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[Matlab 2009a / Mac OS 10.6.4 / 64-bit] MEX linking problem; does not find std

I'm running Matlab 2009a in 64-bit mode on Mac OS 10.6.4. I am trying to compile/link a bunch of files, but for some reason, MEX does not appear to link against STD. Below the commands I run and the error I get:

==================================
/Applications/MATLAB_R2009b.app/bin/mex -c CC=g++ CXX=g++ LD=g++ ARCH=maci64 CXXFLAGS\#'-O2 -g -I. -fPIC -D__STDC_CONSTANT_MACROS -m64 -o mexClientPopen2.mexmaci64.o' mexClientPopen2.cpp
/Applications/MATLAB_R2009b.app/bin/mex -c CC=g++ CXX=g++ LD=g++ ARCH=maci64 CXXFLAGS\#'-O2 -g -I. -fPIC -D__STDC_CONSTANT_MACROS -m64 -o debug.mexmaci64.o' debug.cpp 
/Applications/MATLAB_R2009b.app/bin/mex -c CC=g++ CXX=g++ LD=g++ ARCH=maci64 CXXFLAGS\#'-O2 -g -I. -fPIC -D__STDC_CONSTANT_MACROS -m64 -o popen2.mexmaci64.o' popen2.cpp
/Applications/MATLAB_R2009b.app/bin/mex -cxx CC=g++ CXX=g++ LD=g++ ARCH=maci64 CXXFLAGS\#'-O2 -g -fPIC -m64' mexClientPopen2.mexmaci64.o debug.mexmaci64.o popen2.mexmaci64.o -output echoPopen2.mexmaci64
Undefined symbols:
  "std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)", referenced from:
      _mexFunction in mexClientPopen2.mexmaci64.o
      _mexFunction in mexClientPopen2.mexmaci64.o
      _mexFunction in mexClientPopen2.mexmaci64.o
      _mexFunction in mexClientPopen2.mexmaci64.o
      _mexFunction in mexClientPopen2.mexmaci64.o
      _mexFunction in mexClientPopen2.mexmaci64.o
      _mexFunction in mexClientPopen2.mexmaci64.o
      VideoIO::readMessageHeader(__sFILE*)      in mexClientPopen2.mexmaci64.o
      VideoIO::readMessageHeader(__sFILE*)      in mexClientPopen2.mexmaci64.o
  "std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<void const*>(void const*)", referenced from:
      VideoIO::readMessageHeader(__sFILE*)      in mexClientPopen2.mexmaci64.o
  "std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<unsigned long>(unsigned long)", referenced from:
      VideoIO::writeBinaryDataLowLevel(void const*, unsigned long, __sFILE*)in mexClientPopen2.mexmaci64.o
      VideoIO::writeBinaryDataLowLevel(void const*, unsigned long, __sFILE*)in mexClientPopen2.mexmaci64.o
ld: symbol(s) not found
collect2: ld returned 1 exit status

    mex: link of ' "echoPopen2.mexmaci64"' failed.
==================================

Curiously, if I build the same code in 32-bit mode (with Matlab 2008b), linking against STD works perfectly. Unfortunately, a full 32-bit build is not an option, because in a later stage, I'm also linking against a 64-bit version of ffmpeg. So I really do not to reolve this linking error.

Any ideas on how to resolve the above error? I tried stuff like adding /usr/lib to LD_LIBRARY_PATH in Matlab, but that did not help...
0
lvdmaaten (3)
9/17/2010 2:07:08 AM
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Hi...

I had the very same problem when linking mex wrapper for a library I needed in Matlab2009b. After researching a little bit a noticed that Snow Leopard (10.6.4) keeps two versions of the OS sdk (and thus, the std c++ lib):

/Developer/SDKs/MacOSX10.5.sdk/ and
/Developer/SDKs/MacOSX10.6.sdk/

You should check which version is being linked in the mex instruction. Try to run your linking line again with -v option to get the verbose details: Check in the CFLAGS variable which is the isysroot path pointing to. In my case I had to change it from the 5 version to the 6, and it worked:

-isysroot /Developer/SDKs/MacOSX10.6.sdk

To change the mex options you could just try to edit by hand the options file matlab is using, which is shown together with the verbose mex instruction. In my case was:

/Users/username/.matlab/R2009b/mexopts.sh

or try to specify it as a mex argument instead. 

