Error building arb on 10.7

[chris@…]

On OS X 10.7, building arb fails. I've tried this with 2.0.0 rc1 and svn rev 80898. I've attached main.log. All of the prerequisites built fine.

[jmroot (Joshua Root)]

As per the ticket guidelines, please remember to cc the maintainer, and don't set the Milestone field.

[chris@…]

Running the make separately, error with missing /bin/xmkmf. I symlinked to /opt/local/bin/xmkmf, but didn't get much further. Now getting this:

make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_arb/arb/work/arbsrc_6779'
------------------------------------------------------------
ARBHOME is set to '/opt/local/share/arb'
GCC version check:
The environment variable ARBHOME has to point to the top arb source directory.
  - Your version is '4.2.1'
If you use bash enter:
  - Supported gcc version '4.2.1' detected - fine!

/usr/bin/make check_same_GCC_VERSION
          export ARBHOME='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_arb/arb/work/arbsrc_6779'
------------------------------------------------------------
make: *** [check_ARBHOME] Error 1
make: *** Waiting for unfinished jobs....
make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_arb/arb/work/arbsrc_6779'
/opt/local/share/arb/SOURCE_TOOLS/check_same_gcc_version.pl 4.2.1
make[1]: /opt/local/share/arb/SOURCE_TOOLS/check_same_gcc_version.pl: No such file or directory
make[1]: *** [check_same_GCC_VERSION] Error 1
make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_arb/arb/work/arbsrc_6779'
make: *** [check_GCC_VERSION] Error 2
All tools needed for ARB compilation have been located.
make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_arb/arb/work/arbsrc_6779'

[chris@…]

Removing ARBHOME, cleaning, and reinstalling did not help. Attaching new log file.

[chris@…]

main.log (after removing arbhome, cleaning, reinstall)

[matt.cottrell@…]

Replying to chris@…:

Removing ARBHOME, cleaning, and reinstalling did not help. Attaching new log file.

Works for me with MacPorts-2.0.0-rc1-10.7-Lion.

[chris@…]

Replying to matt.cottrell@…:

Replying to chris@…:

Removing ARBHOME, cleaning, and reinstalling did not help. Attaching new log file.

Works for me with MacPorts-2.0.0-rc1-10.7-Lion.

Hmm, that's unfortunate. I've removed MacPorts per ​http://guide.macports.org/#installing.macports.uninstalling, have reinstalled from the 2.0.0-rc1 dmg, and am setting up arb again. More when it finishes.

[chris@…]

Replying to matt.cottrell@…:

Replying to chris@…:

Removing ARBHOME, cleaning, and reinstalling did not help. Attaching new log file.

Works for me with MacPorts-2.0.0-rc1-10.7-Lion.

Just did this again, and it fails in the same place. I run the make manually, I see the following:

The following tools are missing:
    /bin/xmkmf
These tools are vital to compile ARB, so
please ensure that these tools are installed and that either
- their installation directory is in PATH or
- they are linked into the PATH

If I change the makefile line 313 to:

XMKMF := /opt/local/bin/xmkmf 

and run the make again, I see this:

ARBHOME is set to ''
All tools needed for ARB compilation have been located.
GCC version check:
The environment variable ARBHOME has to point to the top arb source directory.
  - Your version is '4.2.1'
If you use bash enter:
  - Supported gcc version '4.2.1' detected - fine!

/usr/bin/make check_same_GCC_VERSION
          export ARBHOME='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_arb/arb/work/arbsrc_6779'

If I set ARBHOME and run make, I see this:

The environment variable PATH has to contain /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_arb/arb/work/arbsrc_6779/bin
All tools needed for ARB compilation have been located.
GCC version check:
If you use bash enter:
  - Your version is '4.2.1'
			export PATH=$ARBHOME/bin:$PATH

If i set the path and run make again, I see this (see newest make.log). Things that are strage (to me) are:

ld: warning: directory not found for option '-L/lib'

I realize that there's a lot going on with macports since the Lion release. I'm also assuming you're running your tests with the Lion version of macports actually on lion. I would be excellent if we could solve this ASAP, since I'll be away for some courses using ARB next week. Thanks!

[chris@…]

Replying to chris@…:

Replying to matt.cottrell@…:

Replying to chris@…:

Removing ARBHOME, cleaning, and reinstalling did not help. Attaching new log file.

Works for me with MacPorts-2.0.0-rc1-10.7-Lion.

ld: warning: directory not found for option '-L/lib'

Oops, manual make doesn't know about macports global $(PREFIX). Still not working, however.

