I am trying to compile FormCalc 9.9 on a MacOS 10.10.5.
Compilation consists in running a bash script on terminal. I redirect both stdout and sterr to a log file, but this is all the output I get:
$ ./compile
Compiling for system type MacOSX-x86-64
cp -p ./bin/MacOSX-x86-64/* MacOSX-x86-64/
gcc -O3 -fomit-frame-pointer -ffast-math -Wall -Wextra -m64 -o MacOSX-x86-64/ToForm ./FormCalc/ToForm.c
./FormCalc/ToForm.c:72:9: warning: declaration does not declare anything [-Wmissing-declarations]
__attribute__ ((fallthrough));
^
>
1 warning generated.
strip MacOSX-x86-64/ToForm
gcc -O3 -fomit-frame-pointer -ffast-math -Wall -Wextra -m64 -o MacOSX-x86-64/ToFortran ./FormCalc/ToFortran.c
strip MacOSX-x86-64/ToFortran
gcc -O3 -fomit-frame-pointer -ffast-math -Wall -Wextra -m64 -o MacOSX-x86-64/ToC ./FormCalc/ToC.c
strip MacOSX-x86-64/ToC
gcc -O3 -fomit-frame-pointer -ffast-math -Wall -Wextra -m64 -o MacOSX-x86-64/reorder ./tools/reorder.c
strip MacOSX-x86-64/reorder
looking for gcc... /usr/bin/clang
looking for g++... /usr/bin/clang++
looking for fortran... /usr/local/bin/gfortran
extracting the Fortran libraries... ok
does gfortran append underscores... error linking Fortran and C
How can I get more information about the linking error?
Related
Please I need help, I need to install this library quickly for a project I am working on (https://github.com/LuaDist/mapm) and I don't understand makefile. Per the instructions I run the command "make" and get the following output:
gcc -c -Wall -O2 mapmhsin.c
gcc -c -Wall -O2 mapm_pow.c
gcc -c -Wall -O2 mapm_log.c
gcc -c -Wall -O2 mapm_lg2.c
gcc -c -Wall -O2 mapm_lg4.c
gcc -c -Wall -O2 mapm_exp.c
gcc -c -Wall -O2 mapm_lg3.c
gcc -c -Wall -O2 mapmasin.c
gcc -c -Wall -O2 mapmasn0.c
gcc -c -Wall -O2 mapm_sin.c
gcc -c -Wall -O2 mapm5sin.c
gcc -c -Wall -O2 mapmrsin.c
gcc -c -Wall -O2 mapm_cpi.c
gcc -c -Wall -O2 mapmsqrt.c
gcc -c -Wall -O2 mapmcbrt.c
gcc -c -Wall -O2 mapmgues.c
gcc -c -Wall -O2 mapmfact.c
gcc -c -Wall -O2 mapm_gcd.c
gcc -c -Wall -O2 mapmipwr.c
gcc -c -Wall -O2 mapmpwr2.c
gcc -c -Wall -O2 mapm_rnd.c
gcc -c -Wall -O2 mapm_flr.c
gcc -c -Wall -O2 mapm_fpf.c
gcc -c -Wall -O2 mapm_rcp.c
gcc -c -Wall -O2 mapmstck.c
gcc -c -Wall -O2 mapm_div.c
gcc -c -Wall -O2 mapm_mul.c
gcc -c -Wall -O3 mapmfmul.c
gcc -c -Wall -O2 mapm_fft.c
gcc -c -Wall -O2 mapm_add.c
gcc -c -Wall -O2 mapmistr.c
gcc -c -Wall -O2 mapm_set.c
gcc -c -Wall -O2 mapm_fam.c
gcc -c -Wall -O3 mapmutil.c
gcc -c -Wall -O2 mapmutl2.c
gcc -c -Wall -O2 mapmutl1.c
gcc -c -Wall -O2 mapmcnst.c
rm -f libmapm.a
ar rc libmapm.a mapmhasn.o mapmhsin.o mapm_pow.o mapm_log.o mapm_lg2.o mapm_lg4.o mapm_exp.o mapm_lg3.o mapmasin.o mapmasn0.o mapm_sin.o mapm5sin.o mapmrsin.o mapm_cpi.o mapmsqrt.o mapmcbrt.o mapmgues.o mapmfact.o mapm_gcd.o mapmipwr.o mapmpwr2.o mapm_rnd.o mapm_flr.o mapm_fpf.o mapm_rcp.o mapmstck.o mapm_div.o mapm_mul.o mapmfmul.o mapm_fft.o mapm_add.o mapmistr.o mapm_set.o mapm_fam.o mapmutil.o mapmutl2.o mapmutl1.o mapmcnst.o
gcc -c -Wall -O2 calc.c
gcc -s -static -o calc calc.o libmapm.a -lm
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
make: *** [Makefile:63: calc] Error 1
It looks like everything goes fine until the end:
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
Is there any way I fix this, and what does the command -lm and -lc do?
