%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  ActivePathways
%global packver   2.0.5
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          2.0.5
Release:          1%{?dist}%{?buildtag}
Summary:          Integrative Pathway Enrichment Analysis of Multivariate Omics Data

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


BuildRequires:    R-devel >= 3.6
Requires:         R-core >= 3.6
BuildArch:        noarch
BuildRequires:    R-CRAN-data.table 
BuildRequires:    R-CRAN-ggplot2 
Requires:         R-CRAN-data.table 
Requires:         R-CRAN-ggplot2 

%description
Framework for analysing multiple omics datasets in the context of
molecular pathways, biological processes and other types of gene sets. The
package uses p-value merging to combine gene- or protein-level signals,
followed by ranked hypergeometric tests to determine enriched pathways and
processes. Genes can be integrated using directional constraints that
reflect how the input datasets are expected interact with one another.
This approach allows researchers to interpret a series of omics datasets
in the context of known biology and gene function, and discover
associations that are only apparent when several datasets are combined.
The recent version of the package is part of the following publication:
Directional integration and pathway enrichment analysis for multi-omics
data. Slobodyanyuk M^, Bahcheli AT^, Klein ZP, Bayati M, Strug LJ, Reimand
J. Nature Communications (2024) <doi:10.1038/s41467-024-49986-4>.

%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}