[matt.cottrell@…]

Replying to chris@…:

Replying to chris@…:

Replying to matt.cottrell@…:

Replying to chris@…:

Removing ARBHOME, cleaning, and reinstalling did not help. Attaching new log file.

Works for me with MacPorts-2.0.0-rc1-10.7-Lion.

ld: warning: directory not found for option '-L/lib'

Oops, manual make doesn't know about macports global $(PREFIX). Still not working, however.

It's going to take some time for me to see if I can reproduce your problem. I upgraded my personal computer to Lion, performed a fresh MacPorts installation and then installed ARB. Worked fine. Of course I did that on my personal computer not the one in the lab at work where I actually use ARB because Lion is not yet supported by MacPorts. I'm cloning that machine now so I can test your problem again on a different computer.

Are you having this problem on new hardware that came with Lion installed? Did you upgrade to Lion? Did you have ARB installed before upgrading to Lion. Tell me more about your set up.

[chris@…]

Replying to matt.cottrell@…:

Replying to chris@…:

Replying to chris@…:

Replying to matt.cottrell@…:

Replying to chris@…:

Removing ARBHOME, cleaning, and reinstalling did not help. Attaching new log file.

Works for me with MacPorts-2.0.0-rc1-10.7-Lion.

ld: warning: directory not found for option '-L/lib'

Oops, manual make doesn't know about macports global $(PREFIX). Still not working, however.

It's going to take some time for me to see if I can reproduce your problem. I upgraded my personal computer to Lion, performed a fresh MacPorts installation and then installed ARB. Worked fine. Of course I did that on my personal computer not the one in the lab at work where I actually use ARB because Lion is not yet supported by MacPorts. I'm cloning that machine now so I can test your problem again on a different computer.

Are you having this problem on new hardware that came with Lion installed? Did you upgrade to Lion? Did you have ARB installed before upgrading to Lion. Tell me more about your set up.

Like you, I also upgraded my personal computer to Lion. I had a working arb install from macports before the upgrade, removed macports (in various incarnations) and then installed arb. Except for Lion, nothing else has changed. ;-)

[matt.cottrell@…]

Replying to chris@…:

Replying to matt.cottrell@…:

Replying to chris@…:

Replying to chris@…:

Replying to matt.cottrell@…:

Replying to chris@…:

Removing ARBHOME, cleaning, and reinstalling did not help. Attaching new log file.

Works for me with MacPorts-2.0.0-rc1-10.7-Lion.

ld: warning: directory not found for option '-L/lib'

Oops, manual make doesn't know about macports global $(PREFIX). Still not working, however.

It's going to take some time for me to see if I can reproduce your problem. I upgraded my personal computer to Lion, performed a fresh MacPorts installation and then installed ARB. Worked fine. Of course I did that on my personal computer not the one in the lab at work where I actually use ARB because Lion is not yet supported by MacPorts. I'm cloning that machine now so I can test your problem again on a different computer.

Are you having this problem on new hardware that came with Lion installed? Did you upgrade to Lion? Did you have ARB installed before upgrading to Lion. Tell me more about your set up.

Like you, I also upgraded my personal computer to Lion. I had a working arb install from macports before the upgrade, removed macports (in various incarnations) and then installed arb. Except for Lion, nothing else has changed. ;-)

Did you try running the existing installation of ARB after upgrading to Lion? What prompted you to remove MacPorts after upgrading to Lion?

On my machine with ARB installed before the Lion upgrade ARB continued to run just fine. I did the fresh MacPorts and ARB install to figure out what your problem might be.

[chris@…]

Replying to matt.cottrell@…:

Did you try running the existing installation of ARB after upgrading to Lion? What prompted you to remove MacPorts after upgrading to Lion?

On my machine with ARB installed before the Lion upgrade ARB continued to run just fine. I did the fresh MacPorts and ARB install to figure out what your problem might be.

I didn't. Figured better safe than sorry, plus the migration docs and talking with some folks on the freenode channel. Recommended course of action was to reinstall base with 2.0.0 then reinstall the ports. I could try to do this with 1.9.2, I guess, it just take so darn long to compile.

[chris@…]

Replying to chris@…:

Replying to matt.cottrell@…:

Did you try running the existing installation of ARB after upgrading to Lion? What prompted you to remove MacPorts after upgrading to Lion?

On my machine with ARB installed before the Lion upgrade ARB continued to run just fine. I did the fresh MacPorts and ARB install to figure out what your problem might be.