I am having serious trouble compiling Qt with the OCI plugin.
The Qt version is 5.6.1, and the Oracle instant client version is 12.1.0.2.0. I have installed both the basic and SDK versions, as the Qt online manual asks.
I then try to run the following command:
./configure -I /usr/include/oracle/12.1/client64/ -L /usr/lib/oracle/12.1/client64/lib -prefix /online/daq/antonin/qt_build -plugin-sql-oci -qt-xcb -v
Which produces this output:
+ cd qtbase
+ /online/daq/antonin/qt_source/5.6/Src/qtbase/configure -top-level -I /usr/include/oracle/12.1/client64/ -L /usr/lib/oracle/12.1/client64/lib -prefix /online/daq/antonin/qt_build -plugin-sql-oci -qt-xcb -v
Which edition of Qt do you want to use ?
Type 'c' if you want to use the Commercial Edition.
Type 'o' if you want to use the Open Source Edition.
o
This is the Qt Open Source Edition.
You are licensed to use this software under the terms of
the Lesser GNU General Public License (LGPL) versions 2.1.
You are also licensed to use this software under the terms of
the GNU Lesser General Public License (LGPL) versions 3.
Type '3' to view the GNU Lesser General Public License version 3.
Type 'L' to view the Lesser GNU General Public License version 2.1.
Type 'yes' to accept this license offer.
Type 'no' to decline this license offer.
Do you accept the terms of either license? yes
Running configuration tests (phase 1)...
Precompiled-headers support enabled.
g++ -c -fvisibility=hidden fvisibility.c
Symbol visibility control enabled.
cc1plus: error: unrecognized command line option "-fuse-ld=gold"
g++ -o libtest.so -shared -Wl,-Bsymbolic-functions -fPIC bsymbolic_functions.c
Symbolic function binding enabled.
DEFAULT_INCDIRS="/usr/include/c++/4.4.7
/usr/include/c++/4.4.7/x86_64-redhat-linux
/usr/include/c++/4.4.7/backward
/usr/local/include
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include
/usr/include
"
DEFAULT_LIBDIRS="/lib64
/usr/lib64
/online/daq/lib
/usr/lib
/lib
/usr/lib/gcc/x86_64-redhat-linux/4.4.7
"
Done running configuration tests.
Creating qmake...
gmake: Nothing to be done for `first'.
Running configuration tests (phase 2)...
Found pkg-config from $PATH: /usr/bin/pkg-config
Determining architecture... ()
g++ -c -pipe -g -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../mkspecs/linux-g++ -o arch.o arch.cpp
g++ -o arch arch.o -L/usr/lib/oracle/12.1/client64/lib
Found architecture in binary
CFG_ARCH="x86_64"
CFG_CPUFEATURES=" mmx sse sse2"
System architecture: 'x86_64'
Host architecture: 'x86_64'
C++11 auto-detection... ()
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o c++11.o c++11.cpp
g++ -Wl,-O1 -o c++11 c++11.o -L/usr/lib/oracle/12.1/client64/lib
C++11 enabled.
C++14 auto-detection... ()
g++ -c -pipe -O2 -std=gnu++1y -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o c++14.o c++14.cpp
cc1plus: error: unrecognized command line option "-std=gnu++1y"
gmake: *** [c++14.o] Error 1
C++14 disabled.
default C++ standard edition auto-detection... ()
g++ -pipe -O2 -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o c++default.ii -E c++default.cpp
default C++ standard edition enabled.
64-bit std::atomic auto-detection... ()
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o atomic64.o atomic64.cpp
atomic64.cpp:34:18: error: atomic: No such file or directory
atomic64.cpp:37: error: expected unqualified-id before '<' token
atomic64.cpp:37: error: expected ')' before '<' token
atomic64.cpp:37: error: expected initializer before '<' token
gmake: *** [atomic64.o] Error 1
64-bit std::atomic disabled.
