From murdoch at stats.uwo.ca  Fri Aug 24 03:15:05 2007
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Thu, 23 Aug 2007 21:15:05 -0400
Subject: [Rd] compiling R under cygwin
In-Reply-To: <F160BE32A2E5E04497668BBDFE83FEDF11CF87A5@EXCHVS1.medctr.ad.wfubmc.edu>
References: <66CE7F4ACF0C74439F9F6E0A5682930202FF5CA7@INDMAIL.lands.resnet.qg>	<Pine.LNX.4.64.0708230724220.15873@gannet.stats.ox.ac.uk>
	<F160BE32A2E5E04497668BBDFE83FEDF11CF87A5@EXCHVS1.medctr.ad.wfubmc.edu>
Message-ID: <46CE3119.4060909@stats.uwo.ca>

On 23/08/2007 3:33 PM, Latchezar (Lucho) Dimitrov wrote:
>  
> 
>> -----Original Message-----
>> From: r-devel-bounces at r-project.org 
>> [mailto:r-devel-bounces at r-project.org] On Behalf Of Prof Brian Ripley
>> Sent: Thursday, August 23, 2007 2:54 AM
>> To: Denham Robert
>> Cc: r-devel at r-project.org; Duncan Murdoch
>> Subject: Re: [Rd] compiling R under cygwin
>>
>> On Thu, 23 Aug 2007, Denham Robert wrote:
>>
>>>>> For various reasons,
>>>> I think it is only courteous to mention some good reasons 
>> if you want
>>> to take up people's time.
>>>
>>> Some of the reasons we would like a cygwin version aren't 
>> necessarily 
>>> good reasons.  We have been using cygwin for sometime, 
>> mostly to deal 
>>> with scripting in a combined windows/unix environment.  We have a 
>>> setup which allows windows users to run many scripts in the 
>> same way 
>>> as unix users.  These scripts are often python or shell 
>> scripts.  We 
>>> have R installed on the unix machines, and the system 
>> administrators 
>>> would like to be able to have R on windows in the same 
>> environment.  
>>> This set up also means that the administrator can fairly easily 
>>> maintain the version of software used on all user's machines.  
>>> Probably this could all be managed and still use the native windows 
>>> version of R, but the administrator is familiar with cygwin 
>> and they 
>>> could manage this software in the same way they manage 
>> other packages.
>>
>> Yes, it could almost certainly be done with Rterm.exe.
>>
>> The issue I came across was the so-called 'posix file paths' 
>> that Cygwin uses.  Most (but not all) Windows programs accept 
>> file paths with / as the path separator, and most (but not 
>> all, e.g. tar) Cygwin programs accept paths of the forn 
>> c:/path/to/file.  So provided you use that as your format, 
>> interworking with Unix and Unix-like shells work fine.  It 
>> used to be the case that if you had just one drive C: then 
>> Cygwin programs produced paths of the form /path/to/file that 
>> also worked on Windows.  Now they produce 
>> /cygdrive/c/path/to/file that works nowhere else.
> 
> I'm not sure what you mean by "produce" above but one can easily setup
> (by mount option) cygwin to use "/" instead of "/cygdrive/" so that your
> example above will become "/c/path/to/file". That's if you insist on
> using drive letters. Otherwise w/ proper mounting (in cygwin) one can
> have "usual" *nix dir tree.

The issue is compatibility with other Windows programs.  /path/to/file 
works in lots of Windows programs, and is interpreted relative to the 
current drive.  In the common situation where the user only has one 
partition which is mounted as C:, it works (as long as they didn't 
switch to a CD or USB drive).

/c/path/to/file wouldn't work anywhere but in Cygwin or similar.

