[Rd] compiling R under cygwin
Latchezar (Lucho) Dimitrov
ldimitro at wfubmc.edu
Thu Aug 23 21:33:28 CEST 2007
> -----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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>
> --
> 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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