I'm unable to build Doxygen on x86_64-linux.
I have Doxygen-1.8.6 unpacked.
I have libiconv-1.14 unpacked, built, installed.
I keep getting:
g++ -c -pipe -fsigned-char -D_LARGEFILE_SOURCE -Wall -W -O2 -I../qtools -I../libmd5 -I. -o ../objects/main.o main.cpp
g++ -o ../bin/doxygen ../objects/main.o -L../lib -ldoxygen -ldoxycfg -lqtools -lmd5 -lpthread
../lib/libdoxycfg.a(portable_c.o): In function `portable_iconv_close':
portable_c.c:(.text+0x1): undefined reference to `libiconv_close'
../lib/libdoxycfg.a(portable_c.o): In function `portable_iconv':
portable_c.c:(.text+0x11): undefined reference to `libiconv'
../lib/libdoxycfg.a(portable_c.o): In function `portable_iconv_open':
portable_c.c:(.text+0x21): undefined reference to `libiconv_open'
collect2: ld returned 1 exit status
Which iconv gives:
/usr/local/bin/iconv
as expected.
Any ideas?
add -liconv to the end of the line in src/doxygen.pro.in:
unix:LIBS += -L../lib -ldoxygen -lvhdlparser -ldoxycfg -lqtools -lmd5 -lpthread %%SQLITE3_LIBS%% %%LIBCLANG_LIBS%% -liconv
Related
I have a legacy Perl 5.8.9 project which I need to run in a docker environment. Since I new it worked on Ubuntu I tried compiling it on an Ubuntu 16.1 and
FROM ubuntu
RUN apt-get update \
&& apt-get install -y curl \
&& apt-get install -y wget \
&& apt-get install -y perlbrew
NAME="Ubuntu"
VERSION="18.04.3 LTS (Bionic Beaver)"
Images
since I couldn't find the version on perlbrew, I tried compiling from perl-5.8.9.tar.bz2 which I downloaded
Compilation failed having something to do with miniperl.
perlio.c:515:2: note: in expansion of macro 'PerlLIO_write'
PerlLIO_write(dbg, s, len);
^~~~~~~~~~~~~
perlio.c: In function 'PerlIO_parse_layers':
perlio.c:995:11: warning: this statement may fall through [-Wimplicit-
fallthrough=]
if (*e++) {
^
perlio.c:1001:4: note: here
case '\0':
^~~~
In file included from perl.h:3169:0,
from perlio.c:57:
perlio.c: In function 'S_more_refcounted_fds':
iperlsys.h:762:39: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
#define PerlLIO_write(fd, buf, count) write((fd), (buf), (count))
^~~~~~~~~~~~~~~~~~~~~~~~~~~
perlio.c:2307:2: note: in expansion of macro 'PerlLIO_write'
PerlLIO_write(PerlIO_fileno(Perl_error_log),
^~~~~~~~~~~~~
`sh cflags "optimize='-O2'" perlapi.o` perlapi.c
CCCMD = cc -DPERL_CORE -c -fno-strict-aliasing -pipe - I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -std=c89 - O2 -Wall -ansi -pedantic -W -Wextra -Wdeclaration-after-statement -Wendif-labels -Wc++-compat -DPERL_GCC_PEDANTIC
`sh cflags "optimize='-O2'" numeric.o` numeric.c
CCCMD = cc -DPERL_CORE -c -fno-strict-aliasing -pipe - I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -std=c89 - O2 -Wall -ansi -pedantic -W -Wextra -Wdeclaration-after-statement -Wendif- labels -Wc++-compat -DPERL_GCC_PEDANTIC
`sh cflags "optimize='-O2'" mathoms.o` mathoms.c
CCCMD = cc -DPERL_CORE -c -fno-strict-aliasing -pipe - I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -std=c89 - O2 -Wall -ansi -pedantic -W -Wextra -Wdeclaration-after-statement -Wendif- labels -Wc++-compat -DPERL_GCC_PEDANTIC
