File R-SSHAARP.spec of Package R-SSHAARP
# Automatically generated by CRAN2OBS
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# Spec file for package SSHAARP
# This file is auto-generated using information in the package source,
# esp. Description and Summary. Improvements in that area should be
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%global packname SSHAARP
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 2.0.8
Release: 0
Summary: Searching Shared HLA Amino Acid Residue Prevalence
Group: Development/Libraries/Other
License: GPL (>= 3)
URL: http://cran.r-project.org/web/packages/%{packname}
Source: SSHAARP_2.0.8.tar.gz
Requires: R-base
Requires: R-data.table
Requires: R-stringr
Requires: R-gtools
Requires: R-gmt
Requires: R-DescTools
Requires: R-dplyr
Requires: R-filesstrings
Requires: R-purrr
Requires: R-stringi
Requires: R-HLAtools
Requires: R-mvtnorm
Requires: R-expm
Requires: R-Rcpp
Requires: R-rstudioapi
Requires: R-Exact
Requires: R-gld
Requires: R-readxl
Requires: R-readr
Requires: R-haven
Requires: R-httr
Requires: R-withr
Requires: R-cli
Requires: R-fs
Requires: R-generics
Requires: R-glue
Requires: R-lifecycle
Requires: R-magrittr
Requires: R-pillar
Requires: R-R6
Requires: R-rlang
Requires: R-tibble
Requires: R-tidyselect
Requires: R-vctrs
Requires: R-checkmate
Requires: R-strex
Requires: R-fmsb
Requires: R-rvest
Requires: R-xfun
Requires: R-backports
Requires: R-rootSolve
Requires: R-e1071
Requires: R-lmom
Requires: R-forcats
Requires: R-hms
Requires: R-cpp11
Requires: R-curl
Requires: R-jsonlite
Requires: R-mime
Requires: R-openssl
Requires: R-utf8
Requires: R-clipr
Requires: R-crayon
Requires: R-vroom
Requires: R-tzdb
Requires: R-cellranger
Requires: R-progress
Requires: R-selectr
Requires: R-xml2
Requires: R-pkgconfig
Requires: R-rematch
Requires: R-proxy
Requires: R-askpass
Requires: R-prettyunits
Requires: R-bit64
Requires: R-sys
Requires: R-bit
# %%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-data.table
BuildRequires: R-stringr
BuildRequires: R-gtools
BuildRequires: R-gmt
BuildRequires: R-DescTools
BuildRequires: R-dplyr
BuildRequires: R-filesstrings
BuildRequires: R-purrr
BuildRequires: R-stringi
BuildRequires: R-HLAtools
BuildRequires: R-mvtnorm
BuildRequires: R-expm
BuildRequires: R-Rcpp-devel
BuildRequires: R-rstudioapi
BuildRequires: R-Exact
BuildRequires: R-gld
BuildRequires: R-readxl
BuildRequires: R-readr
BuildRequires: R-haven
BuildRequires: R-httr
BuildRequires: R-withr
BuildRequires: R-cli
BuildRequires: R-fs
BuildRequires: R-generics
BuildRequires: R-glue
BuildRequires: R-lifecycle
BuildRequires: R-magrittr
BuildRequires: R-pillar
BuildRequires: R-R6
BuildRequires: R-rlang
BuildRequires: R-tibble
BuildRequires: R-tidyselect
BuildRequires: R-vctrs
BuildRequires: R-checkmate
BuildRequires: R-strex
BuildRequires: R-fmsb
BuildRequires: R-rvest
BuildRequires: R-xfun
BuildRequires: R-backports
BuildRequires: R-rootSolve
BuildRequires: R-e1071
BuildRequires: R-lmom
BuildRequires: R-forcats
BuildRequires: R-hms
BuildRequires: R-cpp11-devel
BuildRequires: R-curl
BuildRequires: R-jsonlite
BuildRequires: R-mime
BuildRequires: R-openssl
BuildRequires: R-utf8
BuildRequires: R-clipr
BuildRequires: R-crayon
BuildRequires: R-vroom
BuildRequires: R-tzdb
BuildRequires: R-cellranger
BuildRequires: R-progress
BuildRequires: R-selectr
BuildRequires: R-xml2
BuildRequires: R-pkgconfig
BuildRequires: R-rematch
BuildRequires: R-proxy
BuildRequires: R-askpass
BuildRequires: R-prettyunits
BuildRequires: R-bit64
BuildRequires: R-sys
BuildRequires: R-bit
Suggests: R-knitr
Suggests: R-rmarkdown
%description
Processes amino acid alignments produced by the 'IPD-IMGT/HLA (Immuno
Polymorphism-ImMunoGeneTics/Human Leukocyte Antigen) Database' to
identify user-defined amino acid residue motifs shared across HLA
alleles, HLA alleles, or HLA haplotypes, and calculates frequencies
based on HLA allele frequency data. 'SSHAARP' (Searching Shared HLA
Amino Acid Residue Prevalence) uses 'Generic Mapping Tools (GMT)'
software and the 'GMT' R package to generate global frequency heat maps
that illustrate the distribution of each user-defined map around the
globe. 'SSHAARP' analyzes the allele frequency data described by
Solberg et al. (2008) <doi:10.1016/j.humimm.2008.05.001>, a global set
of 497 population samples from 185 published datasets, representing
66,800 individuals total. Users may also specify their own datasets,
but file conventions must follow the prebundled Solberg dataset, or the
mock haplotype dataset.
%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
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/data
%doc %{rlibdir}/%{packname}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%changelog
