Re: [igraph] some trouble compiling igraph in SL 5.3 with R 2.12.1

[Gábor Csárdi]

I think you need to use the same compiler, that was used to compile R
on your system. R automatically selects this imho, although your R
version is very old, so I cannot tell for sure.

Gabor

On Fri, Sep 5, 2014 at 8:10 PM, Lisa Gerhardt <address@hidden> wrote:
> Hi,
> I'm having some trouble getting igraph to compile with R 2.12.1 in
> scientific linux 5.3. After downloading and untarring the source, I do
>
> export CC=/usr/common/usg/gcc/4.7.0/bin/gcc
> R CMD INSTALL igraph
>
> I get this error:
> * installing to library
> '/global/common/carver/usg/R/R-2.12.1/lib64/R/library'
> * installing *source* package 'igraph' ...
> checking for gcc... icc -std=c99
> checking whether the C compiler works... no
> configure: error: in
> `/global/scratch2/sd/lgerhard/RtmpG5FC8q/downloaded_packages/igraph':
> configure: error: C compiler cannot create executables
> See `config.log' for more details
> ERROR: configuration failed for package 'igraph'
> * removing '/global/common/carver/usg/R/R-2.12.1/lib64/R/library/igraph'
>
> Looking in the config.log I see:
> This file contains any messages produced by compilers while
> running configure, to aid debugging if configure makes a mistake.
>
> It was created by igraph configure @VERSION@, which was
> generated by GNU Autoconf 2.69.  Invocation command line was
>
>   $ ./configure
>
> ## --------- ##
> ## Platform. ##
> ## --------- ##
>
> hostname = cvrsvc02
> uname -m = x86_64
> uname -r = 2.6.32-358.18.1.el6.nersc.x86_64
> uname -s = Linux
> uname -v = #1 SMP Wed Aug 28 02:17:42 PDT 2013
>
> /usr/bin/uname -p = unknown
> /bin/uname -X     = unknown
>
> /bin/arch              = x86_64
> /usr/bin/arch -k       = unknown
> /usr/convex/getsysinfo = unknown
> /usr/bin/hostinfo      = unknown
> /bin/machine           = unknown
> /usr/bin/oslevel       = unknown
> /bin/universe          = unknown
>
> PATH: /usr/common/usg/R/R-2.12.1/bin
> PATH: ./
> PATH: /usr/common/usg/openmpi/1.4.5/pgi/bin
> PATH: /usr/common/usg/OFED/gcc4.7.0/2.0-3.0.0-Mellanox/bin
> PATH: /usr/common/usg/gcc/4.7.0/bin
> PATH: /usr/common/usg/bin
> PATH: /usr/common/mss/bin
> PATH: /usr/common/nsg/bin
> PATH: /usr/syscom/opt/torque/4.2.7.h1/bin
> PATH: /usr/syscom/opt/moab/7.2.7-e7c070d1-b4/bin
> PATH: /usr/syscom/nsg/sbin
> PATH: /usr/syscom/nsg/bin
> PATH: /usr/share/Modules/bin
> PATH: /usr/kerberos/bin
> PATH: /usr/local/bin
> PATH: /bin
> PATH: /usr/bin
>
>
> ## ----------- ##
> ## Core tests. ##
> ## ----------- ##
>
> configure:2489: checking for gcc
> configure:2516: result: icc -std=c99
> configure:2745: checking for C compiler version
> .....
> configure:2854: error: in
> `/global/scratch2/sd/lgerhard/RtmpG5FC8q/downloaded_packages/igraph':
> configure:2856: error: C compiler cannot create executables
> See `config.log' for more details
>
> ## ---------------- ##
> ## Cache variables. ##
> ## ---------------- ##
>
> ac_cv_env_CCC_set=
> ac_cv_env_CCC_value=
> ac_cv_env_CC_set=set
> ac_cv_env_CC_value=/usr/common/usg/gcc/4.7.0/bin/gcc
> ac_cv_env_CFLAGS_set=
>
>
> So it is picking up the gcc set in $CC, but seems to be ignoring it. Any
> suggestions would be greatly appreciated. The full config.log is attached.
>
> Thanks,
> Lisa
>
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