File R-BinMat.spec of Package R-BinMat
# Automatically generated by CRAN2OBS
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# Spec file for package BinMat
# This file is auto-generated using information in the package source,
# esp. Description and Summary. Improvements in that area should be
# discussed with upstream.
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%global packname BinMat
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 0.1.6
Release: 0
Summary: Processes Binary Data Obtained from Fragment Analysis (Such as AFLPs, ISSRs, and RFLPs)
Group: Development/Libraries/Other
License: GPL-3
URL: http://cran.r-project.org/web/packages/%{packname}
Source: BinMat_0.1.6.tar.gz
Requires: R-base
Requires: R-pvclust
Requires: R-ggpubr
Requires: R-tibble
Requires: R-ggplot2
Requires: R-ggrepel
Requires: R-ggsci
Requires: R-tidyr
Requires: R-purrr
Requires: R-dplyr
Requires: R-cowplot
Requires: R-ggsignif
Requires: R-scales
Requires: R-gridExtra
Requires: R-glue
Requires: R-polynom
Requires: R-rlang
Requires: R-rstatix
Requires: R-magrittr
Requires: R-cli
Requires: R-lifecycle
Requires: R-pillar
Requires: R-pkgconfig
Requires: R-vctrs
Requires: R-gtable
Requires: R-generics
Requires: R-R6
Requires: R-tidyselect
Requires: R-isoband
Requires: R-S7
Requires: R-withr
Requires: R-Rcpp
Requires: R-utf8
Requires: R-broom
Requires: R-corrplot
Requires: R-car
Requires: R-farver
Requires: R-labeling
Requires: R-RColorBrewer
Requires: R-viridisLite
Requires: R-stringr
Requires: R-cpp11
Requires: R-backports
Requires: R-carData
Requires: R-abind
Requires: R-Formula
Requires: R-pbkrtest
Requires: R-quantreg
Requires: R-lme4
Requires: R-stringi
Requires: R-minqa
Requires: R-nloptr
Requires: R-reformulas
Requires: R-RcppEigen
Requires: R-numDeriv
Requires: R-doBy
Requires: R-SparseM
Requires: R-MatrixModels
Requires: R-Deriv
Requires: R-modelr
Requires: R-microbenchmark
Requires: R-Rdpack
Requires: R-rbibutils
# %%if 0%%{?sle_version} > 120400 || 0%%{?is_opensuse}
# # Three others commonly needed
# BuildRequires: tex(ae.sty)
# BuildRequires: tex(fancyvrb.sty)
# BuildRequires: tex(inconsolata.sty)
# BuildRequires: tex(natbib.sty)
# %else
# BuildRequires: texlive
# %endif
# BuildRequires: texinfo
BuildRequires: fdupes
BuildRequires: R-base
BuildRequires: R-pvclust
BuildRequires: R-ggpubr
BuildRequires: R-tibble
BuildRequires: R-ggplot2
BuildRequires: R-ggrepel
BuildRequires: R-ggsci
BuildRequires: R-tidyr
BuildRequires: R-purrr
BuildRequires: R-dplyr
BuildRequires: R-cowplot
BuildRequires: R-ggsignif
BuildRequires: R-scales
BuildRequires: R-gridExtra
BuildRequires: R-glue
BuildRequires: R-polynom
BuildRequires: R-rlang
BuildRequires: R-rstatix
BuildRequires: R-magrittr
BuildRequires: R-cli
BuildRequires: R-lifecycle
BuildRequires: R-pillar
BuildRequires: R-pkgconfig
BuildRequires: R-vctrs
BuildRequires: R-gtable
BuildRequires: R-generics
BuildRequires: R-R6
BuildRequires: R-tidyselect
BuildRequires: R-isoband
BuildRequires: R-S7
BuildRequires: R-withr
BuildRequires: R-Rcpp-devel
BuildRequires: R-utf8
BuildRequires: R-broom
BuildRequires: R-corrplot
BuildRequires: R-car
BuildRequires: R-farver
BuildRequires: R-labeling
BuildRequires: R-RColorBrewer
BuildRequires: R-viridisLite
BuildRequires: R-stringr
BuildRequires: R-cpp11-devel
BuildRequires: R-backports
BuildRequires: R-carData
BuildRequires: R-abind
BuildRequires: R-Formula
BuildRequires: R-pbkrtest
BuildRequires: R-quantreg
BuildRequires: R-lme4
BuildRequires: R-stringi
BuildRequires: R-minqa
BuildRequires: R-nloptr
BuildRequires: R-reformulas
BuildRequires: R-RcppEigen-devel
BuildRequires: R-numDeriv
BuildRequires: R-doBy
BuildRequires: R-SparseM
BuildRequires: R-MatrixModels
BuildRequires: R-Deriv
BuildRequires: R-modelr
BuildRequires: R-microbenchmark
BuildRequires: R-Rdpack
BuildRequires: R-rbibutils
Suggests: R-knitr
Suggests: R-rmarkdown
%description
A molecular genetics tool that processes binary data from fragment
analysis. It consolidates replicate sample pairs, outputs summary
statistics, and produces hierarchical clustering trees and nMDS plots.
This package was developed from the publication available here:
<doi:10.1016/j.biocontrol.2020.104426>. The GUI version of this package
is available on the R Shiny online server at:
<https://clarkevansteenderen.shinyapps.io/BINMAT/> or it is accessible
via GitHub by typing: shiny::runGitHub("BinMat", "clarkevansteenderen")
into the console in R. Two real-world datasets accompany the package:
an AFLP dataset of Bunias orientalis samples from Tewes et. al. (2017)
<doi:10.1111/1365-2745.12869>, and an ISSR dataset of Nymphaea
specimens from Reid et. al. (2021) <doi:10.1016/j.aquabot.2021.103372>.
The authors of these publications are thanked for allowing the use of
their data.
%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
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/data
%{rlibdir}/%{packname}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%changelog
