问题
I am trying to install Rcplex in R on a macbook and I'm following the instruction at this link http://jrzubizarreta.com/INSTALL.
On terminal, in the folder where the unzipped Rcplex directory is, I typed
cd /Library/Frameworks/R.framework/Versions/3.4/Resources/library
R CMD INSTALL --configure-args="PKG_CFLAGS='-m64 -fPIC' PKG_CPPFLAGS=-
I/Applications/CPLEX_Studio_Community129/cplex/include PKG_LIBS='-
l/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic
-m64 -lm -lpthread -framework CoreFoundation -framework IOKit'" Rcplex
as by instructions. However, I get the following error:
configure: error: Could not link CPLEX library using -
L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic
-m64 -lm -lpthread -framework CoreFoundation -framework IOKit
The error persist if I use the sudo option before R CMD INSTALL [...].
The config.log states:
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by Rcplex configure 0.3.2, which was
generated by GNU Autoconf 2.59. Invocation command line was
$ ./configure PKG_CFLAGS=-m64 -fPIC PKG_CPPFLAGS=-I/Applications/CPLEX_Studio_Community129/cplex/include PKG_LIBS=-L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit
## --------- ##
## Platform. ##
## --------- ##
hostname = Michele.local
uname -m = x86_64
uname -r = 16.7.0
uname -s = Darwin
uname -v = Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64
/usr/bin/uname -p = i386
/bin/uname -X = unknown
/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
hostinfo = Mach kernel version:
Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64
Kernel configured for up to 4 processors.
2 processors are physically available.
4 processors are logically available.
Processor type: x86_64h (Intel x86-64h Haswell)
Processors active: 0 1 2 3
Primary memory available: 16.00 gigabytes
Default processor set: 365 tasks, 1663 threads, 4 processors
Load average: 2.45, Mach factor: 1.68
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /Users/ssandrews/anaconda/bin
PATH: /Library/Frameworks/Python.framework/Versions/2.7/bin
PATH: /Users/ssandrews/anaconda/bin
PATH: /Library/Frameworks/Python.framework/Versions/3.5/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /sbin
PATH: /opt/X11/bin
PATH: /Library/TeX/texbin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:1631: checking for gcc
configure:1657: result: clang
configure:1901: checking for C compiler version
configure:1904: clang --version </dev/null >&5
Apple LLVM version 7.0.0 (clang-700.0.72)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
configure:1907: $? = 0
configure:1909: clang -v </dev/null >&5
Apple LLVM version 7.0.0 (clang-700.0.72)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
configure:1912: $? = 0
configure:1914: clang -V </dev/null >&5
clang: error: argument to '-V' is missing (expected 1 value)
clang: error: no input files
configure:1917: $? = 1
configure:1940: checking for C compiler default output file name
configure:1943: clang -Wall -g -O2 -I/usr/local/include conftest.c >&5
configure:1946: $? = 0
configure:1992: result: a.out
configure:1997: checking whether the C compiler works
configure:2003: ./a.out
configure:2006: $? = 0
configure:2023: result: yes
configure:2030: checking whether we are cross compiling
configure:2032: result: no
configure:2035: checking for suffix of executables
configure:2037: clang -o conftest -Wall -g -O2 -I/usr/local/include conftest.c >&5
configure:2040: $? = 0
configure:2065: result:
configure:2071: checking for suffix of object files
configure:2092: clang -c -Wall -g -O2 -I/usr/local/include conftest.c >&5
configure:2095: $? = 0
configure:2117: result: o
configure:2121: checking whether we are using the GNU C compiler
configure:2145: clang -c -Wall -g -O2 -I/usr/local/include conftest.c >&5
configure:2151: $? = 0
configure:2155: test -z
|| test ! -s conftest.err
configure:2158: $? = 0
configure:2161: test -s conftest.o
configure:2164: $? = 0
configure:2177: result: yes
configure:2183: checking whether clang accepts -g
configure:2204: clang -c -g -I/usr/local/include conftest.c >&5
configure:2210: $? = 0
configure:2214: test -z
|| test ! -s conftest.err
configure:2217: $? = 0
configure:2220: test -s conftest.o
configure:2223: $? = 0
configure:2234: result: yes
configure:2251: checking for clang option to accept ANSI C
configure:2321: clang -c -Wall -g -O2 -I/usr/local/include conftest.c >&5
configure:2327: $? = 0
configure:2331: test -z
|| test ! -s conftest.err
configure:2334: $? = 0
configure:2337: test -s conftest.o
configure:2340: $? = 0
configure:2358: result: none needed
configure:2376: clang -c -Wall -g -O2 -I/usr/local/include conftest.c >&5
conftest.c:2:3: error: unknown type name 'choke'
choke me
^
conftest.c:2:11: error: expected ';' after top level declarator
choke me
^
;
2 errors generated.