`sh cflags "optimize='-O2'" locale.o` locale.c
CCCMD = cc -DPERL_CORE -c -fno-strict-aliasing -pipe - I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -std=c89 - O2 -Wall -ansi -pedantic -W -Wextra -Wdeclaration-after-statement -Wendif- labels -Wc++-compat -DPERL_GCC_PEDANTIC
`sh cflags "optimize='-O2'" pp_pack.o` pp_pack.c
CCCMD = cc -DPERL_CORE -c -fno-strict-aliasing -pipe - I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -std=c89 - O2 -Wall -ansi -pedantic -W -Wextra -Wdeclaration-after-statement -Wendif- labels -Wc++-compat -DPERL_GCC_PEDANTIC
pp_pack.c: In function 'S_pack_rec':
pp_pack.c:2716:7: warning: variable 'was_utf8' set but not used [- Wunused-but-set-variable]
U32 was_utf8;
^~~~~~~~
`sh cflags "optimize='-O2'" pp_sort.o` pp_sort.c
CCCMD = cc -DPERL_CORE -c -fno-strict-aliasing -pipe - I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -std=c89 - O2 -Wall -ansi -pedantic -W -Wextra -Wdeclaration-after-statement -Wendif- labels -Wc++-compat -DPERL_GCC_PEDANTIC
`sh cflags "optimize='-O2'" opmini.o` -DPERL_EXTERNAL_GLOB opmini.c
CCCMD = cc -DPERL_CORE -c -fno-strict-aliasing -pipe -vI/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -std=c89 - O2 -Wall -ansi -pedantic -W -Wextra -Wdeclaration-after-statement -Wendif- labels -Wc++-compat -DPERL_GCC_PEDANTIC
opmini.c: In function 'Perl_list':
opmini.c:977:5: warning: this statement may fall through [-Wimplicit- fallthrough=]
if (!o->op_next && cUNOPo->op_first->op_type == OP_FLOP) {
^
opmini.c:981:5: note: here
case OP_LIST:
^~~~
opmini.c: In function 'Perl_mod':
opmini.c:1277:11: warning: this statement may fall through [-Wimplicit-v
fallthrough=]
PL_hints |= HINT_BLOCK_SCOPE;
opmini.c:1278:5: note: here
case OP_SASSIGN:
^~~~
opmini.c: In function 'Perl_fold_constants':
opmini.c:2119:40: warning: argument 'o' might be clobbered by 'longjmp' or 'vfork' [-Wclobbered]
Perl_fold_constants(pTHX_ register OP *o)
^
cc -L/usr/local/lib -o miniperl \
`echo gv.o toke.o perly.o op.o pad.o regcomp.o dump.o util.o mg.o reentr.o hv.o av.o perl.o run.o pp_hot.o sv.o pp.o scope.o pp_ctl.o pp_sys.o doop.o doio.o regexec.o utf8.o taint.o deb.o universal.o xsutils.o globals.o perlio.o perlapi.o numeric.o mathoms.o locale.o pp_pack.o pp_sort.o | sed 's/ op.o / /'` \
miniperlmain.o opmini.o
pp.o: In function `Perl_pp_pow':
pp.c:(.text+0x2d84): undefined reference to `pow'
pp.o: In function `Perl_pp_modulo':
pp.c:(.text+0x3b80): undefined reference to `fmod'
pp.o: In function `Perl_pp_atan2':
pp.c:(.text+0x8884): undefined reference to `atan2'
pp.o: In function `Perl_pp_sin':
pp.c:(.text+0x8978): undefined reference to `sqrt'
pp.c:(.text+0x8a23): undefined reference to `log'
pp.c:(.text+0x8a4e): undefined reference to `cos'
pp.c:(.text+0x8afb): undefined reference to `sin'
pp.c:(.text+0x8b13): undefined reference to `exp'
collect2: error: ld returned 1 exit status
makefile:313: recipe for target 'miniperl' failed
make: *** [miniperl] Error 1
Is there a ready docker image?
If not how do I install on ubuntu or preferably on alpine or another light container.
