span age trend plots with estimated age-adjusted centiles
and facilitates the generation of covariate-corrected residuals for
analytical purposes. Methods for harmonization are based on approaches
described in Johnson et al., (2007) <doi:10.1093/biostatistics/kxj037>,
Beer et al., (2020) <doi:10.1016/j.neuroimage.2020.117129>, Pomponio et
al., (2020) <doi:10.1016/j.neuroimage.2019.116450>, and Chen et al.,
(2021) <doi:10.1002/hbm.25688>.

%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}