64-bit std::atomic in -latomic auto-detection... ()
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o atomic64.o atomic64.cpp
atomic64.cpp:34:18: error: atomic: No such file or directory
atomic64.cpp:37: error: expected unqualified-id before '<' token
atomic64.cpp:37: error: expected ')' before '<' token
atomic64.cpp:37: error: expected initializer before '<' token
gmake: *** [atomic64.o] Error 1
64-bit std::atomic in -latomic disabled.
sse2 auto-detection... ()
g++ -c -pipe -msse2 -g -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o sse2.o sse2.cpp
g++ -o sse2 sse2.o -L/usr/lib/oracle/12.1/client64/lib
sse2 enabled.
sse3 auto-detection... ()
g++ -c -pipe -msse3 -g -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o sse3.o sse3.cpp
g++ -o sse3 sse3.o -L/usr/lib/oracle/12.1/client64/lib
sse3 enabled.
ssse3 auto-detection... ()
g++ -c -pipe -mssse3 -g -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o ssse3.o ssse3.cpp
g++ -o ssse3 ssse3.o -L/usr/lib/oracle/12.1/client64/lib
ssse3 enabled.
sse4_1 auto-detection... ()
g++ -c -pipe -msse4.1 -g -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o sse4_1.o sse4_1.cpp
g++ -o sse4_1 sse4_1.o -L/usr/lib/oracle/12.1/client64/lib
sse4_1 enabled.
sse4_2 auto-detection... ()
g++ -c -pipe -msse4.2 -g -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o sse4_2.o sse4_2.cpp
g++ -o sse4_2 sse4_2.o -L/usr/lib/oracle/12.1/client64/lib
sse4_2 enabled.
avx auto-detection... ()
g++ -c -pipe -mavx -g -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o avx.o avx.cpp
g++ -o avx avx.o -L/usr/lib/oracle/12.1/client64/lib
avx enabled.
avx2 auto-detection... ()
g++ -c -pipe -mavx2 -g -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o avx2.o avx2.cpp
cc1plus: error: unrecognized command line option "-mavx2"
gmake: *** [avx2.o] Error 1
avx2 disabled.
ipc_sysv auto-detection... ()
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o ipc.o ipc.cpp
g++ -Wl,-O1 -o ipc_sysv ipc.o -L/usr/lib/oracle/12.1/client64/lib
ipc_sysv enabled.
zlib auto-detection... ()
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o zlib.o zlib.cpp
g++ -Wl,-O1 -o zlib zlib.o -L/usr/lib/oracle/12.1/client64/lib -lz
zlib enabled.
mtdev auto-detection... ()
Project ERROR: mtdev development package not found
mtdev disabled.
libjpeg auto-detection... ()
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o libjpeg.o libjpeg.cpp
libjpeg.cpp: In function 'int main(int, char**)':
libjpeg.cpp:43: warning: 'cinfo' is used uninitialized in this function
g++ -Wl,-O1 -o libjpeg libjpeg.o -L/usr/lib/oracle/12.1/client64/lib -ljpeg
libjpeg enabled.
libpng auto-detection... ()
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o libpng.o libpng.cpp
g++ -Wl,-O1 -o libpng libpng.o -L/usr/lib/oracle/12.1/client64/lib -lpng
libpng enabled.
libdl auto-detection... ()
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o libdl.o libdl.cpp
g++ -Wl,-O1 -o libdl libdl.o -L/usr/lib/oracle/12.1/client64/lib -ldl
libdl enabled.
DB2 auto-detection... ()
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o db2.o db2.cpp
db2.cpp:34:20: error: sqlcli.h: No such file or directory
db2.cpp:35:21: error: sqlcli1.h: No such file or directory
gmake: *** [db2.o] Error 1
DB2 disabled.
InterBase auto-detection... ()
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o ibase.o ibase.cpp
ibase.cpp:34:19: error: ibase.h: No such file or directory
gmake: *** [ibase.o] Error 1
InterBase disabled.
MySQL (thread-safe) auto-detection... ()
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -isystem /usr/include/mysql -I../../../mkspecs/linux-g++ -o mysql.o ../mysql/mysql.cpp
g++ -Wl,-O1 -o mysql_r mysql.o -L/usr/lib/oracle/12.1/client64/lib -L/usr/lib64/mysql -lz -lcrypt -lnsl -lm -lpthread -lssl -lcrypto -lmysqlclient_r
MySQL (thread-safe) enabled.
