Hi all,
The systems guys here in the stat dept don't seem to be able to
compile R on the Dec Alphas or on the SGIs. Can anyone give them a hand?
-Greg
-------------------------------------------------------------------------------
Gregory R. Warnes | It is high time that the ideal of success
warnes at biostat.washington.edu | be replaced by the ideal of service.
| Albert Einstein
-------------------------------------------------------------------------------
---------- Forwarded message ----------
Date: Tue, 9 Feb 1999 10:06:57 -0800 (PST)
From: Richard Fairfield <rcf at ms.washington.edu>
To: "Adrian E. Raftery" <raftery at stat.washington.edu>
Cc: Statistics Help <help at stat.washington.edu>
Subject: Re: installing R on monto
Adrian:
We are unable to compile this software on either platform. I don't think
there is anything more we can do at this time.
Here are several options for the future:
1) If you know of anyone who has successfully compiled this software on
either DEC Alpha (running Dunix 4.0) or on a 64 bit SGI (running Irix 6.2)
then maybe they would share their work with us.
2) We can watch for future versions of the software. A newer version may
fix the comilation problems.
3) Maybe you have a grad student who knows Fortran who could work on the
code?
that's all for now,
rcf
On Fri, 5 Feb 1999, Adrian E. Raftery wrote:
> Thanks, Rick. - Adrian
>
> On Fri, 5 Feb 1999, Richard Fairfield wrote:
>
> > Today I tried to build "R" on both a DEC Alpha and on an
SGI. It failed
> > in both cases. There errors looked a bit less formidable on the Alpha
than
> > on the SGI. We are going to have one of our grad students employees
look
> > at the DEC Alpha version to see if he can isolate the error.
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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On Tue, 9 Feb 1999, Gregory R. Warnes wrote:> > Hi all, > > The systems guys here in the stat dept don't seem to be able to > compile R on the Dec Alphas or on the SGIs. Can anyone give them a hand? > > -GregI attached my "config.site" file. I am using it with R 0.63.2 on my Alphas (DU 4.0E) with no problems during compiling. It contains the needed fortran and ld options. You have to do only a "./configure" and "make". I hope this helps. BTW, there are binary packages available at our ftp server ftp://ftp.uni-klu.ac.at/pub/uni-klu.ac.at/rpms/osf1/alpha/ but currently they are not up to date, and because these packages are in RPM format you would first need to install rpm 2.5 and some basic freeware rpm packages for DU 4.0. (These are Digital Unix (4.0) RPMs and no Linux/Alpha RPMs!) Best wishes Albrecht Gebhardt ..................................................................... | Albrecht Gebhardt Tel.: (++43 463) 2700/837 | | Institut fuer Mathematik Fax : (++43 463) 2700/834 | | Universitaet Klagenfurt mailto:albrecht.gebhardt at uni-klu.ac.at | | Villacher Str. 161 http://www-stat.uni-klu.ac.at/~agebhard | | A-9020 Klagenfurt, Austria | `--------------------------------------------------------------------' -------------- next part -------------- #! /bin/sh ### This file is part of R. ### ### R is free software; you can redistribute it and/or modify it under ### the terms of the GNU General Public License as published by the Free ### Software Foundation; either version 2 of the License, or (at your ### option) any later version. ### ### R is distributed in the hope that it will be useful, but WITHOUT ANY ### WARRANTY; without even the implied warranty of MERCHANTABILITY or ### FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public ### License for more details. ### ### You should have received a copy of the GNU General Public License ### along with R; if not, you can obtain it via the World Wide Web at ### `http://www.gnu.org/copyleft/gpl.html', or by writing to the Free ### Software Foundation, 59 Temple Place -- Suite 330, Boston, MA ### 02111-3307, USE. # By means of this file you can (also) provide default values for the # configuration process. To set variables, uncomment the VAR=DEFAULT # lines and set DEFAULT according to your needs. # The command used to