Good Luck

"Laurens " <lvdmaaten@hotmail.com> wrote in message <i6uigc$27v$1@fred.mathworks.com>...
> I'm running Matlab 2009a in 64-bit mode on Mac OS 10.6.4. I am trying to compile/link a bunch of files, but for some reason, MEX does not appear to link against STD. Below the commands I run and the error I get:
> 
> ==================================
> /Applications/MATLAB_R2009b.app/bin/mex -c CC=g++ CXX=g++ LD=g++ ARCH=maci64 CXXFLAGS\#'-O2 -g -I. -fPIC -D__STDC_CONSTANT_MACROS -m64 -o mexClientPopen2.mexmaci64.o' mexClientPopen2.cpp
> /Applications/MATLAB_R2009b.app/bin/mex -c CC=g++ CXX=g++ LD=g++ ARCH=maci64 CXXFLAGS\#'-O2 -g -I. -fPIC -D__STDC_CONSTANT_MACROS -m64 -o debug.mexmaci64.o' debug.cpp 
> /Applications/MATLAB_R2009b.app/bin/mex -c CC=g++ CXX=g++ LD=g++ ARCH=maci64 CXXFLAGS\#'-O2 -g -I. -fPIC -D__STDC_CONSTANT_MACROS -m64 -o popen2.mexmaci64.o' popen2.cpp
> /Applications/MATLAB_R2009b.app/bin/mex -cxx CC=g++ CXX=g++ LD=g++ ARCH=maci64 CXXFLAGS\#'-O2 -g -fPIC -m64' mexClientPopen2.mexmaci64.o debug.mexmaci64.o popen2.mexmaci64.o -output echoPopen2.mexmaci64
> Undefined symbols:
>   "std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)", referenced from:
>       _mexFunction in mexClientPopen2.mexmaci64.o
>       _mexFunction in mexClientPopen2.mexmaci64.o
>       _mexFunction in mexClientPopen2.mexmaci64.o
>       _mexFunction in mexClientPopen2.mexmaci64.o
>       _mexFunction in mexClientPopen2.mexmaci64.o
>       _mexFunction in mexClientPopen2.mexmaci64.o
>       _mexFunction in mexClientPopen2.mexmaci64.o
>       VideoIO::readMessageHeader(__sFILE*)      in mexClientPopen2.mexmaci64.o
>       VideoIO::readMessageHeader(__sFILE*)      in mexClientPopen2.mexmaci64.o
>   "std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<void const*>(void const*)", referenced from:
>       VideoIO::readMessageHeader(__sFILE*)      in mexClientPopen2.mexmaci64.o
>   "std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<unsigned long>(unsigned long)", referenced from:
>       VideoIO::writeBinaryDataLowLevel(void const*, unsigned long, __sFILE*)in mexClientPopen2.mexmaci64.o
>       VideoIO::writeBinaryDataLowLevel(void const*, unsigned long, __sFILE*)in mexClientPopen2.mexmaci64.o
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
> 
>     mex: link of ' "echoPopen2.mexmaci64"' failed.
> ==================================
> 
> Curiously, if I build the same code in 32-bit mode (with Matlab 2008b), linking against STD works perfectly. Unfortunately, a full 32-bit build is not an option, because in a later stage, I'm also linking against a 64-bit version of ffmpeg. So I really do not to reolve this linking error.
> 
> Any ideas on how to resolve the above error? I tried stuff like adding /usr/lib to LD_LIBRARY_PATH in Matlab, but that did not help...
0
10/26/2010 3:04:05 PM
Same problem here (on R2010b). Suggested solution worked fine for me.
thanks, georg

"Jose Carlos Rubio " <josecrubio@yahoo.com> wrote in message 
> I had the very same problem when linking mex wrapper for a library I needed in Matlab2009b. After researching a little bit a noticed that Snow Leopard (10.6.4) keeps two versions of the OS sdk (and thus, the std c++ lib):
> 
> /Developer/SDKs/MacOSX10.5.sdk/ and
> /Developer/SDKs/MacOSX10.6.sdk/
> 
> To change the mex options you could just try to edit by hand the options file matlab is using, which is shown together with the verbose mex instruction. 
0
georg
3/2/2011 12:54:05 PM
Reply:

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What is the best way to import Excel files, with stock data, into Matlab? I’m using Matlab R2010b (64-bit) I’m trying to import historical prices of stock data. Matlab keeps cutting off the header of each column; it gives me only values. I am thinking that this is a data-type-mixing-issue, or whatever it’s called. I have ‘Dates’ in ColumnA, and ‘MSFT’, ‘PWER’, ‘KO’, and ‘SBUX’, in ColumnB-ColumnE. Basically, if I put the Excel file in my Matlab folder and double-click the file, I see the values in a matrix (no dates and no headers), I hit ‘Next’. Then, I see only one option; one radio button is enabled – ‘Create variable matching preview’. The other two options, ‘Create vectors from each column using column names’ and ‘Create vectors from each row using row names’ – both are greyed out. I’ve seen videos, on YouTube and on the Matlab site, where people import excel data and these options are NOT greyed out. No matter what I do, there options are ALWAYS greyed out. The problem is, when I click ‘Finish’ in my ‘Workspace’ I have a variable named ‘data’ all values in a 575x4 matrix, but I have NO DATES and I have NO HEADERS on the columns. All of this seems to go into another variable, called ‘textdata’; all dates and headers ate in textdata. This is VERY inconvenient. I’m trying to analyze some stock data and I have no headers, so I have no idea which stock is which (I can figure it out, but I think Matlab should do this for me). Also, I have no dates corresponding to ...