OCI auto-detection... ()
g++ -c -pipe -O2 -std=gnu++0x -Wall -W -fPIC -I. -isystem /usr/include/oracle/12.1/client64 -I../../../mkspecs/linux-g++ -o oci.o oci.cpp
g++ -Wl,-O1 -o oci oci.o -L/usr/lib/oracle/12.1/client64/lib -lclntsh
/usr/lib/oracle/12.1/client64/lib/libclntsh.so: undefined reference to `lxXmlCvEsc0'
/usr/lib/oracle/12.1/client64/lib/libclntsh.so: undefined reference to `lxXmlGEntEscImpl'
/usr/lib/oracle/12.1/client64/lib/libclntsh.so: undefined reference to `slnxmul'
/usr/lib/oracle/12.1/client64/lib/libclntsh.so: undefined reference to `zt_init'
/usr/lib/oracle/12.1/client64/lib/libclntsh.so: undefined reference to `slnxadd'
/usr/lib/oracle/12.1/client64/lib/libclntsh.so: undefined reference to `slnxsub'
collect2: ld returned 1 exit status
gmake: *** [oci] Error 1
OCI disabled.
Oracle (OCI) support cannot be enabled due to functionality tests!
Turn on verbose messaging (-v) to /online/daq/antonin/qt_source/5.6/Src/qtbase/configure to see the final report.
If you believe this message is in error you may use the continue
switch (-continue) to /online/daq/antonin/qt_source/5.6/Src/qtbase/configure to continue.
As you can see, there are several undefined references for one of the the OCI .so files. I have tried checking online, but I have found barely any references to these symbols.
Any idea what could be causing this? A missing .so file? Wrong version of the library?
I've tested this on GCC 4.8.3, 4.9.2 and trunk 20141210. When using -Werror=write-strings, it correctly enables the warning, but doesn't turn it into an error. The command line I'm using is:
g++ -std=c99 -x c -Werror=write-strings -O2 -Wall -pedantic main.cpp
warning: initialization discards 'const' qualifier from pointer target type
char *s = "test";
However, it turns it into an error in C++ mode:
g++ -Werror=write-strings -O2 -Wall -pedantic -pthread main.cpp
main.cpp:8:15: error: deprecated conversion from string constant to 'char*'
[-Werror=write-strings]
char *s = "test";
Is there something I'm missing or is this just a missing feature?
I've seen the deleted answer, but bear with me…it was actually correct (at least, under my testing). I think what you've found is interesting, and close to being a bug.
As far as my testing goes (GCC 4.9.1 built on Mac OS X 10.9.4 Mavericks, running on Mac OS X 10.10.2 Yosemite), it appears that the -Werror=write-strings does not make the warning into an error (which I regard as being probably a bug, though you may find that the GCC team has a different view on it). It only becomes an error when -Werror is in effect.
Here's what I ran:
$ cat x.c
#include <stdio.h>
int main(void)
{
char *test = "data";
printf("%s\n", test);
return 0;
}
$ gcc -O3 -g -std=c11 -c x.c
$ gcc -O3 -g -std=c11 -c x.c -Wwrite-strings
x.c: In function ‘main’:
x.c:5:18: warning: initialization discards ‘const’ qualifier from pointer target type
char *test = "data";
^
$ gcc -O3 -g -std=c11 -c x.c -Werror=write-strings
x.c: In function ‘main’:
x.c:5:18: warning: initialization discards ‘const’ qualifier from pointer target type
char *test = "data";
^
$ gcc -O3 -g -std=c11 -c x.c -Werror -Wwrite-strings
x.c: In function ‘main’:
x.c:5:18: error: initialization discards ‘const’ qualifier from pointer target type [-Werror]
char *test = "data";
^
cc1: all warnings being treated as errors
$ gcc -O3 -g -std=c11 -c x.c -Wall -Wextra -Werror=write-strings
x.c: In function ‘main’:
x.c:5:18: warning: initialization discards ‘const’ qualifier from pointer target type
char *test = "data";
^
$ gcc -O3 -g -std=c11 -c x.c -Wall -Wextra -Werror
$ gcc -O3 -g -std=c11 -c x.c -Wall -Wextra -Werror -Wwrite-strings
x.c: In function ‘main’:
x.c:5:18: error: initialization discards ‘const’ qualifier from pointer target type [-Werror]
char *test = "data";
^
cc1: all warnings being treated as errors
$ gcc -O3 -g -std=c11 -c x.c -Wall -Wextra -Werror -Werror=write-strings
x.c: In function ‘main’:
x.c:5:18: error: initialization discards ‘const’ qualifier from pointer target type [-Werror]
char *test = "data";
^