configure:2382: $? = 1
configure: failed program was:
| #ifndef __cplusplus
| choke me
| #endif
configure:2520: checking how to run the C preprocessor
configure:2638: result: clang -E
configure:2662: clang -E -I/usr/local/include conftest.c
configure:2668: $? = 0
configure:2700: clang -E -I/usr/local/include conftest.c
conftest.c:9:10: fatal error: 'ac_nonexistent.h' file not found
#include <ac_nonexistent.h>
^
1 error generated.
configure:2706: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "Rcplex"
| #define PACKAGE_TARNAME "rcplex"
| #define PACKAGE_VERSION "0.3.2"
| #define PACKAGE_STRING "Rcplex 0.3.2"
| #define PACKAGE_BUGREPORT ""
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:2756: checking for egrep
configure:2766: result: grep -E
configure:2771: checking for ANSI C header files
configure:2796: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2802: $? = 0
configure:2806: test -z
|| test ! -s conftest.err
configure:2809: $? = 0
configure:2812: test -s conftest.o
configure:2815: $? = 0
configure:2904: clang -o conftest -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c -L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit >&5
conftest.c:26:7: warning: implicitly declaring library function 'exit' with type 'void (int) __attribute__((noreturn))'
exit(2);
^
conftest.c:26:7: note: include the header <stdlib.h> or explicitly provide a declaration for 'exit'
1 warning generated.
configure:2907: $? = 0
configure:2909: ./conftest
configure:2912: $? = 0
configure:2927: result: yes
configure:2951: checking for sys/types.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for sys/stat.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for stdlib.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for string.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for memory.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for strings.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for inttypes.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for stdint.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:2951: checking for unistd.h
configure:2967: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:2973: $? = 0
configure:2977: test -z
|| test ! -s conftest.err
configure:2980: $? = 0
configure:2983: test -s conftest.o
configure:2986: $? = 0
configure:2997: result: yes
configure:3019: checking ilcplex/cplex.h usability
configure:3031: clang -c -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c >&5
configure:3037: $? = 0
configure:3041: test -z
|| test ! -s conftest.err
configure:3044: $? = 0
configure:3047: test -s conftest.o
configure:3050: $? = 0
configure:3060: result: yes
configure:3064: checking ilcplex/cplex.h presence
configure:3074: clang -E -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c
configure:3080: $? = 0
configure:3100: result: yes
configure:3135: checking for ilcplex/cplex.h
configure:3142: result: yes
configure:3154: checking for library containing CPXversion
configure:3184: clang -o conftest -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c -L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit >&5
Undefined symbols for architecture x86_64:
"_CPXversion", referenced from:
_main in conftest-074e04.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
configure:3190: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "Rcplex"
| #define PACKAGE_TARNAME "rcplex"
| #define PACKAGE_VERSION "0.3.2"
| #define PACKAGE_STRING "Rcplex 0.3.2"
| #define PACKAGE_BUGREPORT ""
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h. */
|
| /* Override any gcc2 internal prototype to avoid an error. */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
