File R-MPGE.spec of Package R-MPGE
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# Spec file for package MPGE
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%global packname MPGE
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 1.0.1
Release: 0
Summary: A Two-Step Approach to Testing Overall Effect of Gene-Environment Interaction for Multiple Phenotypes
Group: Development/Libraries/Other
License: GPL-3
URL: http://cran.r-project.org/web/packages/%{packname}
Source: MPGE_1.0.1.tar.gz
Requires: R-base
Requires: R-car
Requires: R-purrr
Requires: R-carData
Requires: R-abind
Requires: R-Formula
Requires: R-pbkrtest
Requires: R-quantreg
Requires: R-lme4
Requires: R-scales
Requires: R-cli
Requires: R-lifecycle
Requires: R-magrittr
Requires: R-rlang
Requires: R-vctrs
Requires: R-Rdpack
Requires: R-minqa
Requires: R-nloptr
Requires: R-reformulas
Requires: R-Rcpp
Requires: R-RcppEigen
Requires: R-broom
Requires: R-dplyr
Requires: R-numDeriv
Requires: R-doBy
Requires: R-SparseM
Requires: R-MatrixModels
Requires: R-farver
Requires: R-glue
Requires: R-labeling
Requires: R-R6
Requires: R-RColorBrewer
Requires: R-viridisLite
Requires: R-backports
Requires: R-generics
Requires: R-stringr
Requires: R-tibble
Requires: R-tidyr
Requires: R-cowplot
Requires: R-Deriv
Requires: R-forecast
Requires: R-ggplot2
Requires: R-modelr
Requires: R-microbenchmark
Requires: R-pillar
Requires: R-tidyselect
Requires: R-rbibutils
Requires: R-gtable
Requires: R-colorspace
Requires: R-fracdiff
Requires: R-lmtest
Requires: R-timeDate
Requires: R-urca
Requires: R-withr
Requires: R-zoo
Requires: R-RcppArmadillo
Requires: R-isoband
Requires: R-S7
Requires: R-utf8
Requires: R-stringi
Requires: R-pkgconfig
Requires: R-cpp11
# %%if 0%%{?sle_version} > 120400 || 0%%{?is_opensuse}
# # Three others commonly needed
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BuildRequires: R-purrr
BuildRequires: R-carData
BuildRequires: R-abind
BuildRequires: R-Formula
BuildRequires: R-pbkrtest
BuildRequires: R-quantreg
BuildRequires: R-lme4
BuildRequires: R-scales
BuildRequires: R-cli
BuildRequires: R-lifecycle
BuildRequires: R-magrittr
BuildRequires: R-rlang
BuildRequires: R-vctrs
BuildRequires: R-Rdpack
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BuildRequires: R-broom
BuildRequires: R-dplyr
BuildRequires: R-numDeriv
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BuildRequires: R-SparseM
BuildRequires: R-MatrixModels
BuildRequires: R-farver
BuildRequires: R-glue
BuildRequires: R-labeling
BuildRequires: R-R6
BuildRequires: R-RColorBrewer
BuildRequires: R-viridisLite
BuildRequires: R-backports
BuildRequires: R-generics
BuildRequires: R-stringr
BuildRequires: R-tibble
BuildRequires: R-tidyr
BuildRequires: R-cowplot
BuildRequires: R-Deriv
BuildRequires: R-forecast
BuildRequires: R-ggplot2
BuildRequires: R-modelr
BuildRequires: R-microbenchmark
BuildRequires: R-pillar
BuildRequires: R-tidyselect
BuildRequires: R-rbibutils
BuildRequires: R-gtable
BuildRequires: R-colorspace
BuildRequires: R-fracdiff
BuildRequires: R-lmtest
BuildRequires: R-timeDate
BuildRequires: R-urca
BuildRequires: R-withr
BuildRequires: R-zoo
BuildRequires: R-RcppArmadillo-devel
BuildRequires: R-isoband
BuildRequires: R-S7
BuildRequires: R-utf8
BuildRequires: R-stringi
BuildRequires: R-pkgconfig
BuildRequires: R-cpp11-devel
Suggests: R-knitr
Suggests: R-rmarkdown
Suggests: R-spelling
Suggests: R-testthat
%description
Interaction between a genetic variant (e.g., a single nucleotide
polymorphism) and an environmental variable (e.g., physical activity)
can have a shared effect on multiple phenotypes (e.g., blood lipids).
We implement a two-step method to test for an overall interaction
effect on multiple phenotypes. In first step, the method tests for an
overall marginal genetic association between the genetic variant and
the multivariate phenotype. The genetic variants which show an evidence
of marginal overall genetic effect in the first step are prioritized
while testing for an overall gene-environment interaction effect in the
second step. Methodology is available from: A Majumdar, KS Burch, T
Haldar, S Sankararaman, B Pasaniuc, WJ Gauderman, JS Witte (2020)
<doi:10.1093/bioinformatics/btaa1083>.
%prep
%setup -q -c -n %{packname}
# the next line is needed, because we build without --clean in between two packages
rm -rf ~/.R
%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
%fdupes -s %{buildroot}%{rlibdir}
#%%check
#%%{_bindir}/R CMD check %%{packname}
%files
%dir %{rlibdir}/%{packname}
%doc %{rlibdir}/%{packname}/DESCRIPTION
%{rlibdir}/%{packname}/INDEX
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%doc %{rlibdir}/%{packname}/NEWS.md
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/WORDLIST
%{rlibdir}/%{packname}/data
%doc %{rlibdir}/%{packname}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%changelog