cc1: all warnings being treated as errors
$
For your convenience, and for easier viewing, these are the GCC commands I ran:
gcc -O3 -g -std=c11 -c x.c
gcc -O3 -g -std=c11 -c x.c -Wwrite-strings
gcc -O3 -g -std=c11 -c x.c -Werror=write-strings
gcc -O3 -g -std=c11 -c x.c -Werror -Wwrite-strings
gcc -O3 -g -std=c11 -c x.c -Wall -Wextra -Werror=write-strings
gcc -O3 -g -std=c11 -c x.c -Wall -Wextra -Werror
gcc -O3 -g -std=c11 -c x.c -Wall -Wextra -Werror -Wwrite-strings
gcc -O3 -g -std=c11 -c x.c -Wall -Wextra -Werror -Werror=write-strings
If you can't run with -Werror normally, then you're probably going to have to do trial builds with -Werror -Wwrite-strings which will fail because of other problems, but this will also identify the writable strings problems, which you can fix and check. Then, when you're OK on the -Wwrite-strings errors, you can go back to not including -Werror in the compilation (keeping -Wwrite-strings or even -Werror=write-strings in the command line so that if you make a mistake and/or the putative compiler bug is fixed, then you can have it all working the way you really wanted).
My GNU scientific library (http://www.gnu.org/software/gsl/) installed in the path: /home/myname/gsl-1.6
My mlRho 1.7-stat prog (http://guanine.evolbio.mpg.de/mlRho/mlRho_1.7.tgz) which uses GNU scientific library-installed in:/home/myname/MlRho_1.7
my operating system: Fedora 16
original make file in mlRho
cd /home/myname/MlRho_1.7/
vim make
CC=gcc
CFLAGS= -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 \
-I/opt/local/include/ -L/opt/local/lib/
I have changed path in mlRho
CC=gcc
CFLAGS= -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 \
-I/home/myname/gsl-1.6 -L/home/myname/gsl-1.6
after making changes, I tried running make, it gives error
make
gcc -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 -I/home/myname/gsl-1.6/include/ -L/home/myname/gsl-1.6/lib/ -c -o mlRho.o mlRho.c
In file included from mlRho.c:16:0:
mlComp.h:7:30: fatal error: gsl/gsl_sf_gamma.h: No such file or directory
compilation terminated.
make: *** [mlRho.o] Error 1
when i do make test- it gives me error below
make test
make[1]: Entering directory `/home/myname/MlRho_1.7/TestMlPi'
gcc -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 -I/opt/local/include/ -L/opt/local/lib/ -c -o testMlPi.o testMlPi.c
testMlPi.c: In function ‘main’:
testMlPi.c:62:67: warning: variable ‘sderr’ set but not used [-Wunused-but-set-variable]
testMlPi.c:62:60: warning: variable ‘sdhet’ set but not used [-Wunused-but-set-variable]
gcc -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 -I/opt/local/include/ -L/opt/local/lib/ -c -o interface.o interface.c
gcc -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 -I/opt/local/include/ -L/opt/local/lib/ -c -o eprintf.o eprintf.c
gcc -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 -I/opt/local/include/ -L/opt/local/lib/ -c -o ranNum.o ranNum.c
gcc -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 -I/opt/local/include/ -L/opt/local/lib/ -o testMlPi testMlPi.o interface.o eprintf.o ranNum.o -lm
make[1]: Leaving directory `/home/myname/MlRho_1.7/TestMlPi'
Output from testMlPi:
pi: 5.00e-05 epsilon: 4.90e-04 -log(L): 1.40e+05
Output from mlRho:
make: ./mlRho: Command not found
make: *** [testPi] Error 127
Output from mlRho:
make: ./mlRho: Command not found
make: *** [testPi] Error 127
It somehow GNU library not linking to mlRho programme. How to fix it?
We are a team working on an R package containing C/C++ code. The package can successfully be installed on all the machines but one. These all run the same version of Mac OS X. I have provided the log files for the installation of the package on my computer (success) and a colleague's computer (error). The package depends on the Rcpp package and the GSL library, both of which were successfully installed on both machines.
My Computer
WARNING: ignoring environment value of R_HOME
* installing to library '/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15'
* installing *source* package 'mrenci' ...
