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
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:2754: icc -std=c99 --version >&5
./configure: line 2756: icc: command not found
configure:2765: $? = 127
configure:2754: icc -std=c99 -v >&5
./configure: line 2756: icc: command not found
configure:2765: $? = 127
configure:2754: icc -std=c99 -V >&5
./configure: line 2756: icc: command not found
configure:2765: $? = 127
configure:2754: icc -std=c99 -qversion >&5
./configure: line 2756: icc: command not found
configure:2765: $? = 127
configure:2785: checking whether the C compiler works
configure:2807: icc -std=c99 -pthread -O3 -I/usr/local/include conftest.c >&5
./configure: line 2809: icc: command not found
configure:2811: $? = 127
configure:2849: result: no
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "igraph"
| #define PACKAGE_TARNAME "igraph"
| #define PACKAGE_VERSION "@VERSION@"
| #define PACKAGE_STRING "igraph @VERSION@"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE_URL ""
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| ;
| return 0;
| }
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=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=set
ac_cv_env_CXX_value=g++
ac_cv_env_FCFLAGS_set=
ac_cv_env_FCFLAGS_value=
ac_cv_env_FC_set=set
ac_cv_env_FC_value=gfortran
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_prog_ac_ct_CC='icc -std=c99'
## ----------------- ##
## Output variables. ##
## ----------------- ##
CC='icc -std=c99'
CFLAGS='-pthread -O3'
CPP=''
CPPFLAGS='-I/usr/local/include'
CXX='icpc'
CXXCPP=''
CXXFLAGS='-O3 -pthread'
DEFS=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
FC='ifort -pthread'
FCFLAGS='-g -O2 -Kieee'
GLPK_LIBS=''
GMP_LIBS=''
GREP=''
HAVE_GLPK=''
HAVE_GMP=''
HAVE_LIBXML=''
LDFLAGS=''
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
OBJEXT=''
PACKAGE_BUGREPORT='[email protected]'
PACKAGE_NAME='igraph'
PACKAGE_STRING='igraph @VERSION@'
PACKAGE_TARNAME='igraph'
PACKAGE_URL=''
PACKAGE_VERSION='@VERSION@'
PATH_SEPARATOR=':'
SHELL='/bin/sh'
XML2CONFIG=''
XML2_CFLAGS=''
XML2_LIBS=''
ac_ct_CC='icc -std=c99'
ac_ct_CXX=''
ac_ct_FC=''
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='NONE'
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='NONE'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
/* confdefs.h */
#define PACKAGE_NAME "igraph"
#define PACKAGE_TARNAME "igraph"
#define PACKAGE_VERSION "@VERSION@"
#define PACKAGE_STRING "igraph @VERSION@"
#define PACKAGE_BUGREPORT "[email protected]"
#define PACKAGE_URL ""
configure: exit 77
_______________________________________________
igraph-help mailing list
[email protected]
https://lists.nongnu.org/mailman/listinfo/igraph-help
