%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  PTXQC
%global packver   1.1.1
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          1.1.1
Release:          1%{?dist}%{?buildtag}
Summary:          Quality Report Generation for MaxQuant and mzTab Results

License:          BSD_3_clause + file LICENSE
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 3.3.0
Requires:         R-core >= 3.3.0
BuildArch:        noarch
BuildRequires:    R-CRAN-ggplot2 >= 2.2
BuildRequires:    R-CRAN-knitr >= 1.10
BuildRequires:    R-CRAN-rmzqc >= 0.5.0
BuildRequires:    R-CRAN-data.table 
BuildRequires:    R-CRAN-ggdendro 
BuildRequires:    R-grid 
BuildRequires:    R-CRAN-gridExtra 
BuildRequires:    R-grDevices 
BuildRequires:    R-CRAN-gtable 
BuildRequires:    R-CRAN-htmlTable 
BuildRequires:    R-CRAN-magrittr 
BuildRequires:    R-methods 
BuildRequires:    R-CRAN-plyr 
BuildRequires:    R-CRAN-R6 
BuildRequires:    R-CRAN-R6P 
BuildRequires:    R-CRAN-RColorBrewer 
BuildRequires:    R-CRAN-reshape2 
BuildRequires:    R-CRAN-rmarkdown 
BuildRequires:    R-CRAN-seqinr 
BuildRequires:    R-stats 
BuildRequires:    R-utils 
BuildRequires:    R-CRAN-UpSetR 
BuildRequires:    R-CRAN-xml2 
BuildRequires:    R-CRAN-yaml 
Requires:         R-CRAN-ggplot2 >= 2.2
Requires:         R-CRAN-knitr >= 1.10
Requires:         R-CRAN-rmzqc >= 0.5.0
Requires:         R-CRAN-data.table 
Requires:         R-CRAN-ggdendro 
Requires:         R-grid 
Requires:         R-CRAN-gridExtra 
Requires:         R-grDevices 
Requires:         R-CRAN-gtable 
Requires:         R-CRAN-htmlTable 
Requires:         R-CRAN-magrittr 
Requires:         R-methods 
Requires:         R-CRAN-plyr 
Requires:         R-CRAN-R6 
Requires:         R-CRAN-R6P 
Requires:         R-CRAN-RColorBrewer 
Requires:         R-CRAN-reshape2 
Requires:         R-CRAN-rmarkdown 
Requires:         R-CRAN-seqinr 
Requires:         R-stats 
Requires:         R-utils 
Requires:         R-CRAN-UpSetR 
Requires:         R-CRAN-xml2 
Requires:         R-CRAN-yaml 

%description
Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS
data analyzed with the MaxQuant software suite (from .txt files) or mzTab
files (ideally from OpenMS 'QualityControl' tool). Reports are
customizable (target thresholds, subsetting) and available in HTML or PDF
format. Published in J. Proteome Res., Proteomics Quality Control: Quality
Control Software for MaxQuant Results (2015)
<doi:10.1021/acs.jproteome.5b00780>.

%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}