From simon.urbanek at r-project.org  Fri May 30 02:06:21 2008
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Thu, 29 May 2008 20:06:21 -0400
Subject: [Rd] problem building R packages on RHEL 4 Linux with Intel
	compilers
In-Reply-To: <6b93d1830805291511l3529c13m364af64d7b1467e6@mail.gmail.com>
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	<CE1BED64-1B89-4937-BE06-0A1A41791318@r-project.org>
	<6b93d1830805291445n7d253c30w9e4fd9a9b351cd9a@mail.gmail.com>
	<631AB4B3-BBC9-4607-B03C-3A889B0C9AE5@r-project.org>
	<6b93d1830805291511l3529c13m364af64d7b1467e6@mail.gmail.com>
Message-ID: <472B44AA-D75F-4DED-AFF9-2FA2835AD97D@r-project.org>


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.
>

You'll get that *if* the package is not broken and you compiled R with  
icc. However, many packages don't use autoconf properly which results  
in broken configure scripts (the configure will use a different  
compiler and flags than R, effectively making it useless).

So, in order to furter help you, you have to be more specific (which  
package we're talking about for example)...

Cheers,
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
>
>



[Rd] problem building R packages on RHEL 4 Linux with Intel compilers
Simon Urbanek