Run the following commands in the terminal one after another.
sudo apt-get install perlbrew
perlbrew available
perlbrew install perl-5.8.9
If it fails to download, create a directory as shown below
mkdir -p perl5/perlbrew/dists
Try again the following command
perlbrew install perl-5.8.9
For more info , please refer this:
https://askubuntu.com/questions/425427/how-to-install-perl-php-mysql-and-ruby-packages-on-ubuntu
In case you don't want to use perlbrew, here is another way-
From https://stackoverflow.com/a/44441545/2001559
In your docker file -
RUN apt-get install -y gcc
ADD http://www.cpan.org/src/5.0/perl-5.8.9.tar.gz /shared
RUN tar -xzf perl-5.8.9.tar.gz
WORKDIR /shared/perl-5.8.9
RUN ./Configure -des -Dprefix=/opt/perl-5.8.9/localperl
RUN make
RUN make test
RUN make install
perl-5.8.0
I solved the issue when created 2 directories:
mkdir -p /home/<username>/perl5/perlbrew/dists/
mkdir -p /home/<username>/perl5/perlbrew/build/perl-5.8.0
Gave rwx-rwx-rwx (to avoid any problems with the access):
chmod -Rf 0777 /home/<username>/perl5/perlbrew/dists
chmod -Rf 0777 /home/<username>/perl5/perlbrew/build/perl-5.8.0
My question is about linking errors I get when compiling with external libraries using mex. I'm trying to compile C++ code using the external library fftw3 using Matlab's mex on MacOS using clang++. Here is an example
main.cpp
#include "fftw3.h"
int main(){
double * test = (double *) fftw_malloc(10*sizeof(double));
}
compiling this works
$ clang++ main.cpp -L/usr/local/lib -lfftw3
Now I try something similar with mex
mex.cpp
#include "math.h"
#include "matrix.h"
#include "mex.h"
#include "fftw3.h"
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
double * test = (double *) fftw_malloc(10*sizeof(double));
}
in MATLAB
>> mex -setup C++;
>> mex -L/usr/local/lib -lfftw3 CXXFLAGS='-L/usr/local/lib -lfftw3' mex.cpp
Building with 'Xcode Clang++'.
Error using mex
clang: warning: -lfftw3: 'linker' input unused
clang: warning: argument unused during compilation: '-L/usr/local/lib'
/path/to/file/mex.cpp:4:10:
fatal error: 'fftw3.h' file not found
#include "fftw3.h"
^
1 error generated.
using the -v flag I get more detailed errors
Verbose mode is on.
Neither -compatibleArrayDims nor -largeArrayDims is selected.
Using -compatibleArrayDims. In the future, MATLAB will require the use of
-largeArrayDims and remove the -compatibleArrayDims option.
For more information:
http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html.
... Looking for compiler 'Xcode Clang++' ...
... Looking for environment variable 'DEVELOPER_DIR' ...No.
... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer').
... Looking for folder '/Applications/Xcode.app/Contents/Developer' ...Yes.
... Executing command 'which xcrun' ...Yes ('/usr/bin/xcrun').
... Looking for folder '/usr/bin' ...Yes.
... Executing command 'defaults read com.apple.dt.Xcode IDEXcodeVersionForAgreedToGMLicense' ...No.
... Executing command 'defaults read /Library/Preferences/com.apple.dt.Xcode IDEXcodeVersionForAgreedToGMLicense' ...Yes ('7.1.1').
... Executing command '
agreed=7.1.1
if echo $agreed | grep -E '[\.\"]' >/dev/null; then
lhs=`expr "$agreed" : '\([0-9]*\)[\.].*'`
rhs=`expr "$agreed" : '[0-9]*[\.]\(.*\)$'`
if echo $rhs | grep -E '[\."]' >/dev/null; then
rhs=`expr "$rhs" : '\([0-9]*\)[\.].*'`
fi
if [ $lhs -gt 4 ] || ( [ $lhs -eq 4 ] && [ $rhs -ge 3 ] ); then
echo $agreed
else
exit 1
fi
fi' ...Yes ('7.1.1').
... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer').
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk' ...Yes.
... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer').
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk' ...Yes.
... Executing command 'echo /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk | rev | cut -c1-10 | rev | egrep -oh '[0-9]+\.[0-9]+'' ...Yes ('10.11').
