%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  iq
%global packver   1.9.12
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.9.12
Release:          1%{?dist}%{?buildtag}
Summary:          Protein Quantification in Mass Spectrometry-Based Proteomics

License:          BSD_3_clause + file LICENSE
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 2.10
Requires:         R-core >= 2.10
BuildRequires:    R-CRAN-Rcpp 
BuildRequires:    R-CRAN-RcppEigen 

%description
An implementation of the MaxLFQ algorithm by Cox et al. (2014)
<doi:10.1074/mcp.M113.031591> in a comprehensive pipeline for processing
proteomics data in data-independent acquisition mode (Pham et al. 2020
<doi:10.1093/bioinformatics/btz961>). It offers additional options for
protein quantification using the N most intense fragment ions, using all
fragment ions, and a wrapper for the median polish algorithm by Tukey
(1977, ISBN:0201076160). In general, the tool can be used to integrate
multiple proportional observations into a single quantitative value.

%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}