| builtin and then its argument prototype would still apply. */
| char CPXversion ();
| int
| main ()
| {
| CPXversion ();
| ;
| return 0;
| }
configure:3239: clang -o conftest -Wall -g -O2 -m64 -fPIC -I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include conftest.c -lcplex -L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit >&5
ld: library not found for -lcplex
clang: error: linker command failed with exit code 1 (use -v to see invocation)
configure:3245: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "Rcplex"
| #define PACKAGE_TARNAME "rcplex"
| #define PACKAGE_VERSION "0.3.2"
| #define PACKAGE_STRING "Rcplex 0.3.2"
| #define PACKAGE_BUGREPORT ""
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h. */
|
| /* Override any gcc2 internal prototype to avoid an error. */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
| builtin and then its argument prototype would still apply. */
| char CPXversion ();
| int
| main ()
| {
| CPXversion ();
| ;
| return 0;
| }
configure:3273: result: no
configure:3279: error: Could not link CPLEX library using -L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_c_compiler_gnu=yes
ac_cv_env_CC_set=
ac_cv_env_CC_value=
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_LDFLAGS_set=
ac_cv_env_LDFLAGS_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_exeext=
ac_cv_header_ilcplex_cplex_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_objext=o
ac_cv_prog_CPP='clang -E'
ac_cv_prog_ac_ct_CC=clang
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_stdc=
ac_cv_prog_egrep='grep -E'
ac_cv_search_CPXversion=no
## ----------------- ##
## Output variables. ##
## ----------------- ##
AWK=''
CC='clang'
CFLAGS='-Wall -g -O2 -m64 -fPIC'
CPLEX_BIN=''
CPP='clang -E'
CPPFLAGS='-I/usr/local/include -I/Applications/CPLEX_Studio_Community129/cplex/include'
DEFS=''
ECHO_C='ECHO_N=''
ECHO_T=''
EGREP='grep -E'
EXEEXT=''
LDFLAGS=''
LIBOBJS=''
LIBS='-L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit'
LTLIBOBJS=''
OBJEXT='o'
PACKAGE_BUGREPORT=''
PACKAGE_NAME='Rcplex'
PACKAGE_STRING='Rcplex 0.3.2'
PACKAGE_TARNAME='rcplex'
PACKAGE_VERSION='0.3.2'
PATH_SEPARATOR=':'
PKG_CFLAGS='-m64 -fPIC'
PKG_CPPFLAGS='-I/Applications/CPLEX_Studio_Community129/cplex/include'
PKG_LIBS='-L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit'
SHELL='/bin/sh'
ac_ct_CC='clang'
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${prefix}/share'
exec_prefix='NONE'
host_alias=''
includedir='${prefix}/include'
infodir='${prefix}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localstatedir='${prefix}/var'
mandir='${prefix}/man'
oldincludedir='/usr/include'
prefix='NONE'
program_transform_name='s,x,x,'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
#define HAVE_INTTYPES_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STDINT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRINGS_H 1
#define HAVE_STRING_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_UNISTD_H 1
#define PACKAGE_BUGREPORT ""
#define PACKAGE_NAME "Rcplex"
#define PACKAGE_STRING "Rcplex 0.3.2"
#define PACKAGE_TARNAME "rcplex"
#define PACKAGE_VERSION "0.3.2"
#define STDC_HEADERS 1
configure: exit 1
The makefile carries the following information:
SYSTEM = x86-64_osx LIBFORMAT = static_pic
#------------------------------------------------------------
#
# When you adapt this makefile to compile your CPLEX programs
# please copy this makefile and set CPLEXDIR and CONCERTDIR to
# the directories where CPLEX and CONCERT are installed.
#
#------------------------------------------------------------
CPLEXDIR = ../../..