I didn't. Figured better safe than sorry, plus the migration docs and talking with some folks on the freenode channel. Recommended course of action was to reinstall base with 2.0.0 then reinstall the ports. I could try to do this with 1.9.2, I guess, it just take so darn long to compile.

This is all pretty weird to me, too, but maybe not to you...

make[3]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_arb/arb/work/arbsrc_6779/AWTC'
Undefined symbols for architecture x86_64:
  "_llvm.eh.catch.all.value578", referenced from:
      anon in lto.o
      anon in lto.o
      anon in lto.o
      anon in lto.o
      anon in lto.o
      anon in lto.o
      anon in lto.o
      ...
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[2]: *** [bin/arb_phylo] Error 1
Undefined symbols for architecture x86_64:
  "_llvm.eh.catch.all.value950", referenced from:
      anon in lto.o
      anon in lto.o
      anon in lto.o
      anon in lto.o
      anon in lto.o
      anon in lto.o
      anon in lto.o
      ...
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[2]: *** [bin/arb_dist] Error 1

[matt.cottrell@…]

Greek to me. What version of xcode are you using?

[chris@…]

Replying to matt.cottrell@…:

Greek to me. What version of xcode are you using?

4.1

[chris@…]

Replying to chris@…:

Replying to matt.cottrell@…:

Greek to me. What version of xcode are you using?

4.1

More specifically:

Developer Information:

  Version:	4.1 (4B110)
  Location:	/Developer
  Applications:
  Xcode:	4.1 (516)
  Instruments:	4.1 (4138)
  Dashcode:	3.0.2 (336)
  SDKs:
  Mac OS X:
  10.6:	(10J567)
  10.7:	(11A511a)
  iPhone OS:
  4.3:	(8H7)
  iPhone Simulator:
  4.3:	(8H7)

[matt.cottrell@…]

Replying to chris@…:

Replying to matt.cottrell@…:

Greek to me. What version of xcode are you using?

4.1

I'm using xcode 3.26. But I don't know why that would be causing the strange errors that you are getting.

[chris@…]

Strange. 3.2.6 stopped working after my upgrade, and is not supported in Lion (only 4.1) for installation. You're one of the few people I've seen who have a working 3.2.6 after upgrading. 4.1 is a free upgrade for Lion users. Any chance you could install it and see if your working one breaks? ;-)

[matt.cottrell@…]

Nope.

[chris@…]

Replying to matt.cottrell@…:

Nope.

OK. So, what now?

[matt.cottrell@…]

Still waiting for that clone to finish...

[chris@…]

Replying to chris@…:

Replying to matt.cottrell@…:

Nope.

OK. So, what now?

Cool. Standing by...

[matt.cottrell@…]

I'll have to work on this tomorrow. The App Store is too busy to download Lion now. Getting the dreaded "Internal Error 500."

[chris@…]

Replying to matt.cottrell@…:

I'll have to work on this tomorrow. The App Store is too busy to download Lion now. Getting the dreaded "Internal Error 500."

Stupid app store. I appreciate it. Until tomorrow...

[matt.cottrell@…]

This failure to build arb was caused by Xcode 4 introducing a default compiler that did not work with arb. I submitted a patch that will solve this problem. It may be a couple of days before it is approved and committed, but then you should do a "port selfupdate" and "port update all" and all will be well with arb.

[chris@…]

Replying to matt.cottrell@…:

This failure to build arb was caused by Xcode 4 introducing a default compiler that did not work with arb. I submitted a patch that will solve this problem. It may be a couple of days before it is approved and committed, but then you should do a "port selfupdate" and "port update all" and all will be well with arb.

Thanks!

[ryandesign (Ryan Carsten Schmidt)]

I have corrected the WikiFormatting in a lot of the preceding comments. Please remember to use WikiFormatting so your posts are legible especially when showing terminal output.

The ticket containing the patches for arb for 10.7 is #30342.

[matt.cottrell@…]

Replying to ryandesign@…:

I have corrected the WikiFormatting in a lot of the preceding comments. Please remember to use WikiFormatting so your posts are legible especially when showing terminal output.

The ticket containing the patches for arb for 10.7 is #30342.

ARB now builds on OS X Lion with XCode 4.

[matt.cottrell@…]

This ticket refers to a compiler problem that arose during a revision to the arb 5.2 port. That issue was resolved and the current version is arb 5.3 ​ticket 32054, so this ticket can be closed now.