From maechler at stat.math.ethz.ch  Fri May 30 09:30:58 2008
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Fri, 30 May 2008 09:30:58 +0200
Subject: [Rd] problem building R packages on RHEL 4 Linux with Intel
	compilers
In-Reply-To: <472B44AA-D75F-4DED-AFF9-2FA2835AD97D@r-project.org>
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Message-ID: <18495.44338.732777.194730@stat.math.ethz.ch>

>>>>> "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}

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



[Rd] problem building R packages on RHEL 4 Linux with Intel compilers
Martin Maechler