Found installed compiler 'Xcode Clang++'.
Options file details
-------------------------------------------------------------------
Compiler location: /Applications/Xcode.app/Contents/Developer
Options file: ~/.matlab/R2014b/mex_C++_maci64.xml
CMDLINE100 : /usr/bin/xcrun -sdk macosx10.11 clang++ -c -DMX_COMPAT_32 -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include" -L/usr/local/lib -lfftw3 -O2 -DNDEBUG /path/to/file/mex.cpp -o /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
CMDLINE200 : /usr/bin/xcrun -sdk macosx10.11 clang++ -Wl,-twolevel_namespace -undefined error -arch x86_64 -mmacosx-version-min=10.11 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -framework Cocoa -bundle -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map" -O -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map" /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o -lfftw3 -L/usr/local/lib -L"/Applications/MATLAB_R2014b.app/bin/maci64" -lmx -lmex -lmat -o mex.mexmaci64
CMDLINE300 : rm -f /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
CXX : /usr/bin/xcrun -sdk macosx10.11 clang++
DEFINES : -DMX_COMPAT_32 -DMATLAB_MEX_FILE
MATLABMEX : -DMATLAB_MEX_FILE
CXXFLAGS : -L/usr/local/lib -lfftw3
INCLUDE : -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include"
CXXOPTIMFLAGS : -O2 -DNDEBUG
CXXDEBUGFLAGS : -g
LDXX : /usr/bin/xcrun -sdk macosx10.11 clang++
LDFLAGS : -Wl,-twolevel_namespace -undefined error -arch x86_64 -mmacosx-version-min=10.11 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -framework Cocoa -bundle -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map"
LDBUNDLE : -bundle
LINKEXPORT : -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map"
LINKLIBS : -lfftw3 -L/usr/local/lib -L"/Applications/MATLAB_R2014b.app/bin/maci64" -lmx -lmex -lmat
LDOPTIMFLAGS : -O
LDDEBUGFLAGS : -g
OBJEXT : .o
LDEXT : .mexmaci64
DEVELOPER_DIR_CHECK :
XCODE_DIR : /Applications/Xcode.app/Contents/Developer
XCRUN_DIR : /usr/bin
XCODE_AGREED_VERSION : 7.1.1
ISYSROOT : /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk
SDKVER : 10.11
MATLABROOT : /Applications/MATLAB_R2014b.app
ARCH : maci64
SRC : /path/to/file/mex.cpp
OBJ : /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
OBJS : /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
SRCROOT : /path/to/file/mex
DEF : /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.def
EXP : mex.exp
LIB : mex.lib
EXE : mex.mexmaci64
ILK : mex.ilk
MANIFEST : mex.mexmaci64.manifest
TEMPNAME : mex
EXEDIR :
EXENAME : mex
OPTIM : -O2 -DNDEBUG
LINKOPTIM : -O
-------------------------------------------------------------------
Building with 'Xcode Clang++'.
/usr/bin/xcrun -sdk macosx10.11 clang++ -c -DMX_COMPAT_32 -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include" -L/usr/local/lib -lfftw3 -O2 -DNDEBUG /path/to/file/mex.cpp -o /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
Error using mex
clang: warning: -lfftw3: 'linker' input unused
clang: warning: argument unused during compilation: '-L/usr/local/lib'
/path/to/file/mex.cpp:4:10:
fatal error: 'fftw3.h' file not found
#include "fftw3.h"
^
1 error generated.
The warnings
clang: warning: -lfftw3: 'linker' input unused
clang: warning: argument unused during compilation: '-L/usr/local/lib'
are there because you are setting CXXFLAGS to contain these flags. This variable is for compiler flags, but -L and -l are linker flags. Simply remove the CXXFLAGS definition from your mex command.
