From Bill.Glessner at cwu.EDU  Tue Jun  8 19:48:21 2010
From: Bill.Glessner at cwu.EDU (Bill.Glessner at cwu.EDU)
Date: Tue, 08 Jun 2010 10:48:21 -0700 (PDT)
Subject: [Rd] Question on trying to build R 2.11.1 on Tru64(aka OSF1) system
Message-ID: <01NO2O3KE43O8WXU3K@cluster.cwu.edu>


Hello,

I am trying to build the R-2.11.1 software for university faculty to use in
research projects on a DEC/Compaq/HP AlphaServer model GS160 16CPU/64GB memory
running Tru64Unix aka OSF1 version 5.1B-5.
Is it known whether it is possible to build the R-2.11.1 software on the 
platform I am using? 
In my attempts to build the R-2.11.1 software, I first used the native C 
and Fortran 77/90/95 components and GNU make version 3.81:

# cc -V
Compaq C V6.5-011 on HP Tru64 UNIX V5.1B (Rev. 2650)
Compiler Driver V6.5-003 (sys) cc Driver
# f77 -version
 HP Fortran V5.6-104654
 HP Fortran Compiler V5.6-104654-48F7C
# f90 -version
 HP Fortran V5.6-104654
 HP Fortran Compiler V5.6-104654-48F7C
# f95 -version
 HP Fortran V5.6-104654
 HP Fortran Compiler V5.6-104654-48F7C

The build was configured with the command:

./configure "ac_cv_prog_cc_c99=" --prefix=/usr/local/R --disable-nls \
 --with-readline --with-libpng --with-jpeglib \
 --with-system-zlib --with-system-bzlib --with-system-pcre \
 --with-system-xz --with-recommended-packages

The configure executed successfully.
The build attempt exited with an error:

gnumake[1]: Entering directory `/usrX/JunqueYard/R-2.11.1/src/library/Recommende
d'
gnumake[2]: Entering directory `/usrX/JunqueYard/R-2.11.1/src/library/Recommende
d'
begin installing recommended package MASS
/usrX/JunqueYard/R-2.11.1/bin/Rcmd: @: not found
gnumake[2]: *** [MASS.ts] Error 1
gnumake[2]: Leaving directory `/usrX/JunqueYard/R-2.11.1/src/library/Recommended
'
gnumake[1]: *** [recommended-packages] Error 2
gnumake[1]: Leaving directory `/usrX/JunqueYard/R-2.11.1/src/library/Recommended
'
gnumake: *** [stamp-recommended] Error 2

With the configure command:

./configure "ac_cv_prog_cc_c99=" --prefix=/usr/local/R --disable-nls \
 --with-readline --with-libpng --with-jpeglib \
 --with-system-zlib --with-system-bzlib --with-system-pcre \
 --with-system-xz --with-recommended-packages=no

the build completes successfully, but the 'gnumake check' fails with the 
same error

"/usrX/JunqueYard/R-2.11.1/bin/Rcmd: @: not found"

The second attempt was made using gcc/gfortran:

# gcc --version
gcc (GCC) 4.0.2 (TWW)
Copyright (C) 2005 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

# gfortran --version
GNU Fortran 95 (GCC 4.0.2 (TWW))
Copyright (C) 2005 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

The build was configured with the command:

./configure --prefix=/usr/local/R --disable-nls \
 --with-readline --with-libpng --with-jpeglib \
 --with-system-zlib --with-system-bzlib --with-system-pcre \
 --with-system-xz --with-recommended-packages

The configure executed successfully.
The build attempt exited with the same error as attempt 1.
Running ./configure with "--with-recommended-packages=no" again allows the
build to complete successfully, but with the same error

"/usrX/JunqueYard/R-2.11.1/bin/Rcmd: @: not found"

as before when trying 'gnumake check'.
Although the 'gnumake check' didn't, I did a 'gnumake install'. The R
environment seems to work; however, anything involving packages fails
with the "/usrX/JunqueYard/R-2.11.1/bin/Rcmd: @: not found".

Can anyone suggest what I am doing incorrectly in configuring/building R?