spool PostScript files to the printer. # If unspecified, the system will look for either "lpr" or "lp" # R_PRINTCMD=lpr # The paper size for the local (PostScript) printer. # It must either be left blank or set to one of "a4" or "letter". # If left blank the system will use "a4". # R_PAPERSIZE=a4 # The default behavior of R if it encounters EOF in batch mode. # Set this to one of "--save" or "--no-save" depending whether you # want automatic saving of `.RData' or not. # R_BATCHSAVE # The command which runs the C compiler. # If unspecified, a search is made for gcc and cc (in that order). # To override this choice, specify the name of the command which runs # the compiler here, for example `c89'. CC="cc" # Debugging and optimization options for the C compiler. # Use this to specify CFLAGS for the version of the C compiler specified # above. If unspecified, defaults to "-g -O2" for gcc, and "-g" in all # other cases. CFLAGS="-g -I/usr/local/include" # Header file search directory (`-IDIR') and any other miscellaneous # options for the C preprocessor and compiler. # CPPFLAGS # The command which runs the the FORTRAN compiler. # If unspecified, a search is made for g77, fort77, f77, f90, xlf, cf77, # and fc (in that order). If none of these is found, f2c is used if # found; otherwise, R cannot be compiled. The search mechanism can be # changed using the `--with-g77', `--with-f77', and `--with-f2c' command # line options to configure. FC="f77" # Options for the FORTRAN compiler. # Use this to specify FFLAGS for the version of the compiler specified # above. If unspecified, defaults to "-O2" for g77, and "" otherwise. FFLAGS="-g -fpe3" # The command to be used to load the main R binary. # This is usually the FORTRAN or C compiler, but the automatic choice # can be overriden by means of this variable. LDCMD="f77 -g -nofor_main -fpe3 " # For `-l' and `-L' options to pass to the linker. # LIBS # The flags which are necessary for loading main program which will load # DLLs at runtime. HP-UX and Linux-elf are examples of platforms which # use this. These platforms are already taken care of by configure. # DLLFLAGS # Any special flags which must be used when compiling C code to be # turned into a shared library. This is typically something like -fpic # or -fPIC. If this variable is left unspecified an attempt is made to # automatically detect the correct value by configure. # CPICFLAGS # The following variable can be used to provide any PIC flags for the # FORTRAN compiler (if you are using one). If not specified, the value # of CPICFLAGS above is used. # FPICFLAGS # Any special flags which are required by "ld" when creating shared # libraries. This is usually automatically detected by configure. SHLIBLDFLAGS='-shared -expect_unresolved "*"'
On Tue, 9 Feb 1999, Gregory R. Warnes wrote:> > Hi all, > > The systems guys here in the stat dept don't seem to be able to > compile R on the Dec Alphas or on the SGIs. Can anyone give them a hand? > > -GregSomeone on this list gave me the hint to try f2c and DEC's cc to compile under DU (I don't have fortran on the dec). I have done this and R compiles on my Alpha. The f2c combination and gcc did NOT work on the alpha. I wish I could thank that person but I cleaned up my desk!!! Jonathan Yuen phone: 46 18 672369 Swedish University of Agricultural Sciences fax: 46 18 672890 Box 7044 email replies to S 750 07 Uppsala, SWEDEN Jonathan.Yuen at tvs.slu.se -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
I've "compiled" R on an OSF1 alpha and on Irix 6.2 and 6.5
(R4000):
$ uname -a
OSF1 atlantic.bio.dfo.ca V4.0 878 alpha
./configure --prefix=$HOME
[...]
R is now configured for alpha-dec-osf4.0
Source directory: .
Installation directory: /usr2/gwhite
C compiler: cc -ieee_with_inexact -g
FORTRAN compiler: f77
$ uname -a
IRIX newton 6.5 05190003 IP22 mips
$ ./configure --prefix=$HOME
[...]
R is now configured for mips-sgi-irix6.5
Source directory: .
Installation directory: /usr/people/gwhite
C compiler: cc -g
FORTRAN compiler: f90
$ uname -a
IRIX caligo 6.2 03131015 IP22
./configure
[...]
R is now configured for mips-sgi-irix6.2
Source directory: .
