%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  maldipickr
%global packver   1.3.1
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.3.1
Release:          1%{?dist}%{?buildtag}
Summary:          Dereplicate and Cherry-Pick Mass Spectrometry Spectra

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


BuildRequires:    R-devel >= 3.2.0
Requires:         R-core >= 3.2.0
BuildArch:        noarch
BuildRequires:    R-CRAN-dplyr 
BuildRequires:    R-CRAN-lifecycle 
BuildRequires:    R-CRAN-magrittr 
BuildRequires:    R-CRAN-MALDIquant 
BuildRequires:    R-CRAN-readBrukerFlexData 
BuildRequires:    R-CRAN-rlang 
BuildRequires:    R-stats 
BuildRequires:    R-CRAN-tibble 
BuildRequires:    R-CRAN-tidyr 
BuildRequires:    R-CRAN-tidyselect 
BuildRequires:    R-tools 
BuildRequires:    R-utils 
Requires:         R-CRAN-dplyr 
Requires:         R-CRAN-lifecycle 
Requires:         R-CRAN-magrittr 
Requires:         R-CRAN-MALDIquant 
Requires:         R-CRAN-readBrukerFlexData 
Requires:         R-CRAN-rlang 
Requires:         R-stats 
Requires:         R-CRAN-tibble 
Requires:         R-CRAN-tidyr 
Requires:         R-CRAN-tidyselect 
Requires:         R-tools 
Requires:         R-utils 

%description
Convenient wrapper functions for the analysis of matrix-assisted laser
desorption/ionization-time-of-flight (MALDI-TOF) spectra data in order to
select only representative spectra (also called cherry-pick). The package
covers the preprocessing and dereplication steps (based on Strejcek,
Smrhova, Junkova and Uhlik (2018) <doi:10.3389/fmicb.2018.01294>) needed
to cluster MALDI-TOF spectra before the final cherry-picking step. It
enables the easy exclusion of spectra and/or clusters to accommodate
complex cherry-picking strategies. Alternatively, cherry-picking using
taxonomic identification MALDI-TOF data is made easy with functions to
import inconsistently formatted reports.

%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}