From ripley at stats.ox.ac.uk  Fri May 30 10:07:38 2008
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Fri, 30 May 2008 09:07:38 +0100 (BST)
Subject: [Rd] problem building R packages on RHEL 4 Linux with Intel
 compilers
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Message-ID: <alpine.LFD.1.10.0805300851290.30023@gannet.stats.ox.ac.uk>

On Fri, 30 May 2008, Martin Maechler wrote:

[Adding Mark Kimpel back to the recipients]

>>>>>> "SU" == Simon Urbanek <simon.urbanek at r-project.org>
>>>>>>     on Thu, 29 May 2008 20:06:21 -0400 writes:
>
>    SU> On May 29, 2008, at 6:11 PM, Mark Kimpel wrote:
>
>    >> Esmail and Simon, I would direct you to the very first sentence of my
>    >> original post, "I would like to build R and packages with the Intel
>    >> 10.1
>    >> compilers in RHEL4." I DO NOT want to build with gcc, that is the
>    >> very point
>    >> of this thread. Does anyone have an answer to my original question?
>    >> I need
>    >> to know what flags to put with configure so that packages will be
>    >> compiled
>    >> with Intel 10.1 when I do "install.packages" from within R.
>    >>
>
>    SU> You'll get that *if* the package is not broken and you compiled R with
>    SU> icc.
>
> But if I read Mark's very first post correctly,
> he tried to build R with icc (and ifort, and their libraries)
> that he didn't succeed  already there,
> but rather gave the ./configure .... error message he'd
> reported.
>
> Is that correct Mark?
> {Not that I could really help further here with the configure problem}

That was my reading of the text but not of the subject line.

If so, we need access to config.log to see the problem.  Please put it on 
a website somewhere.

It would also help to know why Mark Kimpel wants to do this -- people have 
not found the Intel compilers particularly effective and there are quite a 
few reports of wrong answers using them.  I suspect -fast is not going to 
work, as on our Intel 9 compilers it forces static linking.

A very useful general strategy is to start with a minimal set (often none) 
of extra flags and build up to the optimization level required.  So please 
try that before supplying config.log.


