%global __brp_check_rpaths %{nil}
%global packname  SuRF.vs
%global packver   1.1.0.1
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.1.0.1
Release:          1%{?dist}%{?buildtag}
Summary:          Subsampling Ranking Forward Selection (SuRF)

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


BuildRequires:    R-devel >= 3.2.3
Requires:         R-core >= 3.2.3
BuildArch:        noarch
BuildRequires:    R-CRAN-glmnet 
BuildRequires:    R-CRAN-survival 
BuildRequires:    R-CRAN-dplyr 
Requires:         R-CRAN-glmnet 
Requires:         R-CRAN-survival 
Requires:         R-CRAN-dplyr 

%description
Performs variable selection based on subsampling, ranking forward
selection. Details of the method are published in Lihui Liu, Hong Gu,
Johan Van Limbergen, Toby Kenney (2020) SuRF: A new method for sparse
variable selection, with application in microbiome data analysis
Statistics in Medicine 40 897-919 <doi:10.1002/sim.8809>. Xo is the matrix
of predictor variables. y is the response variable. Currently only binary
responses using logistic regression are supported. X is a matrix of
additional predictors which should be scaled to have sum 1 prior to
analysis. fold is the number of folds for cross-validation. Alpha is the
parameter for the elastic net method used in the subsampling procedure:
the default value of 1 corresponds to LASSO. prop is the proportion of
variables to remove in the each subsample. weights indicates whether
observations should be weighted by class size. When the class sizes are
unbalanced, weighting observations can improve results. B is the number of
subsamples to use for ranking the variables. C is the number of
permutations to use for estimating the critical value of the null
distribution. If the 'doParallel' package is installed, the function can
be run in parallel by setting ncores to the number of threads to use. If
the default value of 1 is used, or if the 'doParallel' package is not
installed, the function does not run in parallel. display.progress
indicates whether the function should display messages indicating its
progress. family is a family variable for the glm() fitting. Note that the
'glmnet' package does not permit the use of nonstandard link functions, so
will always use the default link function. However, the glm() fitting will
use the specified link. The default is binomial with logistic regression,
because this is a common use case. pval is the p-value for inclusion of a
variable in the model. Under the null case, the number of false positives
will be geometrically distributed with this as probability of success, so
if this parameter is set to p, the expected number of false positives
should be p/(1-p).

%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}