The error
/path/to/file/mex.cpp:4:10:
fatal error: 'fftw3.h' file not found
#include "fftw3.h"
^
1 error generated.
is because the compiler cannot find the fftw4.h header file. You need to tell the compiler where to find it:
mex -I/usr/local/include -L/usr/local/lib -lfftw3 mex.cpp
Note that in your first case, where you call clang++ directly, it is likely that CLang is configured to look for header files in /usr/local/include, it's a standard place. But when mex invokes your compiler (I don't even know if it's the same one?) apparently this location is not added to the search path.
So I have been trying to compile this code using mex to on avail. The issue is it can not seem to find lstdc++ and lpthread and libm are for whatever reason incompatible. My /usr/lib32 folder looks like the following:
iggy#ThinkpadX1:~/Applications/Matlab_2012a/bin$ ls /usr/lib32/
crt1.o libanl.so libc_nonshared.a libg.a libmcheck.a libnss_files.so libpthread.so librt.so libz.so.1
crti.o libBrokenLocale.a libcrypt.a libgcc_s.so.1 libm.so libnss_hesiod.so libquadmath.so.0 libstdc++.so.6 libz.so.1.2.3.4
crtn.o libBrokenLocale.so libcrypt.so libgomp.so.1 libnsl.a libnss_nisplus.so libquadmath.so.0.0.0 libstdc++.so.6.0.16 Mcrt1.o
gconv libbsd-compat.a libc.so libgomp.so.1.0.0 libnsl.so libnss_nis.so libresolv.a libthread_db.so Scrt1.o
gcrt1.o libc.a libdl.a libieee.a libnss_compat.so libpthread.a libresolv.so libutil.a
libanl.a libcidn.so libdl.so libm.a libnss_dns.so libpthread_nonshared.a librt.a libutil.so
And the errors I am recieving are the following:
K>> make_csolve
**************************************************************************
Warning: Neither -compatibleArrayDims nor -largeArrayDims is selected.
Using -compatibleArrayDims. In the future, MATLAB will require
the use of -largeArrayDims and remove the -compatibleArrayDims
option. For more information, see:
http://www.mathworks.com/help/techdoc/matlab_external/bsflnue-1.html
**************************************************************************
/home/iggy/Applications/Matlab_2012a/bin/mex: 1: /home/iggy/Applications/Matlab_2012a/bin/util/oscheck.sh: /lib64/libc.so.6: not found
/home/iggy/Applications/Matlab_2012a/bin/mex: 1: /home/iggy/Applications/Matlab_2012a/bin/util/oscheck.sh: /lib64/libc.so.6: not found
-> mexopts.sh sourced from directory (DIR = $MATLAB/bin)
FILE = /home/iggy/Applications/Matlab_2012a/bin/mexopts.sh
----------------------------------------------------------------
-> MATLAB = /home/iggy/Applications/Matlab_2012a
-> CC = gcc-4.4
-> CC flags:
CFLAGS = -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread
CDEBUGFLAGS = -g
COPTIMFLAGS = -O -DNDEBUG
CLIBS = -Wl,-rpath-link,/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -L/usr/lib32 -L/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -lmx -lmex -lmat -lm -lstdc++
arguments = -DMX_COMPAT_32
-> CXX = g++-4.4
-> CXX flags:
CXXFLAGS = -ansi -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread
CXXDEBUGFLAGS = -g
CXXOPTIMFLAGS = -O -DNDEBUG
CXXLIBS = -Wl,-rpath-link,/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -L/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -lmx -lmex -lmat -lm
arguments = -DMX_COMPAT_32
-> FC = gfortran
-> FC flags:
FFLAGS = -fexceptions -fbackslash -fPIC -fno-omit-frame-pointer
FDEBUGFLAGS = -g
FOPTIMFLAGS = -O
FLIBS = -Wl,-rpath-link,/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -L/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -lmx -lmex -lmat -lm
