[Rd] problem building R packages on RHEL 4 Linux with Intel compilers
Martin Maechler
maechler at stat.math.ethz.ch
Fri May 30 09:30:58 CEST 2008
>>>>> "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
>>
>>
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