From ldimitro at wfubmc.edu  Fri Aug 24 04:10:23 2007
From: ldimitro at wfubmc.edu (Latchezar (Lucho) Dimitrov)
Date: Thu, 23 Aug 2007 22:10:23 -0400
Subject: [Rd] compiling R under cygwin
In-Reply-To: <46CE3119.4060909@stats.uwo.ca>
References: <66CE7F4ACF0C74439F9F6E0A5682930202FF5CA7@INDMAIL.lands.resnet.qg>	<Pine.LNX.4.64.0708230724220.15873@gannet.stats.ox.ac.uk>
	<F160BE32A2E5E04497668BBDFE83FEDF11CF87A5@EXCHVS1.medctr.ad.wfubmc.edu>
	<46CE3119.4060909@stats.uwo.ca>
Message-ID: <F160BE32A2E5E04497668BBDFE83FEDF11CF87A9@EXCHVS1.medctr.ad.wfubmc.edu>

 

> -----Original Message-----
> From: Duncan Murdoch [mailto:murdoch at stats.uwo.ca] 
> Sent: Thursday, August 23, 2007 9:15 PM
> To: Latchezar (Lucho) Dimitrov
> Cc: Prof Brian Ripley; Denham Robert; r-devel at r-project.org
> Subject: Re: [Rd] compiling R under cygwin
> 
> 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).

As I said _if_ you insist on using c (which btw is absolutely not
necessary)

Please see the output of 'ls' and 'dir' bellow:

C:\Documents and Settings\Latchezar M Dimitrov>dir "u:\home\Latchezar M
Dimitrov\cygwin"
 Volume in drive U is Users':
 Volume Serial Number is 7FC9-20D1

 Directory of u:\home\Latchezar M Dimitrov\cygwin

07/30/2007  07:00 PM    <DIR>          .
07/30/2007  07:00 PM    <DIR>          ..
07/31/2005  07:39 PM             7,664 .alias
07/29/2005  10:29 AM             7,664 .alias~
07/22/2005  11:24 AM    <DIR>          .autosave
02/13/2007  04:46 PM             2,791 .bashrc
01/27/2007  08:47 PM             2,631 .bashrc~
08/20/2007  11:55 AM            25,966 .bash_history
01/27/2007  08:48 PM               959 .bash_profile
05/28/2005  06:18 PM               959 .bash_profile~
10/27/2003  09:09 PM               569 .emacs
05/28/2005  06:18 PM               608 .inputrc
11/03/2004  07:17 PM               135 .saves-2440-TheComputer
09/13/2005  01:40 PM    <DIR>          .semanticdb
07/22/2005  11:24 AM    <DIR>          .ssh
02/09/2002  11:43 PM             1,003 .Xdefaults
02/22/2006  01:33 AM    <DIR>          .xemacs

$ls /home/Latchezar\ M\ Dimitrov/cygwin/
total 962
-rwxrwxrwx   1 Latchezar M Dimitrov None   1003 Feb  9  2002 .Xdefaults*
-rwxrwxrwx   1 Latchezar M Dimitrov None   7664 Jul 31  2005 .alias*
-rwxrwxrwx   1 Latchezar M Dimitrov None   7664 Jul 29  2005 .alias~*
drwxrwxrwx+  2 Latchezar M Dimitrov None      0 Jul 22  2005 .autosave/
-rwxrwxrwx   1 Latchezar M Dimitrov None  25966 Aug 20 11:55
.bash_history*
-rwxrwxrwx   1 Latchezar M Dimitrov None    959 Jan 27  2007
.bash_profile*
-rwxrwxrwx   1 Latchezar M Dimitrov None    959 May 28  2005
.bash_profile~*
-rwxrwxrwx   1 Latchezar M Dimitrov None   2791 Feb 13  2007 .bashrc*
-rwxrwxrwx   1 Latchezar M Dimitrov None   2631 Jan 27  2007 .bashrc~*
-rwxrwxrwx   1 Latchezar M Dimitrov None    569 Oct 27  2003 .emacs*
-rwxrwxrwx   1 Latchezar M Dimitrov None    608 May 28  2005 .inputrc*
-rwxrwxrwx   1 Latchezar M Dimitrov None    135 Nov  3  2004
.saves-2440-TheComputer*
drwxr-xr-x+  2 Latchezar M Dimitrov None      0 Sep 13  2005
.semanticdb/
drwxrwxrwx+  2 Latchezar M Dimitrov None      0 Jul 22  2005 .ssh/
drwxrwxrwx+  2 Latchezar M Dimitrov None      0 Feb 22  2006 .xemacs/

$ls ~
total 962
-rwxrwxrwx   1 Latchezar M Dimitrov None   1003 Feb  9  2002 .Xdefaults*
-rwxrwxrwx   1 Latchezar M Dimitrov None   7664 Jul 31  2005 .alias*
-rwxrwxrwx   1 Latchezar M Dimitrov None   7664 Jul 29  2005 .alias~*
drwxrwxrwx+  2 Latchezar M Dimitrov None      0 Jul 22  2005 .autosave/
-rwxrwxrwx   1 Latchezar M Dimitrov None  25966 Aug 20 11:55
.bash_history*
-rwxrwxrwx   1 Latchezar M Dimitrov None    959 Jan 27  2007
.bash_profile*
-rwxrwxrwx   1 Latchezar M Dimitrov None    959 May 28  2005
.bash_profile~*
-rwxrwxrwx   1 Latchezar M Dimitrov None   2791 Feb 13  2007 .bashrc*
-rwxrwxrwx   1 Latchezar M Dimitrov None   2631 Jan 27  2007 .bashrc~*
-rwxrwxrwx   1 Latchezar M Dimitrov None    569 Oct 27  2003 .emacs*
-rwxrwxrwx   1 Latchezar M Dimitrov None    608 May 28  2005 .inputrc*
-rwxrwxrwx   1 Latchezar M Dimitrov None    135 Nov  3  2004
.saves-2440-TheComputer*
drwxr-xr-x+  2 Latchezar M Dimitrov None      0 Sep 13  2005
.semanticdb/
drwxrwxrwx+  2 Latchezar M Dimitrov None      0 Jul 22  2005 .ssh/
drwxrwxrwx+  2 Latchezar M Dimitrov None      0 Feb 22  2006 .xemacs/
-rw-r--r--   1 Latchezar M Dimitrov None 114993 Jul  4 22:21
2NonSelf.txt.columns
drwxrwxrwx+  2 Latchezar M Dimitrov None      0 Jul 22  2005 Copy of
.xemacs/
drwxrwxrwx+  3 Latchezar M Dimitrov None      0 Jul 22  2005 LaTeX/

No '/u/'. Convincing? No?

Again, this is not apologetics to cygwin. Just counter-argument. E
pluribus unum as we say (or at least inscribe) here :-)

Latchezar

> 
> /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
Latchezar (Lucho