arguments = -DMX_COMPAT_32
-> LD = gcc-4.4
-> Link flags:
LDFLAGS = -pthread -shared -Wl,--version-script,/home/iggy/Applications/Matlab_2012a/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined
LDDEBUGFLAGS = -g
LDOPTIMFLAGS = -O
LDEXTENSION = .mexa64
arguments =
-> LDCXX =
-> Link flags:
LDCXXFLAGS =
LDCXXDEBUGFLAGS =
LDCXXOPTIMFLAGS =
LDCXXEXTENSION =
arguments =
----------------------------------------------------------------
-> gcc-4.4 -c -I/home/iggy/Applications/Matlab_2012a/extern/include -I/home/iggy/Applications/Matlab_2012a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMX_COMPAT_32 -O -DNDEBUG "csolve.c"
-> gcc-4.4 -c -I/home/iggy/Applications/Matlab_2012a/extern/include -I/home/iggy/Applications/Matlab_2012a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMX_COMPAT_32 -O -DNDEBUG "ldl.c"
-> gcc-4.4 -c -I/home/iggy/Applications/Matlab_2012a/extern/include -I/home/iggy/Applications/Matlab_2012a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMX_COMPAT_32 -O -DNDEBUG "matrix_support.c"
-> gcc-4.4 -c -I/home/iggy/Applications/Matlab_2012a/extern/include -I/home/iggy/Applications/Matlab_2012a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMX_COMPAT_32 -O -DNDEBUG "solver.c"
-> gcc-4.4 -c -I/home/iggy/Applications/Matlab_2012a/extern/include -I/home/iggy/Applications/Matlab_2012a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMX_COMPAT_32 -O -DNDEBUG "util.c"
-> gcc-4.4 -O -pthread -shared -Wl,--version-script,/home/iggy/Applications/Matlab_2012a/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined -o "csolve.mexa64" csolve.o ldl.o matrix_support.o solver.o util.o -Wl,-rpath-link,/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -L/usr/lib32 -L/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -lmx -lmex -lmat -lm -lstdc++
/usr/bin/ld: skipping incompatible /usr/lib32/libm.so when searching for -lm
/usr/bin/ld: skipping incompatible /usr/lib32/libm.a when searching for -lm
/usr/bin/ld: cannot find -lstdc++
/usr/bin/ld: skipping incompatible /usr/lib32/libpthread.so when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib32/libpthread.a when searching for -lpthread
collect2: ld returned 1 exit status
mex: link of ' "csolve.mexa64"' failed.
Error using mex (line 206)
Unable to complete successfully.
Error in make_csolve (line 10)
mex -v csolve.c ldl.c matrix_support.c solver.c util.c
Any advice would be greatly appreciated (I am on Ubuntu 12.04 64-bit running MATLAB R2012a).
The libraries in /use/lib32 are incompatible because they are the wrong architecture (32-bit instead of 64-bit). Try running mex -setup again first. I'm assuming you're using 64-bit MATLAB (check with ver) since there are glnxa64 folders in the current setup.
However, the real error seems to be the following:
/home/iggy/Applications/Matlab_2012a/bin/mex: 1: /home/iggy/Applications/Matlab_2012a/bin/util/oscheck.sh: /lib64/libc.so.6: not found
Since oscheck.sh fails to find /lib64/libc.so.6, you might need to go into the package manage and look for libc and libstdc++, install them and try again. But first try to make a link to any existing libc.so.6 in another folder. Typical locations for Ubuntu are below.
64-bit Ubuntu:
sudo ln -s /lib/x86_64-linux-gnu/libc.so.6 /lib64/libc.so.6
32-bit Ubuntu:
sudo ln -s /lib/i386-linux-gnu/libc.so.6 /lib/libc.so.6
While calling make on libmemcached-1.0.18 I got these messages and the compilation stop
...