Installation directory: /usr/local
C compiler: gcc -O2 -I/usr/local/include.bugs
FORTRAN compiler: g77 -O2
The Irix 6.2 system is a mess due to the number of patches that have
been applied, reversed, etc. Some headers are just missing and had to
be copied from another system into "/usr/local/include.bugs".
On the Irix 6.5 system, there were some name clashes which required
additions to the "SGI nonsense" section of src/include/Mathlib.h:
...3.2/src/include $ diff -C 3 Mathlib.h.000 Mathlib.h
*** Mathlib.h.000 Wed Dec 23 05:54:25 1998
--- Mathlib.h Tue Feb 2 14:18:26 1999
***************
*** 154,159 ****
--- 154,165 ----
#ifdef qexp
#undef qexp
#endif
+ #ifdef qgamma
+ #undef qgamma
+ #undef qlgamma
+ #undef qsigngam
+ #endif
+
/* Name Hiding to Avoid Clashes with Fortran */
---------------------------
There are problems with both the OSF1 and Irix 6.5 versions. In both
cases I used the vendor's compilers. Both these systems are very fresh,
out of the box installations with no patches applied. SGI provides perl
5, but OSF1 (at least with the options installed on the system available
to me) does not, so I don't get documentation on OSF1. Furthermore, tick
marks and some other lines (e.g., in boxplots) are missing from plots when
I use the x11 device, but present using the PS device.
The SGI version gives:
> demo(lm.glm)
[...]> anova(lmwg <- lm(weight ~ group))
Analysis of Variance Table
Response: weight
Warning: NAs introduced by coercion
Error: names attribute must be the same length as the vector
I made more headway using Irix 6.2 and GNU compilers, but had to use GNU
rx instead of the SGI regcomp routines, which gave:
> gsub("([ab])", "\\1_\\1_", "abc and ABC")
Error: invalid backreference in regular expression
Finally, I want to use the cluster package, but the "daisy" function
fails on a simple example for:
> codes(as.ordered(NULL))
Error: no applicable method for "codes"
Is this a bug or a change in the definition of "codes"?
--
George White <aa056 at chebucto.ns.ca> tel: 902.426.8509
Bedford Inst. of Oceanography, Nova Scotia, Canada.
On Tue, 9 Feb 1999, Gregory R. Warnes wrote:
>
> Hi all,
>
> The systems guys here in the stat dept don't seem to be able to
> compile R on the Dec Alphas or on the SGIs. Can anyone give them a hand?
>
> -Greg
>
>
-------------------------------------------------------------------------------
> Gregory R. Warnes | It is high time that the ideal of success
> warnes at biostat.washington.edu | be replaced by the ideal of service.
> | Albert Einstein
>
-------------------------------------------------------------------------------
>
> ---------- Forwarded message ----------
> Date: Tue, 9 Feb 1999 10:06:57 -0800 (PST)
> From: Richard Fairfield <rcf at ms.washington.edu>
> To: "Adrian E. Raftery" <raftery at stat.washington.edu>
> Cc: Statistics Help <help at stat.washington.edu>
> Subject: Re: installing R on monto
>
>
> Adrian:
>
> We are unable to compile this software on either platform. I don't
think
> there is anything more we can do at this time.
>
> Here are several options for the future:
>
> 1) If you know of anyone who has successfully compiled this software on
> either DEC Alpha (running Dunix 4.0) or on a 64 bit SGI (running Irix
6.2)
> then maybe they would share their work with us.
>
> 2) We can watch for future versions of the software. A newer version may
> fix the comilation problems.
>
> 3) Maybe you have a grad student who knows Fortran who could work on the
> code?
>
> that's all for now,
> rcf
>
> On Fri, 5 Feb 1999, Adrian E. Raftery wrote:
>
> > Thanks, Rick. - Adrian
> >
> > On Fri, 5 Feb 1999, Richard Fairfield wrote:
> >
> > > Today I tried to build "R" on both a DEC Alpha and on
an SGI. It failed
> > > in both cases. There errors looked a bit less formidable on the
Alpha than
> > > on the SGI. We are going to have one of our grad students
employees look
> > > at the DEC Alpha version to see if he can isolate the error.
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-help-request at
stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._