Duncan Murdoch

> 
> Regards,
> Latchezar
> 
> PS. I really like the idea of having (the same) bare terminal/command
> window interface to R anywhere as well as anything else (like admin
> tasks above) to be the same. So please put my vote (if you care) to have
> R Windows installation look the same as *nix (up to the point when you
> start R from Start button to have terminal version started instead of
> Rgui as it is now) and keep GUI candies separately for whoever
> wants/needs them. Sorry if that's been already done and I did not know
> about it.
> 
>> In general this is a minor nuisance, but I needed to be able 
>> to cross-build R in an environment where I only have 
>> Cygwin-based cross-compilers, and there the path issues bit 
>> me: I needed a version of R that accepted and returned 
>> Cygwin-style paths.  So I made the configure changes 
>> necessary to build R under Cygwin, and had it running in 20 mins.
>>
>>> We would like to be able to use linux machines on pc's but 
>>> unfortunately we have restrictions imposed on us that 
>> prevent this.  
>>> This restriction also goes as far as the use of virtual 
>> machines.  My 
>>> personal preference would be to run linux on my work pc, and use a 
>>> virtual machine to run windows software, such as ArcGIS and 
>> Imagine, 
>>> that are not available for linux.  This does not seem to be 
>> an option for us.
>>> One thing I was interested in was knowing if there are 
>> others who also 
>>> would like a cygwin version.  From the replies to my post, 
>> and from a 
>>> search of the mailing list archive, I think that there is little 
>>> demand for this.  We would, however, be prepared to help in 
>> some way 
>>> for the few people who are interested.
>> As I said earlier, it builds out of the box in R-devel (with 
>> suitable options documented in the R-admin manual).  No 
>> guarantees that it will continue to do so unless tested in 
>> the alpha/beta phase though.  As no other platform we use 
>> nowadays requires that shared objects/dynamic libraries have 
>> all imports satisfied at build time, this is liable to get broken.
>>
>> But I would encourage people to use Rterm.exe if it can be 
>> made to do what you need.
>>
>>
>>>
>>>
>>> Robert Denham
>>> Environmental Statistician
>>> Remote Sensing Centre
>>> Telephone 07 3896 9899
>>> www.nrw.qld.gov.au
>>>
>>> Department of Natural Resources & Water
>>> QScape Building, 80 Meiers Road, Indooroopilly Qld 4068
>>>
>>> -----Original Message-----
>>> From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
>>> Sent: Tuesday, 21 August 2007 9:53 PM
>>> To: Duncan Murdoch
>>> Cc: Denham Robert; r-devel at r-project.org
>>> Subject: Re: [Rd] compiling R under cygwin
>>>
>>> Yes,
>>>
>>>> What is the advantage of building this?
>>> was my question too.  If you want a Unix-like version of R on PC
>>> hardware running Windows why not run a Unix-like OS under a virtual
>>> machine?
>>>
>>> Quite a lot of the details are wrong: using FLIBS, 
>> BLAS_LIBS and LIBS as
>>> intended will solve most of the problems.  I would use --disable-nls
>>> --disable-mbcs as you don't need them (and in particular you don't
>>> benefit from MBCS support on Windows unless you are in a 
>> CJK locale).
>>> Note that 2.5.1 is released and there is unlikely to be a 
>> 2.5.2, so any
>>> changes would be made only to R-devel.  It there is a 
>> convincing case to
>>> tailor a build for Cygwin there we can probably do so 
>> rather easily, but
>>> the need for ongoing support would be a worry.
>>>
>>> (If platforms are not used and in particular not tested in the
>>> alpha/beta testing phases then the ability to build on them crumbles
>>> away.  We seems to be down to regular testers on Linux, 
>> Windows, MacOS
>>> X, Solaris and FreeBSD, with some help on AIX after a patch 
>> with none.)
>>> On Tue, 21 Aug 2007, Duncan Murdoch wrote:
>>>
>>>> Denham Robert wrote:
>>>>> For various reasons,
>>> I think it is only courteous to mention some good reasons 
>> if you want to
>>> take up people's time.
>>>
>>>>> it suits our workplace to have a cygwin version of R.  I am pretty
>>>>> sure that cygwin is still not a supported environment for 
>> R, but we
>>>>> have managed to compile R-2.5.1 under cygwin without too 
>> many dramas.
