From ripley at stats.ox.ac.uk  Tue Jun  8 20:41:05 2010
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue, 8 Jun 2010 19:41:05 +0100 (BST)
Subject: [Rd] Question on trying to build R 2.11.1 on Tru64(aka OSF1)
 system
In-Reply-To: <01NO2O3KE43O8WXU3K@cluster.cwu.edu>
References: <01NO2O3KE43O8WXU3K@cluster.cwu.edu>
Message-ID: <alpine.LFD.2.00.1006081937120.9569@gannet.stats.ox.ac.uk>

On Tue, 8 Jun 2010, Bill.Glessner at cwu.EDU wrote:

>
> 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?

It is not known: it is years since we have a report on that system.

You seem to have a problem with Rcmd, that is R_HOME/bin/Rcmd. 
Perhaps you could send it to us to have a look at?

> 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
>
> ______________________________________________
> 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



[Rd] Question on trying to build R 2.11.1 on Tru64(aka OSF1) system
Prof Brian Ripley