%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  Allspice
%global packver   1.0.7
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.0.7
Release:          1%{?dist}%{?buildtag}
Summary:          RNA-Seq Profile Classifier

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


BuildRequires:    R-devel
Requires:         R-core
BuildArch:        noarch
BuildRequires:    R-methods 
Requires:         R-methods 

%description
We developed a lightweight machine learning tool for RNA profiling of
acute lymphoblastic leukemia (ALL), however, it can be used for any
problem where multiple classes need to be identified from
multi-dimensional data. The methodology is described in Makinen V-P, Rehn
J, Breen J, Yeung D, White DL (2022) Multi-cohort transcriptomic subtyping
of B-cell acute lymphoblastic leukemia, International Journal of Molecular
Sciences 23:4574, <doi:10.3390/ijms23094574>. The classifier contains
optimized mean profiles of the classes (centroids) as observed in the
training data, and new samples are matched to these centroids using the
shortest Euclidean distance. Centroids derived from a dataset of 1,598 ALL
patients are included, but users can train the models with their own data
as well. The output includes both numerical and visual presentations of
the classification results. Samples with mixed features from multiple
classes or atypical values are also identified.

%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}