From ldimitro at wfubmc.edu  Thu Aug 23 21:33:28 2007
From: ldimitro at wfubmc.edu (Latchezar (Lucho) Dimitrov)
Date: Thu, 23 Aug 2007 15:33:28 -0400
Subject: [Rd] compiling R under cygwin
In-Reply-To: <Pine.LNX.4.64.0708230724220.15873@gannet.stats.ox.ac.uk>
References: <66CE7F4ACF0C74439F9F6E0A5682930202FF5CA7@INDMAIL.lands.resnet.qg>
	<Pine.LNX.4.64.0708230724220.15873@gannet.stats.ox.ac.uk>
Message-ID: <F160BE32A2E5E04497668BBDFE83FEDF11CF87A5@EXCHVS1.medctr.ad.wfubmc.edu>

 

> -----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.

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
> >>>
> >>> 
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> >>
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> >
> 
> -- 
> 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
> 
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[Rd] compiling R under cygwin
Latchezar (Lucho