tmap-3.2.0 - link error on OSX 10.8.2, missing symbols

[2bits]

Hello. I'm reporting this for Homebrew, a package installer for OSX. We are having trouble upgrading to version 3.2.0 of tmap, and we are getting some strange undefined symbols during linking that I'm not able to "find" :-)

I am using OSX 10.8.2 on a Core i5 iMac, with XCode-4.5.1. My deps are:

• autoconf: 2.69
• automake: 1.12.4
• libtool: 2.4.2

My install log showing the error is here.
My config.log is in a gist here.
The nm output from a couple of those object files is here.

You'll see from the logs that I have patched your configure.ac for the purposes of debugging this to remove the debug flag and the optimization flag -g -Wall -O3. On OSX, O3 can optimize out some symbols, but even though I've disabled optimization, they symbols are still either U undefined or T defined with a weird address of zero, eg. 0x0000000000 The problem occurs even if I don't patch anything and just try to build this by extracting, configuring, making without using Homebrew at all.

I would offer a patch, but I'm out of ideas atm.

[nh13]

Works with gcc/g++ but not cc/c++. Any ideas? Try "./configure CC=cc CXX=c++" to force it to use the cc/c++ compilers.

[2bits]

I should have said that I tired compiling with clang-4.1 and llvm-gcc-4.2.1, which are the only two compilers that come with XCode these days. Also the default cc and cxx are set up like this on OSX 10.7 and 10.8:

$ ls -l `which cc`
lrwxr-xr-x  1 root  wheel  5 Oct  5 21:17 /usr/bin/cc -> clang
$ ls -l `which c++`
lrwxr-xr-x  1 root  wheel  7 Oct  5 21:17 /usr/bin/c++ -> clang++

So the clang output I gave you matches what would happen if I set CC and CXX. All the 2000+ apps that Homebrew can build have to compile with the default compilers unfortunately. If possible I'd like to stop tmap from being delisted by solving this, but I'm really at a loss to understand why the symbols would not exist. Maybe the compilers have a bug. It would not be the first time. I'll fire up gcc-4.6 and see what I can learn.

[iontorrent-dev]

Agreed we need to find a fix but be a little patient as this has just come to my attention. I am at a loss as tol why these new apple provided compilers are not working. Perhaps it has something to do with the stdlib versions? Thanks for digging.

On Oct 17, 2012, at 5:42 PM, "2bits" <[email protected]mailto:[email protected]> wrote:

I should have said that I tired compiling with clang-4.1 and llvm-gcc-4.2.1, which are the only two compilers that come with XCode these days. Also the default cc and cxx are set up like this on OSX 10.7 and 10.8:

$ ls -l which cc
lrwxr-xr-x 1 root wheel 5 Oct 5 21:17 /usr/bin/cc -> clang
$ ls -l which c++
lrwxr-xr-x 1 root wheel 7 Oct 5 21:17 /usr/bin/c++ -> clang++

So the clang output I gave you matches what would happen if I set CC and CXX. All the 2000+ apps that Homebrew can build have to compile with the default compilers unfortunately. If possible I'd like to stop tmap from being delisted by solving this, but I'm really at a loss to understand why the symbols would not exist. Maybe the compilers have a bug. It would not be the first time. I'll fire up gcc-4.6 and see what I can learn.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/3#issuecomment-9549513.

[2bits]

No rush at all. I found a fix for the missing symbols by using llvm-gcc after you mentioned it worked with gcc. If it's okay, I'll open another issue with a build error I get when I --enable-perftools that's unrelated.