>>>>> Our procedure is described below.  We still have a few problems
>>>>> compiling libraries without manually changing files from 
>> .so to .dll,
>>>>> but it seems ok.
>>>>>
>>>> I would expect other subtle problems as well, because 
>> Cygwin is not a
>>>> normal Unix.  I don't know whether any of these 
>> differences matter to
>>>> R, but some things to look out for are:
>>>>
>>>> - you can't unlink a file while it is open
>>>> - filenames are not case sensitive
>>>> - file permissions have strange defaults (everything is executable)
>>>> - I think the executable format still needs to be Windows format
>>>> - There's no such thing as a ptty
>>>> - You'll probably need X11 for graphics, and will lose support for
>>>> Windows metafile output (wmf)
>>>>> I was wondering whether this information is likely to be useful to
>>>>> others, and if we should spend any time looking in to 
>> ways in which
>>>>> the configure/build/install code could be modified to allow a
>>>>> standard install.
>>>>>
>>>> What is the advantage of building this?  I don't think we want to
>>>> support platforms just for the sake of supporting more 
>> platforms, but
>>>> if there's a real need for it, that would be different.
>>>>
>>>> Duncan Murdoch
>>>>> Notes on building R under cygwin:
>>>>>
>>>>> export FFLAGS=-O3
>>>>> export CFLAGS=-O3
>>>>> export CXXFLAGS=-O3
>>>>> export OBJCFLAGS=-O3
>>>>> export FCFLAGS=-O3
>>>>> export LDFLAGS='-lblas -lg2c -lintl'
>>>>>
>>>>> export R_OSTYPE=unix
>>>>>
>>>>> ./configure --prefix=/opt/freeware/R/R-2.5.1 \
>>>>> --with-tcl-config=/usr/lib/tclConfig.sh \
>>>>> --with-tk-config=/usr/lib/tkConfig.sh \ --with-blas=-lblas \
>>>>> --with-lapack=-llapack \ --enable-R-shlib
>>>>>
>>>>> comment out Win32 in src/include/config.h and set Unix to 
>> 1, change
>>>>> .so to .dll. change .so to .dll and in Makeconf.
>>>>> in src/extra/xdr/rpc/types.h comment out defn of malloc.
>>>>>
>>>>> Change .so to .dll in Makefile's
>>>>>
>>>>> edit Makeconf and set R_OSTYPE to unix
>>>>>
>>>>> make -j2
>>>>>
>>>>> when blas doesn't link, re-run command with -lblas -lg2c 
>> on end and
>>>>> change output to .dll
>>>>>
>>>>> edit Rstrptime.c and change wcstod to atof.
>>>>>
>>>>> in modules:
>>>>> when X11 and internet falls over add -lintl to link line. 
>> add -lg2c
>>>>> and -lblas to lapack
>>>>>
>>>>> comment out library/base/R/library.R lines 47-51 to avoid 
>> arch check
>>>>> which seems to go wrong!
>>>>>
>>>>> make -j2
>>>>> make install
>>>>>
>>>>> edit  /opt/freeware/R/R-2.5.1/lib/R/etc/Makeconf and add '-lintl
>>>>> -lg2c -lblas' to the end of ALL_LIBS so the module building works.
>>>>> Change .so to .dll also (can't see how to to this for the build
>>>>> tho...)
>>>>>
>>>>>
>>>>> Our cygwin info is:
>>>>>              sysname              release              version
>>>>>      "CYGWIN_NT-5.1" "1.5.20s(0.155/4/2)"  "20060527 19:21:22"
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Robert Denham
>>>>> Environmental Statistician
>>>>> Remote Sensing Centre
>>>>> Telephone 07 3896 9899
>>>>> www.nrw.qld.gov.au <http://www.nrw.qld.gov.au/>
>>>>>
>>>>> Department of Natural Resources & Water QScape Building, 80 Meiers
>>>>> Road, Indooroopilly Qld 4068
>>>>>
>>>>>
>> *********************************************************************
>>>>> *** The information in this email together with any attachments is
>>>>> intended only for the person or entity to which it is 
>> addressed and
>>>>> may contain confidential and/or privileged material.
>>>>> Any form of review, disclosure, modification, distribution and/or
>>>>> publication of this email message is prohibited, unless as a
>>>>> necessary part of Departmental business.
>>>>> If you have received this message in error, you are asked 
>> to inform
>>>>> the sender as quickly as possible and delete this message and any
>>>>> copies of this message from your computer and/or your 
>> computer system
>>>>> network.
>>>>>
>>>>> ______________________________________________
>>>>> R-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>>
>> -- 
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>> University of Oxford,             Tel:  +44 1865 272861 (self)
>> 1 South Parks Road,                     +44 1865 272866 (PA)
>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] compiling R under cygwin
Duncan Murdoch