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[igraph] some trouble compiling igraph in SL 5.3 with R 2.12.1
From: |
Lisa Gerhardt |
Subject: |
[igraph] some trouble compiling igraph in SL 5.3 with R 2.12.1 |
Date: |
Fri, 05 Sep 2014 17:10:58 -0700 |
User-agent: |
Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:24.0) Gecko/20100101 Thunderbird/24.6.0 |
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
config.log
Description: Text document
- [igraph] some trouble compiling igraph in SL 5.3 with R 2.12.1,
Lisa Gerhardt <=