CONCERTDIR = ../../../../concert
# ---------------------------------------------------------------------
# Compiler selection
# ---------------------------------------------------------------------
CCC = clang++ -O0
CC = clang -O0
JAVAC = javac
# ---------------------------------------------------------------------
# Compiler options
# ---------------------------------------------------------------------
CCOPT = -m64 -O -fPIC -fexceptions -DNDEBUG -DIL_STD -stdlib=libc++
COPT = -m64 -fPIC
JOPT = -classpath $(CPLEXDIR)/lib/cplex.jar -O
# ---------------------------------------------------------------------
# Link options and libraries
# ---------------------------------------------------------------------
CPLEXBINDIR = $(CPLEXDIR)/bin/$(BINDIST)
CPLEXJARDIR = $(CPLEXDIR)/lib/cplex.jar
CPLEXLIBDIR = $(CPLEXDIR)/lib/$(SYSTEM)/$(LIBFORMAT)
CONCERTLIBDIR = $(CONCERTDIR)/lib/$(SYSTEM)/$(LIBFORMAT)
# For dynamic linking
CPLEXBINDIR = $(CPLEXDIR)/bin/$(SYSTEM)
CPLEXLIB = cplex$(dynamic:yes=1290)
run = $(dynamic:yes=DYLD_LIBRARY_PATH=$(CPLEXBINDIR))
CCLNDIRS = -L$(CPLEXLIBDIR) -L$(CONCERTLIBDIR) $(dynamic:yes=-L$(CPLEXBINDIR))
CLNDIRS = -L$(CPLEXLIBDIR) $(dynamic:yes=-L$(CPLEXBINDIR))
CCLNFLAGS = -lconcert -lilocplex -l$(CPLEXLIB) -m64 -lm -lpthread -framework CoreFoundation -framework IOKit -stdlib=libc++
CLNFLAGS = -l$(CPLEXLIB) -m64 -lm -lpthread -framework CoreFoundation -framework IOKit
JAVA = java -d64 -Djava.library.path=$(CPLEXDIR)/bin/x86-64_osx -classpath $(CPLEXJARDIR):
all:
make all_c
make all_cpp
make all_java
execute: all
make execute_c
make execute_cpp
make execute_java
CONCERTINCDIR = $(CONCERTDIR)/include
CPLEXINCDIR = $(CPLEXDIR)/include
EXDIR = $(CPLEXDIR)/examples
EXINC = $(EXDIR)/include
EXDATA = $(EXDIR)/data
EXSRCC = $(EXDIR)/src/c
EXSRCCX = $(EXDIR)/src/c_x
EXSRCCPP = $(EXDIR)/src/cpp
EXSRCJAVA = $(EXDIR)/src/java
CFLAGS = $(COPT) -I$(CPLEXINCDIR)
CCFLAGS = $(CCOPT) -I$(CPLEXINCDIR) -I$(CONCERTINCDIR)
JCFLAGS = $(JOPT)
Any idea on how to fix this issue? Thank you
回答1:
It says
error: unable to open output file '/Volumes/Andrews/R working
Could it be that the blank in the file/folder name causes trouble? Try to install into a path that does not have blanks in its name. And make sure that path exists and you have write permissions for it.
Update after question was updated with new error message: Now the error is this:
error: Could not link CPLEX library using -L/Applications/CPLEX_Studio_Community129/cplex/examples/x86-64_osx/static_pic -m64 -lm -lpthread -framework CoreFoundation -framework IOKit
This is the wrong path. The CPLEX libraries are not in examples/x86-64_osx/static_pic but are either in bin/x86-64_osx (dynamic library) or in lib/x86-64_osx/static_pic (static library). I don't know which of the two libraries is required, so just put both pathes into the configuration arguments (including the absolute path to your installation, of course). I am not sure whether you also have to put -lcplex or -lcplex129 (depending on whether the static or the dynamic library is required). So if you get the same error without putting these arguments, then try with them.
来源：https://stackoverflow.com/questions/56300644/error-c-compiler-cannot-create-executables