[Rd] problem building R packages on RHEL 4 Linux with Intel compilers
Prof Brian Ripley
ripley at stats.ox.ac.uk
Fri May 30 10:07:38 CEST 2008
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
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