CXX libmemcached/libmemcachedinternal_libmemcachedutilinternal_la-backtrace.lo
CXX libmemcachedutil/libmemcachedinternal_libmemcachedutilinternal_la-flush.lo
CXX libmemcachedutil/libmemcachedinternal_libmemcachedutilinternal_la-pid.lo
CXX libmemcachedutil/libmemcachedinternal_libmemcachedutilinternal_la-ping.lo
CXX libmemcachedutil/libmemcachedinternal_libmemcachedutilinternal_la-pool.lo
CXX libmemcachedutil/libmemcachedinternal_libmemcachedutilinternal_la-version.lo
CXXLD libmemcachedinternal/libmemcachedutilinternal.la
CXX clients/clients_memcapable-memcapable.o
CXX libmemcached/clients_memcapable-byteorder.o
CXXLD clients/memcapable
Undefined first referenced
symbol in file
recv clients/clients_memcapable-memcapable.o
send clients/clients_memcapable-memcapable.o
__xnet_connect clients/clients_memcapable-memcapable.o
__xnet_socket clients/clients_memcapable-memcapable.o
__xnet_getsockopt libmemcached/.libs/libmemcached.a(lt1-libmemcached_libmemcached_la-behavior.o)
getsockname libmemcached/.libs/libmemcached.a(libmemcached_libmemcached_la-server.o)
setsockopt libmemcached/.libs/libmemcached.a(libmemcached_libmemcached_la-connect.o)
getaddrinfo clients/clients_memcapable-memcapable.o
freeaddrinfo clients/clients_memcapable-memcapable.o
gai_strerror clients/clients_memcapable-memcapable.o
__xnet_sendmsg libmemcached/.libs/libmemcached.a(libmemcached_libmemcached_la-do.o)
shutdown libmemcached/.libs/libmemcached.a(libmemcached_libmemcached_la-io.o)
ld: fatal: symbol referencing errors. No output written to clients/memcapable
collect2: ld returned 1 exit status
make[1]: *** [clients/memcapable] Error 1
make[1]: Leaving directory `/home/admin/libmemcached-1.0.18'
make: *** [all] Error 2
This is the ./configure summary
Configuration summary for libmemcached version 1.0.18
* Installation prefix: /usr/local
* System type: pc-solaris2.11
* Host CPU: i386
* C Compiler: gcc (GCC) 4.5.2
* C Flags: -g -O2 -Wno-unknown-pragmas -Wno-pragmas -Wall -Wextra -Wunsuffixed-float-constants -Wjump-misses-init -Wno-attributes -Waddress -Warray-bounds -Wbad-function-cast -Wchar-subscripts -Wcomment -Wfloat-equal -Wformat-security -Wformat=2 -Wformat-y2k -Wlogical-op -Wmissing-field-initializers -Wmissing-noreturn -Wmissing-prototypes -Wnested-externs -Wnormalized=id -Woverride-init -Wpointer-arith -Wpointer-sign -Wredundant-decls -Wshadow -Wsign-compare -Wstrict-overflow=1 -Wswitch-enum -Wundef -Wunsafe-loop-optimizations -funsafe-loop-optimizations -Wclobbered -Wunused -Wunused-result -Wunused-variable -Wunused-parameter -Wwrite-strings -fwrapv -pipe -fPIE -pie -Wpacked
* C++ Compiler: g++ (GCC) 4.5.2
* C++ Flags: -g -O2 -Wno-unknown-pragmas -Wno-pragmas -Wall -Wextra -Wno-attributes -Waddress -Warray-bounds -Wchar-subscripts -Wcomment -Wctor-dtor-privacy -Wfloat-equal -Wformat=2 -Wformat-y2k -Wmissing-field-initializers -Wlogical-op -Wnon-virtual-dtor -Wnormalized=id -Woverloaded-virtual -Wpointer-arith -Wredundant-decls -Wshadow -Wsign-compare -Wstrict-overflow=1 -Wswitch-enum -Wundef -Wunsafe-loop-optimizations -funsafe-loop-optimizations -Wclobbered -Wunused -Wunused-result -Wunused-variable -Wunused-parameter -Wwrite-strings -Wformat-security -fwrapv -pipe -fPIE -pie -Wpacked
* CPP Flags: -fvisibility=hidden
* LIB Flags:
* Assertions enabled: no
* Debug enabled: no
* Shared: yes
* Warnings as failure: no
* SASL support: no
* make -j: 2
* VCS checkout: no
I'm new to Unix/Linux and not sure what it this mean and where should I start looking.
You appear to be missing linking in the networking libraries. Add '-lnsl -lsocket' to your LIB flags.
Up until recently I've been able to compile mex functions fine on my mac osx 10.8.4
but now it gives me the error as follows (for convenience I have included the entire -v invocation):
**************************************************************************
Warning: Neither -compatibleArrayDims nor -largeArrayDims is selected.