The config.site file follows:
#! /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, a copy is available at
### http://www.r-project.org/Licenses/

## 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.
## See etc/Renviron.in for further variables you may wish to set.

## The command used to spool PostScript files to the printer.
## If unspecified, the system will look for either 'lpr' or 'lp'.
## R_PRINTCMD=lpr
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
R_PAPERSIZE=letter

## Set the default behavior of R when ending a session
## Set this to one of '--save' or '--no-save' depending whether you
## want automatic saving of '.RData' or not.
## Note that this applies to interactive and batch use,
## but NOT to the utility R CMD BATCH
## (which defaults to --save irrespective of this setting)
## 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'.
## It is also convenient to set the architecture here, e.g. 'gcc -m32'.
## NB, as from R 2.5.0 configure will append flags for C99 compliance,
## e.g. CC=gcc -std=gnu99
## To avoid this, set contradictory flags (such as -ansi) as part of CFLAGS.
## 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 except icc (for which see R-admin.html).
## CFLAGS=

## Defines for C compilation.
## Use this to specify defines to be used in the compilation of R,
## e.g. -DUSE_TYPE_CHECKING_STRICT
## DEFS=

## The following additional CFLAGS to be used only in the main
## compilation and only in building shared libraries respectively.
## For example, on some systems one needs 'MAIN_CFLAGS=-pg' when
## profiling.
## MAIN_CFLAGS=
## SHLIB_CFLAGS=

## Header file search directory ('-IDIR') and any other miscellaneous
## options (such as defines) for the C preprocessor and compiler.
## If unset defaults to '-I/usr/local/include', with '-I/sw/include'
## prepended on systems using Fink with root '/sw'.
## CPPFLAGS=

## The command which runs the FORTRAN 77 compiler.
## If this is not specified, a search is made for
## f95 fort xlf95 ifort ifc efc pgf95 lf95 gfortran ftn g95
## f90 xlf90 pgf90 pghpf epcf90
## g77 f77 xlf frt pgf77 cf77 fort77 fl32 af77
## On HPUX fort77 is the POSIX compliant FORTRAN compiler, and replaces
## f77 in the search list.
## If CC is gcc, first preference is given to the matching FORTRAN
## compiler (g77 or gfortran).
## If none of these is found, R cannot be compiled.
## F77=
F77=gfortran

## Options for the FORTRAN 77 compiler.
## Use this to specify FFLAGS for the version of the compiler specified
## above.  If unspecified, defaults to '-g -O2' for g77/gfortran,
## otherwise '-g' if this is accepted, otherwise ''.
## FFLAGS=
FFLAGS="-g -O2"

## Options for safe compilation under the FORTRAN 77 compiler.
## Use this to specify FFLAGS for the version of the compiler specified
## above, using as accurate a result as possible, e.g. no optimization
## or using -ffloat-store.
## SAFE_FFLAGS=
SAFE_FFLAGS="-g"

## The following additional FFLAGS to be used only in the main
## compilation and only in building shared libraries respectively.
## For example, on some systems one needs 'MAIN_FFLAGS=-pg' when
## profiling.
## MAIN_FFLAGS=
## SHLIB_FFLAGS=

## The command to be used to load the main R binary.
## This is usually the FORTRAN 77 or C compiler, but the automatic
## choice can be overriden by means of this variable.
## MAIN_LD=

## 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, and anything set here will be in addition unless MAIN_LD
## is given.
## For example, one can set flags for profiling here.
## MAIN_LDFLAGS=

## 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 77 compiler.  If this variable is left
## unspecified an attempt is made to automatically detect the correct
## value by configure.
## FPICFLAGS=

## The command to be used to create shared objects which contain object
## files from a C or FORTRAN 77 compiler only.  This is usually the C
## compiler or 'ld', but the automatic choice can be overridden by means
## of this variable.
## SHLIB_LD=

## Any special flags which are required by the linker when creating
## shared objects containing object files from a C or FORTRAN 77
## compiler only.  This is usually automatically detected by configure,
## and anything set here will be in addition unless SHLIB_LD is given.
## SHLIB_LDFLAGS=