Problem installing Matlab 2007b under Windows 7 64 bits #2
Dear all, I have issues installing Matlab 2007b under a Windows7 64 bits OS. I use the administrator account of the computer (and right click+ install as the administrator to launch the installation), but at the very begining of the setup (before it even installs anything on the computer), when it just copies some files on the harddrive, I have a message stating that I cannot modify some files without the acknowledgement of "all users"... The files list is: cursors Africa America Antartica Asia Atlantic Australia Etc Europe Indian Pacific SystemV Problem is: it is not written anywhere where those files are located, so I cannot set the security to "enable writing, deleting, etc." or change the ownership of the folder these files are in... Did anyone encounter this problem or have a mean to resolve this issue? I didn't find anything on the forum regarding this particular issue... Thanks a lot! Oh and on a side note, this computer is mine, I installed windows 7 myself 2 days ago (recommended settings all the time,and I didn't change anything since then), and there is and has always been only one account (an administrator one): mine. ...

Problems with Catalyst 2950 and Mac OS X 10.4 Systems
Hello, since we have replaced our Catalyst 2924XL switches with Catalyst 2950 we get more and more problems with Apple Macintosh OS X 10.4 Systems with G5 processors. The systems get their static IP addresses from two SuSE Linux DHCP-Servers. In our campus-LAN 76 VLANs are configured. Normally everything works well, but sometimes some Mac OS X 10.4 systems lose suddenly their server mounts. Sometimes other Mac OS X 10.4 systems don´t get an IP address while booting. After a reboot it works regularly. Deactivating the port-security doesn´t help. "Spanningtree portfast" and "switchport nonegotiate" is configured on the switchport. Has anyone a hint on this problem? Thanks in advance! Kai Matthies ---- Our configuration: CatXX#sh vers Cisco Internetwork Operating System Software IOS (tm) C2950 Software (C2950-I6Q4L2-M), Version 12.1(22)EA1b, RELEASE SOFTWARE (fc1) Copyright (c) 1986-2004 by cisco Systems, Inc. Compiled Tue 24-Aug-04 00:12 by yenanh Image text-base: 0x80010000, data-base: 0x8055C000 ROM: Bootstrap program is C2950 boot loader Cat76 uptime is 47 weeks, 6 days, 7 hours, 32 minutes System returned to ROM by power-on System restarted at 15:05:25 MESZ Tue Jun 14 2005 System image file is "flash:/c2950-i6q4l2-mz.121-22.EA1b.bin" cisco WS-C2950G-48-EI (RC32300) processor (revision Q0) with 20873K bytes of memory. Processor board ID XXXXX Last reset from system-reset Running Enhanced Image 48 FastEthernet/IEEE 802.3...

Quark 6.5 on Mac 10.4.8 Printing problems and more...
I am using a Mac 10.4.8 Dual Processor 2.3 Power PC G5 with 2 gb of sdram and with 500 gb of hard drive. I have had this happen to all three Mac in the artroom, It starts with using Quark 6.5 and printing to HP Laserjet 5100dtn. When printing out of Quark it will not duplex. It starts on one printer then goes on to another printer. It seems to be only Quark related. I can duplex with other programs with no problems. This is what I have tried: Tried updating print driver. No change. Tried updating to Quark 6.52. No change. Tried deleting .gz file from the Library/Printer/PPDs/Contents/Resources/en.lproj/HP laserjet 5100series.gz and deleting Preference file out of the HD/Users/Library/Preferences/com.apple.printfiles. Emptied Trash, Restarted and ran Repair Permissions from Disk Utility then reinstalled the new ppd. No change. Tried deleting HD/Users/Library/Preferences/Quark. No Change. Tried deleting HD/Library/Preferences/Quark (thinking there might be hidden files). No Change. Deleted both preferences reinstalled Quark, reinstalled new ppd's. No change. The only way I have found a way to fix this issue is reformatting the hard and doing a clean install. It would be fine for about 2-3 months then comes right back. Now it is effecting DesignMerge software (variable data rinting) Please any suggestions. ...

