Archive:PackagingDrafts/R

How to package R modules

What is R?

The definition from The R-Project website says that R is:

" R is a language and environment for statistical computing and graphics."

R is a GNU project, very similar to the S language developed by Bell Laboratories.

This language is heavily used in research as it provides a lot of statistical and graphical tools. It is also a well developed language for data manipulation.

If you are looking for more information on R, you can go to:

• The R-Project website
• An introduction to R

If you are interested in packaging R modules, or if you are looking for R libraries, you should check here for upstream sources:

• The bioconductor website
• The CRAN website

Spec Templates for R packages

There are two types of R packages: arch-specific and noarch.

Arch specific R packaging spec template

%define packname foo
%define packrel 1

Name:             R-%{packname}
Version:          1.6.6
Release:          1%{?dist}
Source0:          ftp://cran.r-project.org/pub/R/contrib/main/%{packname}_%{version}-%{packrel}.tar.gz
License:          GPL
URL:              http://cran.r-project.org/src/contrib
Group:            Applications/Engineering
Summary:          Adds foo functionality for R
BuildRequires:    R-devel, tetex-latex
BuildRoot:        %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
Requires(post):   R
Requires(postun): R

%description
R Interface to foo, enables bar!

%setup -q -c -n %{packname}

%build

%install
rm -rf $RPM_BUILD_ROOT
mkdir -p $RPM_BUILD_ROOT%{_libdir}/R/library
%{_bindir}/R CMD INSTALL -l $RPM_BUILD_ROOT%{_libdir}/R/library %{packname}
test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
rm -rf $RPM_BUILD_ROOT%{_libdir}/R/library/R.css

%check
%{_bindir}/R CMD check %{packname}

%clean
rm -rf $RPM_BUILD_ROOT

%post
%{_R_make_search_index}

%postun
%{_R_make_search_index}

%files
%defattr(-, root, root, -)
%dir %{_libdir}/R/library/%{packname}
%doc %{_libdir}/R/library/%{packname}/latex
%doc %{_libdir}/R/library/%{packname}/doc
%doc %{_libdir}/R/library/%{packname}/html
%doc %{_libdir}/R/library/%{packname}/man
%doc %{_libdir}/R/library/%{packname}/DESCRIPTION
%{_libdir}/R/library/%{packname}/CONTENTS
%{_libdir}/R/library/%{packname}/INDEX
%{_libdir}/R/library/%{packname}/NAMESPACE
%{_libdir}/R/library/%{packname}/Meta
%{_libdir}/R/library/%{packname}/R
%{_libdir}/R/library/%{packname}/R-ex
%{_libdir}/R/library/%{packname}/help

%changelog
* Fri Jul 6 2007 Tom "spot" Callaway <tcallawa@redhat.com> 1.6.6-1
- Initial package creation

Noarch R packaging spec template

%define packname foo
%define packrel 1

Name:             R-%{packname}
Version:          1.6.6
Release:          1%{?dist}
Source0:          ftp://cran.r-project.org/pub/R/contrib/main/%{packname}_%{version}-%{packrel}.tar.gz
License:          GPL
URL:              http://cran.r-project.org/src/contrib
Group:            Applications/Engineering
Summary:          Adds foo functionality for R
BuildRequires:    R-devel, tetex-latex
BuildRoot:        %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildArch:        noarch
Requires(post):   R
Requires(postun): R
Requires:         R

%description
R Interface to foo, enables bar!

%setup -q -c -n %{packname}

%build

%install
rm -rf $RPM_BUILD_ROOT
mkdir -p $RPM_BUILD_ROOT%{_datadir}/R/library
%{_bindir}/R CMD INSTALL -l $RPM_BUILD_ROOT%{_datadir}/R/library %{packname}
test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
rm -rf $RPM_BUILD_ROOT%{_datadir}/R/library/R.css

