%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  corto
%global packver   1.4.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.4.0
Release:          1%{?dist}%{?buildtag}
Summary:          Inference of Gene Regulatory Networks

License:          LGPL-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-grDevices 
BuildRequires:    R-graphics 
BuildRequires:    R-methods 
BuildRequires:    R-parallel 
BuildRequires:    R-CRAN-pbapply 
BuildRequires:    R-CRAN-plotrix 
BuildRequires:    R-stats 
BuildRequires:    R-utils 
Requires:         R-grDevices 
Requires:         R-graphics 
Requires:         R-methods 
Requires:         R-parallel 
Requires:         R-CRAN-pbapply 
Requires:         R-CRAN-plotrix 
Requires:         R-stats 
Requires:         R-utils 

%description
We present 'corto' (Correlation Tool), a simple package to infer gene
regulatory networks and visualize master regulators from gene expression
data using DPI (Data Processing Inequality) and bootstrapping to recover
edges. An initial step is performed to calculate all significant edges
between a list of source nodes (centroids) and target genes. Then a DPI
step removes edges: by default, for each target only the edge from the
centroid with the strongest correlation is kept; optionally, the ARACNe
rule removes an edge only if it is the weakest in a triplet of two
centroids and one target. A bootstrapping process then calculates the
robustness of the network, eventually re-adding edges previously removed
by DPI. The algorithm has been optimized to run outside a computing
cluster, using a fast correlation implementation. The package finally
provides functions to calculate network enrichment analysis from RNA-Seq
and ATAC-Seq signatures as described in the article by Giorgi lab (2020)
<doi:10.1093/bioinformatics/btaa223>.

%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}