C++ Mex file crashes matlab on 64bit linux, but not 32 bit windows, but program runs fine outside Matlab
Hello, I have written a mex gateway function to a C++ class. If I compile this mex function on 32Bit windows using R2008a I have no problems. If I compile and run on Matlab R2011a running 64bit Scientific Linux (a version of Red Hat Enterprize Linux) matlab exits with a segfault when the mexfunction is called, although it appears to run about halfway through the program. The C++ class can be compiled and run (with a main function) outside of Matlab on both platforms with no errors. I am using Microsoft Visual C++ Express Edition on the windows machine, and gcc 4.4.5 on the Linux machine. Can anyone suggest what the cause of this might be and how I can I fix it? I am having a hard time debugging on Linux as I do not have access to a graphical debugger for use with matlab and am unfamiliar with gdb. This is compounded by the fact that the program compiles and runs fine when compiled as a standalone program. A zip file containing the code and data files necessary to reproduce the problem can be downloaded from http://www.see.ed.ac.uk/~s0237326/downloads/mexcrash.zip. This zip file contains the .m and .cpp source code, and a text file for testing (Temp.fem). The file fmehsersetup.m shows the commands I am using to compile. The file Test_mexfmesher.m runs the mexfunction with an appropriate input for testing. The mex gateway function is mexfmesher.cpp, it calls the fmesher class which is made up of the files in the fmesher directory. Below is a backtrace from the se...

32 bit compiler on Matlab 64 bit
Can you install a 32 bit compiler on 64 bit Matlab? I need to deploy compiled code on a 64 bit machine using 64 bit Matlab to a 32 bit machine. Is there any way I can do this WITHOUT installing 32 bit Matlab on my 64 bit computer? Thanks, Saba "Saba El-Hilo" <selhilo@sfu.ca> wrote in message <j7np4m$mae$1@newscl01ah.mathworks.com>... > Can you install a 32 bit compiler on 64 bit Matlab? > I need to deploy compiled code on a 64 bit machine using 64 bit Matlab to a 32 bit machine. Is there any way I can do this WITHOUT installing 32 bit Matlab on my 64 bit computer? The last time I check: No you still can't. Bruno ...

32-bit Matlab on 64-bit Linux
Hi, I've some mex code(compiled by somebody else on 32-bit machines) but I currently have a 64-bit version of Matlab installed on 64-bit ubuntu. I saw this suggestion from somebody- http://www.mathworks.cn/matlabcentral/newsreader/view_thread/100595 "The fix (since you can't recompile the .mex files) is to run the x86 version of Matlab, which you can install alongside the native x86_64 version. Once you've done that, whenever you need to run your .mexglx files, start Matlab with 'matlab -glnx86'." So I decided to search if this was actually possible and I found two threads from mathworks.com which I personally believe contradict each other with their answers- http://www.mathworks.com/support/solutions/en/data/1-O7POO/ http://www.mathworks.com/support/solutions/en/data/1-1CAT7/ So my question is whether 32-bit matlab can be installed on a 64bit machine ? Thanks On Sep 29, 1:09=A0pm, "Gautam " <gautam.iiith...@gmail.com> wrote: > Hi, > > I've some mex code(compiled by somebody else on 32-bit machines) but I cu= rrently have a 64-bit version of Matlab installed on 64-bit ubuntu. > > I saw this suggestion from somebody-http://www.mathworks.cn/matlabcentral= /newsreader/view_thread/100595 > "The fix (since you can't recompile the .mex files) is to run the x86 ver= sion of Matlab, which you can install alongside the native x86_64 version. = Once you've done that, whenever you need to run your .m...

Matlab 2010b quits unexpectedly on Mac OS X 10.5.8
I recently installed matlab v2010b on my macbook air 15.8. It opens without a problem the first time, but the second time I opened it it only said "Matlab quit unexpectedly" I copied the below from the error report: Dyld Error Message: Library not loaded: libtbb.dylib Referenced from: /Applications/MATLAB_R2010b.app/bin/maci64/libut.dylib Reason: image not found What might be the problem?? Hi, Make sure that the application you are opening is "MATLAB_R2010b.app" in Applications, not "MATLAB.app" in /Applications/MATLAB_R2010b.app/bin/maci64. The latter will give the specific error message below, because its environment hasn't been set up. If the application icon you are opening is in the Dock, right-click or control-click on the Dock icon, and select "Options" -> "Show in Finder" from the context menu. If it opens the folder "maci64", remove it from the Dock, and drag MATLAB_R2010b (.app) from the Applications folder to the Dock. If that doesn't resolve the issue, or if the folder opened by "Show in Finder" is "Applications", then the issue is with MATLAB_R2010b (.app), and you'll need to start troubleshooting the startup sequence, and your shell environment. Googling for this error message will give you several suggestions on how to proceed with that. Good luck, - Brian On 9/20/11 4:20 PM, Jan wrote: > I recently installed matlab v2010b on m...

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