%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  iCellR
%global packver   1.6.7
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.6.7
Release:          1%{?dist}%{?buildtag}
Summary:          Analyzing High-Throughput Single Cell Sequencing Data

License:          GPL-2
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 3.3.0
Requires:         R-core >= 3.3.0
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-CRAN-plotly 
BuildRequires:    R-CRAN-Matrix 
BuildRequires:    R-CRAN-Rtsne 
BuildRequires:    R-CRAN-gridExtra 
BuildRequires:    R-CRAN-ggrepel 
BuildRequires:    R-CRAN-ggpubr 
BuildRequires:    R-CRAN-scatterplot3d 
BuildRequires:    R-CRAN-RColorBrewer 
BuildRequires:    R-CRAN-knitr 
BuildRequires:    R-CRAN-NbClust 
BuildRequires:    R-CRAN-shiny 
BuildRequires:    R-CRAN-pheatmap 
BuildRequires:    R-CRAN-ape 
BuildRequires:    R-CRAN-ggdendro 
BuildRequires:    R-CRAN-plyr 
BuildRequires:    R-CRAN-reshape 
BuildRequires:    R-CRAN-Hmisc 
BuildRequires:    R-CRAN-htmlwidgets 
BuildRequires:    R-methods 
BuildRequires:    R-CRAN-uwot 
BuildRequires:    R-CRAN-hdf5r 
BuildRequires:    R-CRAN-progress 
BuildRequires:    R-CRAN-igraph 
BuildRequires:    R-CRAN-data.table 
BuildRequires:    R-CRAN-Rcpp 
BuildRequires:    R-CRAN-RANN 
BuildRequires:    R-CRAN-jsonlite 
BuildRequires:    R-CRAN-png 
Requires:         R-CRAN-ggplot2 
Requires:         R-CRAN-plotly 
Requires:         R-CRAN-Matrix 
Requires:         R-CRAN-Rtsne 
Requires:         R-CRAN-gridExtra 
Requires:         R-CRAN-ggrepel 
Requires:         R-CRAN-ggpubr 
Requires:         R-CRAN-scatterplot3d 
Requires:         R-CRAN-RColorBrewer 
Requires:         R-CRAN-knitr 
Requires:         R-CRAN-NbClust 
Requires:         R-CRAN-shiny 
Requires:         R-CRAN-pheatmap 
Requires:         R-CRAN-ape 
Requires:         R-CRAN-ggdendro 
Requires:         R-CRAN-plyr 
Requires:         R-CRAN-reshape 
Requires:         R-CRAN-Hmisc 
Requires:         R-CRAN-htmlwidgets 
Requires:         R-methods 
Requires:         R-CRAN-uwot 
Requires:         R-CRAN-hdf5r 
Requires:         R-CRAN-progress 
Requires:         R-CRAN-igraph 
Requires:         R-CRAN-data.table 
Requires:         R-CRAN-Rcpp 
Requires:         R-CRAN-RANN 
Requires:         R-CRAN-jsonlite 
Requires:         R-CRAN-png 

%description
A toolkit that allows scientists to work with data from single cell
sequencing technologies such as scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq
and Spatial Transcriptomics (ST). Single (i) Cell R package ('iCellR')
provides unprecedented flexibility at every step of the analysis pipeline,
including normalization, clustering, dimensionality reduction, imputation,
visualization, and so on. Users can design both unsupervised and
supervised models to best suit their research. In addition, the toolkit
provides 2D and 3D interactive visualizations, differential expression
analysis, filters based on cells, genes and clusters, data merging,
normalizing for dropouts, data imputation methods, correcting for batch
differences, pathway analysis, tools to find marker genes for clusters and
conditions, predict cell types and pseudotime analysis. See
Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.05.05.078550> and
Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.03.31.019109> for more
details.

%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}