%check
%{_bindir}/R CMD check %{packname}

%clean
rm -rf $RPM_BUILD_ROOT

%post
%{_R_make_search_index}

%postun
%{_R_make_search_index}

%files
%defattr(-, root, root, -)
%dir %{_datadir}/R/library/%{packname}
%doc %{_datadir}/R/library/%{packname}/latex
%doc %{_datadir}/R/library/%{packname}/doc
%doc %{_datadir}/R/library/%{packname}/html
%doc %{_datadir}/R/library/%{packname}/man
%doc %{_datadir}/R/library/%{packname}/DESCRIPTION
%{_datadir}/R/library/%{packname}/CONTENTS
%{_datadir}/R/library/%{packname}/INDEX
%{_datadir}/R/library/%{packname}/NAMESPACE
%{_datadir}/R/library/%{packname}/Meta
%{_datadir}/R/library/%{packname}/R
%{_datadir}/R/library/%{packname}/R-ex
%{_datadir}/R/library/%{packname}/help

%changelog
* Fri Jul 6 2007 Tom "spot" Callaway <tcallawa@redhat.com> 1.6.6-1
- Initial package creation

Summary of differences between arch-specific and noarch R packages

• Noarch packages set BuildArch: noarch
• Noarch packages install into %{_datadir}/R/library/%{packname}, arch-specific packages install into %{_libdir}/R/library/%{packname}

R packaging tips

Naming of R packages

Packages of R modules (thus they rely on R as a parent) have their own naming scheme. They should take into account the upstream name of the R module. This makes a package name format of R-$NAME. When in doubt, use the name of the module that you type to import it in R.

Examples:

R-mAr (R module named mAr)
R-RScaLAPACK (R module named RScaLAPACK)
R-waveslim (R module named waveslim)

Empty %build section

Unlike normal Fedora packages, there is normally no separate %build actions (e.g. %configure)that need to be taken for an R package. However, it is important that all R module packages include an empty %build section, as shown in the spec templates.

Installing the R addon bits

Instead of calling make install, to install the R addon components, you need to run R CMD INSTALL -l $RPM_BUILD_ROOT%{_datadir}/R/library %{packname} (noarch) or R CMD INSTALL -l $RPM_BUILD_ROOT%{_libdir}/R/library %{packname} (arch-specific). Proper %install sections for Fedora R packages are demonstrated in the spec templates.

Deleting the R.css file

Most R addon modules generate a new R.css file, but it would conflict with the master R.css file, included in the main R package. You must delete this file, and do not include it in your package.

Generating the search index.txt

R keeps a master index.txt, as a search index of which R libraries are installed on the system. This provides the source for the R html help interface that is accessible through the help.start() command. This index is always located at %{_libdir}/R/doc/html/search/index.txt. All R packages need to update the search index.txt in %post and %postun. The R package provides a macro to make this simple: %{_R_make_search_index}. Simply put this macro in %post and %postun in your R package, and it will update the search index.txt to include arch-specific and noarch R libraries upon install and uninstall. This is demonstrated in the spec templates.

NOTE: R packages will throw the following warning from rpmlint:

W: R-widgetTools one-line-command-in-%post
/usr/lib/rpm/R-make-search-index.sh

Normally, this would be resolved by running %post -p foo, but this will not work with our script. Just ignore this warning.

Cleaning the R directory of binaries

It is important to clean the R directory of binary files (*.o *.so) before running R CMD CHECK. Otherwise, the CHECK command will throw a warning about finding binaries in the source dir. This is accomplished by running (in %install):

test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)

This is demonstrated in the spec templates.

Running %check

Most (if not all) R addon modules come with a built-in check. This can be triggered by running R CMD check. In Fedora, the check should be run in the %check section. Here is an example %check section for a Fedora R package:

%check
%{_bindir}/R CMD check %{packname}

Note that frequently, R packages have circular dependency loops when running R CMD check. If you hit such a case, you can comment out the check to break the dependency loop, and leave a comment explaining the circular dependency problem.

Documentation files

The R CMD INSTALL operation will install all of the files, including documentation files. The latex, doc, html, man, and DESCRIPTION files/directories need to be marked as %doc. Note that other files, such as CONTENTS, INDEX, NAMESPACE, and help/ are not %doc, since proper R functionality depends on their presence. Be careful not to duplicate %doc files in the package, the spec templates provide good examples on how to package the R addon files without duplications.

Optimization flags

R packages inherit their optimization flags from the main R package, which stores them in %{_libdir}/R/etc/Makeconf. The design of R is such that all R addon library modules use the same optimization flags that the main R package was built with. Accordingly, this is why R addon packages do not pass $RPM_OPT_FLAGS. Also, there is no simple way to pass special optimization flags to R CMD INSTALL.