** libs
*** arch - x86_64
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c MRMRTree.cc -o MRMRTree.o
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c Matrix.cc -o Matrix.o
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c MiMBuilder.cc -o MiMBuilder.o
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c SymmetricMatrix.cc -o SymmetricMatrix.o
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c adaptor.cc -o adaptor.o
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c memory.cc -o memory.o
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c tools.cc -o tools.o
/opt/local/bin/g++-mp-4.5 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/lib -o mrenci.so MRMRTree.o Matrix.o MiMBuilder.o SymmetricMatrix.o adaptor.o memory.o tools.o /Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/lib/x86_64/libRcpp.a -fopenmp -fopenmp -L/opt/local/lib/R/lib/x86_64 -lR
installing to /Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/mrenci/libs/x86_64
** R
** preparing package for lazy loading
** testing if installed package can be loaded
* DONE (mrenci)
Colleague's Computer
WARNING: ignoring environment value of R_HOME
* installing to library '/Library/Frameworks/R.framework/Versions/2.15/Resources/library'
* installing *source* package 'mrenci' ...
** libs
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -fPIC -g -O2 -c MRMRTree.cc -o MRMRTree.o
MRMRTree.cc: In member function 'double* const MRMRTree::bootstrap(unsigned int)':
MRMRTree.cc:73: warning: iteration variable 'i' is unsigned
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -fPIC -g -O2 -c Matrix.cc -o Matrix.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -fPIC -g -O2 -c MiMBuilder.cc -o MiMBuilder.o
MiMBuilder.cc: In member function 'Matrix* const MiMBuilder::createMiM(unsigned int*, unsigned int, unsigned int*, unsigned int)':
MiMBuilder.cc:102: warning: iteration variable 'i' is unsigned
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -fPIC -g -O2 -c SymmetricMatrix.cc -o SymmetricMatrix.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -fPIC -g -O2 -c adaptor.cc -o adaptor.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -fPIC -g -O2 -c memory.cc -o memory.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -fPIC -g -O2 -c tools.cc -o tools.o
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o mrenci.so MRMRTree.o Matrix.o MiMBuilder.o SymmetricMatrix.o adaptor.o memory.o tools.o /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/lib/x86_64/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64
** R
** preparing package for lazy loading
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64/mrenci.so':
dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64/mrenci.so, 6): Symbol not found: _GOMP_critical_name_end
Referenced from: /Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64/mrenci.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64/mrenci.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci'
At first, the installation on my colleague's computer would result in the compilation of the package for both architectures, upon which g++ complained about an unknown -arch argument. This issue, however, appears to have been mitigated by forcing the targeting of a single architecture x86_64. It is also worth noting that as a result of these errors, all computers now have several versions of R and g++. Is this an issue with the linker? Does the same compiler need to be used for both R and its packages? In the case of my computer, I never explicitly asked for g++-mp-4.5 to be used rather than the default g++ (version 4.2), so I figured R automatically detects it.
In case this is of any help, here is what my Makevars contains:
PKG_LIBS=`$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(SHLIB_OPENMP_CFLAGS) -fopenmp
PKG_CPPFLAGS=$(SHLIB_OPENMP_CXXFLAGS) -fopenmp
PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS) -fopenmp
The $(SHLIB_OPENMP_*FLAGS) flags seem to be defined only on my computer; -fopenmp flags were explicitly added for the package to work on all the machines.
Has anyone experienced similar issues? Any help would be appreciated.
I changed my colleague's ~/.R/Makevars to conform to my configs
LDFLAGS=-L/opt/local/lib
CC=/opt/local/bin/gcc-mp-4.5 -std=gnu99
CXX=/opt/local/bin/g++-mp-4.5
CPP=/opt/local/bin/gcc-mp-4.5 -std=gnu99 -E
CXXCPP=/opt/local/bin/g++-mp-4.5 -E
CFLAGS=-pipe -O2 -m64
CXXFLAGS=-pipe -O2 -m64
SHLIB_CXXLD=/opt/local/bin/g++-mp-4.5
SHLIB_CXXLDFLAGS=-dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_LD=/opt/local/bin/gcc-mp-4.5 -std=gnu99
SHLIB_LDFLAGS=-dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
Additionally, the --no-multiarch argument was used when issuing the installation command. And it now works on his computer.
The problem was because the use of openMP was hardwired (no checks) inside the code and clang did not support openMP at the same I asked the question. My colleague's R was installed using the default (Xcode) compiler when we were trying to use gcc via Mac Ports.