%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname immunogenetr
%global packver 1.0.0
%global rlibdir /usr/local/lib/R/library
Name: R-CRAN-%{packname}
Version: 1.0.0
Release: 1%{?dist}%{?buildtag}
Summary: A Comprehensive Toolkit for Clinical HLA Informatics
License: GPL (>= 3)
URL: https://cran.r-project.org/package=%{packname}
Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz
BuildRequires: R-devel >= 4.1.0
Requires: R-core >= 4.1.0
BuildArch: noarch
BuildRequires: R-CRAN-tibble >= 3.1.3
BuildRequires: R-CRAN-magrittr >= 2.0.3
BuildRequires: R-CRAN-glue >= 1.8.0
BuildRequires: R-CRAN-stringr >= 1.5.0
BuildRequires: R-CRAN-xml2 >= 1.3.6
BuildRequires: R-CRAN-tidyr >= 1.3.0
BuildRequires: R-CRAN-tidyselect >= 1.2.0
BuildRequires: R-CRAN-rlang >= 1.1.2
BuildRequires: R-CRAN-dplyr >= 1.1.1
BuildRequires: R-CRAN-purrr >= 1.0.2
BuildRequires: R-CRAN-cli >= 1.0.0
Requires: R-CRAN-tibble >= 3.1.3
Requires: R-CRAN-magrittr >= 2.0.3
Requires: R-CRAN-glue >= 1.8.0
Requires: R-CRAN-stringr >= 1.5.0
Requires: R-CRAN-xml2 >= 1.3.6
Requires: R-CRAN-tidyr >= 1.3.0
Requires: R-CRAN-tidyselect >= 1.2.0
Requires: R-CRAN-rlang >= 1.1.2
Requires: R-CRAN-dplyr >= 1.1.1
Requires: R-CRAN-purrr >= 1.0.2
Requires: R-CRAN-cli >= 1.0.0
%description
A comprehensive toolkit for clinical Human Leukocyte Antigen (HLA)
informatics, built on 'tidyverse'
principles and making use of genotype list string (GL string, Mack et al.
(2023) ) for storing and computing HLA genotype
data. Specific functionalities include: coercion of HLA data in tabular
format to and from GL string; calculation of matching and mismatching in
all directions, with multiple output formats; automatic formatting of HLA
data for searching within a GL string; truncation of molecular HLA data to
a specific number of fields; and reading HLA genotypes in HML files and
extracting the GL string.
%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}