## ditto for a dynamic library: DYLIB_LDFLAGS defaults to SHLIB_LDFLAGS
## DYLIB_LD=
## DYLIB_LDFLAGS=

## The appropriate 'lib' dir, normally 'lib', but 'lib64' on Linux on
## x86_64, mips64, ppc64, sparc64, s390x but not ia64.
## LIBnn=

## Stripping ('-s'), path ('-L'), and any other miscellaneous options
## for the linker.
## '-L' options set here will be prepended to LD_LIBRARY_PATH (or its
## system equivalent) at run time.
## If unset defaults to '-L/usr/local/lib', with '-L/sw/lib' prepended
## on systems using Fink with root '/sw'.
## On some Linux 64-bit systems its default is -L/usr/local/lib64.
## If LIBnn is set it defaults to -L/usr/local/$LIBnn.
## LDFLAGS=

## The command which runs the C++ compiler.  It not specified, configure
## uses the values of the environment variables 'CXX' or 'CCC' if set,
## and then looks under the names 'c++', 'g++', 'gcc', 'CC', 'cxx', and
## 'cc++' (in that order).
## CXX=
CXX=g++

## Options for the C++ compiler.
## CXXFLAGS=

## Any special flags which must be used when compiling C++ code to be
## turned into a shared library.  If this variable is left unspecified
## an attempt is made to automatically detect the correct value by
## configure.
## CXXPICFLAGS=

## The command to be used to load shared libraries which contain object
## files from a C++ compiler.  This is usually the C++ compiler/linker,
## but the automatic choice can be overridden by means of this
## variable.
## SHLIB_CXXLD=

## Any special flags which are required when creating shared libraries
## containing object files from a C++ compiler.  This is usually
## automatically detected by configure, and anything set here will be in
## addition unless SHLIB_CXXLD is given.
## SHLIB_CXXLDFLAGS=


## FORTRAN 95 compiler: optional for use in packages.
## Analogous to the F77 and CXX settings.
## FC=
## FCFLAGS=
## FCPICFLAGS=
## SHLIB_FCLD=${FC}
## Unlike SHLIB_CXXLDFLAGS, SHLIB_FCLDFLAGS is never additional
## SHLIB_FCLDFLAGS=${SHLIB_LDFLAGS}

## Tcl/Tk settings.
## Use TCLTK_LIBS for all '-L' and '-l' options needed for linking
## against the Tcl and Tk library.
## TCLTK_LIBS=
## Use TCLTK_CPPFLAGS for all '-I' options needed for finding the tcl.h
## and tk.h headers.
## TCLTK_CPPFLAGS=

## Browser default
## Default setting for the R_BROWSER env variable
## If unset configure searches in turn for (currently)
## firefox mozilla galeon kfmclient opera gnome-moz-remote open
## and uses the full path.
## R_BROWSER=

## BLAS and LAPACK settings
## Use BLAS_LIBS for all '-L' and '-l' options needed for linking
## against an external BLAS implementation.
## BLAS_LIBS=
## Use LAPACK_LIBS for all '-L' and '-l' options needed for linking
## against an external LAPACK implementation.
## Note that (see R-admin) that our main intention is to allow a
## LAPACK-containing BLAS to be used, so this is rarely needed, and
## it is not used if the BLAS already contains LAPACK.
## LAPACK_LIBS=

## Make name.
## Set this if you want to use a make by another name.
## For example, if your GNU make is called 'gmake', use 'MAKE=gmake'.
## MAKE=
MAKE=gnumake

## Tar name
## Set this to prefer a tar which has the capability to automagically
## read compressed archives.  The default is to choose 'gtar' (normally
## GNU tar) then 'tar', but other possibilities include 'bsdtar' from
## the libarchive project.
## TAR=
TAR=gnutar

In looking through the R documentation I didn't see any reference to "@"
as a function/variable/language element/etc.

Thanks for your help,
Bill



[Rd] Question on trying to build R 2.11.1 on Tru64(aka OSF1) system
Bill.Glessner at cwu.EDU