Re: [Rd] config.log told me to report these (PR#12035)

From: Prof Brian Ripley <>
Date: Sat, 09 Aug 2008 07:04:19 +0100 (BST)

This looks like a thoroughly screwed-up compilation system, not an R problem. E.g.

/usr/include/limits.h(125): error #5: could not open source file "limits.h"

configure:5465: icc -E -traditional-cpp -I/opt/intel/cce/10.1.015/include/ conftest.c
<command-line>:11: warning: "__GNUC_PATCHLEVEL__" redefined <built-in>:3: warning: this is the location of the previous definition In file included from /usr/include/features.h:331,

                  from /usr/include/assert.h:38,
                  from conftest.c:20:

/usr/include/sys/cdefs.h:32: error: #error "You need a ISO C conforming compiler to use the glibc headers"

/usr/include/limits.h(125): catastrophic error: could not open source file "limits.h"

conftest.c(74): catastrophic error: could not open source file "dl.h"

conftest.c(77): catastrophic error: could not open source file "floatingpoint.h"

./conftest: error while loading shared libraries: cannot open shared object file: No such file or directory

On Thu, 7 Aug 2008, RichardsTJ2_at_UPMC.EDU wrote:

> This is a multi-part message in MIME format.
> ------_=_NextPart_001_01C8EAD7.27542985
> Content-Type: text/plain;
> charset="iso-8859-1"
> Content-Transfer-Encoding: quoted-printable
> Hello r-bugs,
> I am running openSuse 11.0, with my new Intel 8500 (Penryn) C2D, and I =
> want to use icc and ifort.
> I was able to get a working Goto BLAS, following Dr. Goto's =
> instructions.
> That seems to work OK with gcc and gfortran.
> I get about 10% faster computations by using -O3 rather than -O2.
> I get faster results with Goto BLAS rather than the R BLAS.
> Now I want to make icc and ifort work...
> So I tried this:
> ./configure CC=3Dicc CFLAGS=3D'-O3 -mp' =
> CPPFLAGS=3D-I/opt/intel/cce/10.1.015/include/ F77=3Difort CXX=3Dicc =
> CXXFLAGS=3D'-O3 -mp' FFLAGS=3D'-C90 -w90 -w95 -mp' CPICFLAGS=3D-shared =
> SHLIB_CXXLDFLAGS=3D-shared --with-blas=3D"-L/usr/lib64/GotoBLAS =
> -lgoto_penrynp-r1.26 -lpthread"
> I get six purported "bugs" in the config.log file (attached), but I hope =
> there is something I've overlooked in the past week of agony.
> I have had similar log files with about 100 different combinations of =
> options.
> I hope that you can help.
> Thank you so much.
> Tom Richards
> ------_=_NextPart_001_01C8EAD7.27542985
> Content-Type: text/x-log;
> name="config.log"
> Content-Transfer-Encoding: base64
> Content-Description: config.log
> Content-Disposition: attachment;
> filename="config.log"

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