From ligges at statistik.tu-dortmund.de  Thu Sep  3 10:31:32 2009
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Thu, 03 Sep 2009 10:31:32 +0200
Subject: [Rd] Including a binary Python Interpreter into a binary
 R-package for MS Windows
In-Reply-To: <57821.94131.qm@web65608.mail.ac4.yahoo.com>
References: <57821.94131.qm@web65608.mail.ac4.yahoo.com>
Message-ID: <4A9F7EE4.4020202@statistik.tu-dortmund.de>



gvsteen at yahoo.com wrote:
> 2009/8/30 Uwe Ligges <ligges at statistik.tu-dortmund.de>: [snip]
>> Guido van Steen wrote:
> [snip]
>>> Something that interests me too: What about R's policy with
>>> respect to including binary files? I saw that developers should
>>> include a file
> [snip]
>> Please do not include binary files and carefully watch for licenses
>> of those files (e.g. if GPL'ed, you need to ship sources!). If
>> pyhthon is required, I highly suggest to state it in the
>> SystemDependencies and be fine with it - users can learn to install
>> phython themselves, I'm pretty sure.
> 
> Hi Uwe,
> 
> Note: I will send this email cc. to the R-devel list, which I joined
> today. I think it may be of interest to other people as well.
> 
> Thank you for your answer, although it disappointed me a bit. I had
> already spent quite some time building a stand-alone windows binary
> of a new package "write2xls". This package provides the same R
> interface to Python as the other package "dataframes2xls". As you
> know it enable users to create xls files. The special thing about
> "write2xls" is that it does not have any dependencies at all. It is
> so-to-speak a turn-key solution.
 >
> Of course I should have read a bit more before I started. Only after
> your mail I read the pdf-file "Writing R Extensions". It says "A
> source package if possible should not contain binary executable
> files: they are not portable, and a security risk if they are of the
> appropriate architecture. R CMD check will warn about them unless
> they are listed (one filepath per line) in a file 'BinaryFiles' at
> the top level of the package or bundle. Note that CRAN will no longer
> accept submissions containing binary files even if they are listed."
 >
> So, yes, you are right. I was actually hoping that CRAN could make
> some exceptions, but after some thinking I fully understand that many
> people would object to this for good reasons: R code depending on a C
> compiler will not work without a C Compiler either. For security
> reasons we cannot allow packages to install a binary C compiler. So,
> yes, I understand the reasons but still it is a pity.
>
> The current situation is that many MS Windows users can not easily
> use "dataframes2xls". There are a few reasons:
> 
> * Most users of MS Windows will be unfamiliar with Python, which will
> make them reluctant to install Python.


Guido,

why? If you package asks them to install Python, if your package cannot 
find it in the path, they will certainly do if they find the 
functionality very useful.


> * Installing Python will be impossible on many MS Windows platforms
> due to limited user rights.

Don't know Python on Windows so well, but why can't they install it? You 
can also install R with limited user privileges.


> * Downloading a standard Python installer takes about 15 Megabytes.
> My newly created "write2xls" package just contains 1.3 MB.

Well, but much of that space is useless/wasted for non-Windows users then.


> So only few R users can benefit from "dataframes2xls". An alternative
> to "dataframes2xls" is "write.xls". "dataframes2xls" is technically
> superior, as it allows the specification of proper formatting and
> fonts. "dataframes2xls" also exists longer. However, "write.xls" is
> available to many more R users because it depends on Perl, which is
> installed as a part of the R-tools.

Most R users under Windows won't have Rtools installed, just the 
developers will have.



> So, I think it would be a pity not to provide "write2xls", since I
> have it readily available now. Therefore, I will probably be hosting
> "write2xls" on a different repository, as long as no Python
> Interpreter is included in the R-tools. Does anyone know of a
> alternative repository, which does accept "trustworthy" R packages
> with a binary Python Interpreter.


Can't you add some configure script / Makefile that allows to build the 
binary from sources that you provide in your package?

Otherwise, what you could do is to install the binary on demand from 
another side you are hosting. E.g. library("write2xls") could check if 
the required binary is available and install on demand if it is not 
available. But don't forget to look carefully into all license issues.


> 
> Thanks!
> 
> Best wishes,
> 
> Guido van Steen
> 
> P.S. For those who are interested or who would like to test it, at
> the moment "write2xls" can be downloaded as
> "http://www.heppel.net/write2xls_0.4.4.9.zip". The "source" package
> is available as "http://www.heppel.net/write2xls_0.4.4.9.tar.gz".
> 
> P.P.S. I think that on MS Windows the combination of R and the R
> tools is just as much a potential security risk as allowing to
> include a Python Interpreter in a binary package. The R website
> should pay more serious attention to this.

R tools are just required for developers, and they won't be installed on 
other platforms than Windows, I believe. Additionally, we know who built 
those tools.


> P.P.P.S. Uwe also brings up the issue of licensing. However, this is
> not a problem at all. The Python license is one of the most
> permissive licenses around. For the Python Interpreter that I
> included in the "write2xls" package, I used pyMingW, which is
> distributed under an MIT license. It is a version of Python compiled
> by the MinGW compiler. Thanks to this pyMingW distribution I also
> avoid the need of any Microsoft-owned dlls. "dataframes2xls" and
> "write2xls" are also distributed under a MIT license.

If MIT allows to ship things the way you plan to, then it's fine, but no 
binaries in sources packages on CRAN. We did quite some work to get rid 
of the packages that did (even my own package!) and won't make 
exceptions. We won't revert our decision.

Best wishes,
Uwe Ligges



[Rd] Including a binary Python Interpreter into a binary R-package for MS Windows
Uwe Ligges