Using -compatibleArrayDims. In the future, MATLAB will require
the use of -largeArrayDims and remove the -compatibleArrayDims
option. For more information, see:
http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-
api.html
**************************************************************************
-> mexopts.sh sourced from directory (DIR = .)
FILE = /Users/munanxu/Dropbox/Code/CUDA/mexThomasTDM/mexopts.sh
----------------------------------------------------------------
-> MATLAB = /Applications/MATLAB_R2013a.app
-> CC = xcrun -sdk macosx10.7 clang
-> CC flags:
CFLAGS = -fno-common -arch x86_64 -isysroot
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOS
X10.7.sdk -mmacosx-version-min=10.7 -fexceptions
CDEBUGFLAGS = -g
COPTIMFLAGS = -O2 -DNDEBUG
CLIBS = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -
lstdc++
arguments = -DMX_COMPAT_32
-> CXX = xcrun -sdk macosx10.7 clang++
-> CXX flags:
CXXFLAGS = -fno-common -fexceptions -arch x86_64 -isysroot
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX
10.7.sdk -mmacosx-version-min=10.7
CXXDEBUGFLAGS = -g
CXXOPTIMFLAGS = -O2 -DNDEBUG
CXXLIBS = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -
lstdc++
arguments = -DMX_COMPAT_32
-> FC = gfortran
-> FC flags:
FFLAGS = -fexceptions -m64 -fbackslash
FDEBUGFLAGS = -g
FOPTIMFLAGS = -O
FLIBS = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -L
-lgfortran -L -lgfortranbegin
arguments = -DMX_COMPAT_32
-> LD = xcrun -sdk macosx10.7 clang
-> Link flags:
LDFLAGS = -arch x86_64 -Wl,-
syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/
SDKs/MacOSX10.7.sdk -mmacosx-version-min=10.7 -bundle -Wl,-
exported_symbols_list,/Applications/MATLAB_R2013a.app/extern/lib/maci64/mexFunction.map
LDDEBUGFLAGS = -g
LDOPTIMFLAGS = -O
LDEXTENSION = .mexmaci64
arguments =
-> LDCXX =
-> Link flags:
LDCXXFLAGS =
LDCXXDEBUGFLAGS =
LDCXXOPTIMFLAGS =
LDCXXEXTENSION =
arguments =
----------------------------------------------------------------
-> xcrun -sdk macosx10.7 clang -g -arch x86_64 -Wl,-
syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/
SDKs/MacOSX10.7.sdk -mmacosx-version-min=10.7 -bundle -Wl,-
exported_symbols_list,/Applications/MATLAB_R2013a.app/extern/lib/maci64/mexFunction.map -o
"inputsTest.mexmaci64" "inputsTest.o" -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx
-lmex -lmat -lstdc++
Undefined symbols for architecture x86_64:
"_mexFunction", referenced from:
-exported_symbol[s_list] command line option
ld: symbol(s) not found for architecture x86_64
I had copied the original mexopts.sh file to the local directory to ensure that the mex compiler was using the correct version. I had also previously compiled my cpp file using g++ just to make sure the code was compiled natively for the x86_64 architecture. However, the same result occurs when I attempt to use the mex compiler to do compilation and linking.
Any ideas on what might be going on here? It seems that people have had this issue before, but mostly with missing libraries or definitions. I have definitely defined a mexFunction in my source file.
I think Amro is correct, I would put this as a comment, but it's a bit large, I find this for clang command line options to select target CPU
Registered Targets:
alpha - Alpha [experimental]
arm - ARM
bfin - Analog Devices Blackfin [experimental]
c - C backend ... ...
mblaze - MBlaze
mips - Mips ...
msp430 - MSP430 [experimental] ...
thumb - Thumb
x86 - 32-bit X86: Pentium-Pro and above
x86-64 - 64-bit X86: EM64T and AMD64
xcore - XCoreI'm thinking Amro is correct:
So is -arch x86-64 the right command line switch, rather than x86_64