> Martin Maechler, ETH Zurich
>
>    SU>  However, many packages don't use autoconf properly which results
>    SU> in broken configure scripts (the configure will use a different
>    SU> compiler and flags than R, effectively making it useless).
>
>    SU> So, in order to furter help you, you have to be more specific (which
>    SU> package we're talking about for example)...
>
>
>    SU> Cheers,
>    SU> Simon
>
>
>    >>
>    >> On Thu, May 29, 2008 at 5:54 PM, Simon Urbanek <simon.urbanek at r-project.org
>    >> >
>    >> wrote:
>    >>
>    >>>
>    >>> On May 29, 2008, at 5:45 PM, Mark Kimpel wrote:
>    >>>
>    >>> Simon, I scanned the config.log, which is too voluminous to insert
>    >>> below,
>    >>>> but it seems that gcc is still being looked for as the compiler.
>    >>>> See the
>    >>>> lines from config.log below. Mark
>    >>>>
>    >>>> Thread model: posix
>    >>>> gcc version 3.4.6 20060404 (Red Hat 3.4.6-9)
>    >>>> configure:4824: $? = 0
>    >>>> configure:4831: gcc -V >&5
>    >>>> gcc: `-V' option must have argument
>    >>>> configure:4834: $? = 1
>    >>>> configure:4857: checking for C compiler default output file name
>    >>>> configure:4884: gcc -fast -unroll -wd188 -I/usr/local/include -L -L
>    >>>> -L/usr/local/lib64 conftest.c  >&5
>    >>>> gcc: unrecognized option `-wd188'
>    >>>> cc1: error: unrecognized command line option "-fast"
>    >>>>
>    >>>
>    >>> ^^ there you go: "-fast" is not supported by your gcc and "-wd188" is
>    >>> ignored (whatever you're trying achieve with that) ... it's there
>    >>> in plain
>    >>> english ;).
>    >>>
>    >>> Cheers,
>    >>> Simon
>    >>>
>    >>>
>    >>>
>    >>>
>    >>>> configure:4887: $? = 1
>    >>>> configure:4925: result:
>    >>>> configure: failed program was:
>    >>>> | /* confdefs.h.  */
>    >>>>
>    >>>> # Then the tail end of config.log
>    >>>>
>    >>>> r_cc_lo_rules_frag=''
>    >>>> r_cc_rules_frag=''
>    >>>> r_cxx_rules_frag=''
>    >>>> r_objc_rules_frag=''
>    >>>>
>    >>>> ## ----------- ##
>    >>>> ## confdefs.h. ##
>    >>>> ## ----------- ##
>    >>>>
>    >>>> #define PACKAGE_NAME "R"
>    >>>> #define PACKAGE_TARNAME "R"
>    >>>> #define PACKAGE_VERSION "2.7.0"
>    >>>> #define PACKAGE_STRING "R 2.7.0"
>    >>>> #define PACKAGE_BUGREPORT "r-bugs at R-project.org"
>    >>>> #define PACKAGE "R"
>    >>>> #define VERSION "2.7.0"
>    >>>> #define R_PLATFORM "x86_64-unknown-linux-gnu"
>    >>>> #define R_CPU "x86_64"
>    >>>> #define R_VENDOR "unknown"
>    >>>> #define R_OS "linux-gnu"
>    >>>> #define Unix 1
>    >>>> #define R_ARCH ""
>    >>>>
>    >>>> configure: exit 77
>    >>>>
>    >>>>
>    >>>> On Thu, May 29, 2008 at 5:35 PM, Simon Urbanek <
>    >>>> simon.urbanek at r-project.org> wrote:
>    >>>>
>    >>>> On May 29, 2008, at 5:01 PM, Mark Kimpel wrote:
>    >>>>
>    >>>> I am installing within my home folder, see the ./configure
>    >>>> options. I've
>    >>>> never had a permission problem before and, like I said, if I don't
>    >>>> put all
>    >>>> the Intel-specific flags in the ./configure, everything works fine.
>    >>>>
>    >>>>
>    >>>> This has nothing to do with the executable bit and/or permissions
>    >>>> - this
>    >>>> is about the compiler rejecting your flags. Have a look in
>    >>>> config.log that's
>    >>>> where you'll find out what the compiler didn't like (and the error
>    >>>> clearly
>    >>>> tells you that ;)).
>    >>>>
>    >>>> Cheers,
>    >>>> Simon
>    >>>>
>    >>>>
>    >>>> On Thu, May 29, 2008 at 4:41 PM, Esmail Bonakdarian <esmail.js at gmail.com
>    >>>> >
>    >>>> wrote:
>    >>>>
>    >>>> Mark Kimpel wrote:
>    >>>>
>    >>>>
>    >>>> checking for gcc... gcc
>    >>>> checking for C compiler default output file name...
>    >>>> configure: error: C compiler cannot create executables
>    >>>> See `config.log' for more details.
>    >>>>
>    >>>>
>    >>>> Are you running this as root? Or do you have the right
>    >>>> privileges for the install?
>    >>>>
>    >>>> The "cannot create executables" looks like a permission problem
>    >>>>
>    >>>> Esmail
>    >>>>
>    >>>>
>    >>>>
>    >>>>
>    >>>> --
>    >>>> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
>    >>>> Indiana University School of Medicine
>    >>>>
>    >>>> 15032 Hunter Court, Westfield, IN 46074
>    >>>>
>    >>>> (317) 490-5129 Work, & Mobile & VoiceMail
>    >>>> (317) 663-0513 Home (no voice mail please)
>    >>>>
>    >>>> ******************************************************************
>    >>>>
>    >>>> [[alternative HTML version deleted]]
>    >>>>
>    >>>> ______________________________________________
>    >>>> R-devel at r-project.org mailing list
>    >>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>    >>>>
>    >>>>
>    >>>>
>    >>>>
>    >>>>
>    >>>>
>    >>>> --
>    >>>> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
>    >>>> Indiana University School of Medicine
>    >>>>
>    >>>> 15032 Hunter Court, Westfield, IN 46074
>    >>>>
>    >>>> (317) 490-5129 Work, & Mobile & VoiceMail
>    >>>> (317) 663-0513 Home (no voice mail please)
>    >>>>
>    >>>> ******************************************************************
>    >>>>
>    >>>
>    >>>
>    >>
>    >>
>    >> --
>    >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
>    >> Indiana University School of Medicine
>    >>
>    >> 15032 Hunter Court, Westfield, IN 46074
>    >>
>    >> (317) 490-5129 Work, & Mobile & VoiceMail
>    >> (317) 663-0513 Home (no voice mail please)
>    >>
>    >> ******************************************************************
>    >>
>    >> [[alternative HTML version deleted]]
>    >>
>    >> ______________________________________________
>    >> R-devel at r-project.org mailing list
>    >> https://stat.ethz.ch/mailman/listinfo/r-devel
>    >>
>    >>
>
>    SU> ______________________________________________
>    SU> R-devel at r-project.org mailing list
>    SU> 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



[Rd] problem building R packages on RHEL 4 Linux with Intel compilers
Prof Brian Ripley