arb is not UsingTheRightCompiler for PERL2ARB

[macports.org@…]

On a freshly formatted Macbook Pro, SnowLeopard, with Xcode 4.2, I attempted 'port install arb'.

It died, and I applied the patch (gcc -O3 instead of gcc -O4) found here: ​http://bugs.arb-home.de/changeset/8675/trunk/Makefile

I tried again, and it died in a new way:

/usr/bin/gcc-4.2: No such file or directory

It was building in the 'PERL2ARB' directory, and it got the CC variable from /opt/local/lib/perl5/5.12.4/darwin-thread-multi-2level/Config.pm

It appears that the perl5.12 port needs to find /usr/bin/llvm-gcc-4.2 during installation.

[mf2k (Frank Schima)]

Please clean the failed port and attach the main.log file.

[mf2k (Frank Schima)]

After re-trying the install of course.

[macports.org@…]

Trace of 'port install arb' after patching Makefile to do -O3

[macports.org@…]

The patch to change gcc -O4 to -O3

[ryandesign (Ryan Carsten Schmidt)]

I suspect you either installed perl5.12 while you had Xcode 3 (before you upgraded to Xcode 4), or else you received a pre-compiled binary of perl5.12 from our Snow Leopard buildbot, which uses Xcode 3 at this time.

Because you are using a different Xcode than our buildbot (in particular an Xcode that has a different default compiler, and even more in particular an Xcode that no longer contains the compiler that our buildbot's Xcode uses by default), I suggest you disable the use of pre-compiled binaries in macports.conf (set "buildfromsource" to "always") then rebuild perl5.12:

sudo port clean perl5.12
sudo port -n upgrade --force perl5.12

perl5.12 is not the only port that will "remember" the compiler it was used with, so you might have other ports already installed that you need to rebuild.

[macports.org@…]

This is a fresh install of everything; Xcode went on for the first time today, followed shortly by the first install of Macports on the machine. All settings were as they had been when the Macports installer finished.

I'm actually considering just symlinking llvm-gcc-4.2 to gcc-4.2 to get arb installed, which is the only reason I'm not using Fink right now. Fink removed arb from the list of available packages.

I suggest you make Config.pm into a separate source-only package, and make those compiler-remembering programs either source-only or have precompiled versions for each possible compiler in Xcode. (If "I suggest you (action)..." makes you feel defensive, perhaps you could stop using it yourself.)

I'll give it a try.

[ryandesign (Ryan Carsten Schmidt)]

I apologize if my wording made you feel uncomfortable. I was only trying to explain why the situation arose, and to give my best recommendation of how you can resolve or at least work around it.

[ryandesign (Ryan Carsten Schmidt)]

Replying to macports.org@…:

and make those compiler-remembering programs either source-only or have precompiled versions for each possible compiler in Xcode.

I've ​brought this matter to the macports-dev mailing list for further discussion.

[macports.org@…]

Replying to ryandesign@…:

I apologize if my wording made you feel uncomfortable. I was only trying to explain why the situation arose, and to give my best recommendation of how you can resolve or at least work around it.

Thank you for that; I wasn't uncomfortable, I just saw an opportunity to spruce-up the way a recommendation was phrased. In general putting 'you' into a sentence tends to make the recipient defensive. (​http://suite101.com/article/dos-and-donts-of-email-writing-a407257 )

[macports.org@…]

Replying to jmr@…:

Are you sure the problem is in arb? If perl 5.12 were fixed, arb would be too.

Or is this a way of indicating which packages need testing after the original problem is fixed?

[mattcottrell]

I'm Matt Cottrell, the arb port maintainer. I'm sorry to hear that you are having trouble installing arb using MacPorts.

I recently used MacPorts to build arb package installers for Snow Leopard, Lion and Mountain Lion. A few folks have reported back to me that they work fine. Maybe it is worth trying that approach for your Snow Leopard system.

The package installers are available here:

​http://download.arb-home.de/osx/

The package installer is the familiar installer seen on the Mac. It will install arb in the same location as the version that MacPorts would compile from source. The only difference is the package installer places a previously compiled version on your system instead of compiling arb all over again. You will start arb by typing "arb" in the terminal after setting the necessary environment variables.

Please follow the instructions in the README included in the archive.

[macports.org@…]

Replying to matt.cottrell@…:

Actually, by creating a symbolic link from '/usr/bin/llvm-gcc-4.2' to '/usr/bin/gcc-4.2', I was able to get Arb fully working. I should probably remove the symlink now, and double-check that it's still working, but I suspect it will since arb won't (shouldn't?) be doing any compiling.

Thanks!

[neverpanic (Clemens Lang)]

Replying to matt.cottrell@…:

It will install arb in the same location as the version that MacPorts would compile from source.

You should not be doing this unless you want an entry in the ProblemHotlist (see Image error: /opt/local/bin/xmlwf already exists and does not belong to a registered port).

Please use a MacPorts installation with a prefix different from /opt/local to create those packages to prevent conflicts on systems that already have MacPorts installed in /opt/local.

[mattcottrell]

Replying to cal@…:

Replying to matt.cottrell@…:

It will install arb in the same location as the version that MacPorts would compile from source.

You should not be doing this unless you want an entry in the ProblemHotlist (see Image error: /opt/local/bin/xmlwf already exists and does not belong to a registered port).

Please use a MacPorts installation with a prefix different from /opt/local to create those packages to prevent conflicts on systems that already have MacPorts installed in /opt/local.

Wow, I didn't realize such a conflict could arise from binary installations. Thanks for the tip and I will see what I can do about using a different prefix for package installers in the future.

But right now I"m kinda stuck with the binary installers that I have because the upgrade of MacPorts to libpng15 broke the arb port. Until I solve the libpng15 problem there is no way for me to generate new package installers. I built the ones that I have as a stop gap measure so that folks who needed arb could get their work done.

[mattcottrell]

Replying to macports.org@…:

Replying to matt.cottrell@…:

Actually, by creating a symbolic link from '/usr/bin/llvm-gcc-4.2' to '/usr/bin/gcc-4.2', I was able to get Arb fully working. I should probably remove the symlink now, and double-check that it's still working, but I suspect it will since arb won't (shouldn't?) be doing any compiling.

Thanks!

Does the fast aligner work for you or does arb crash when you try to align DNA sequences?

[mattcottrell]

This ticket can be closed. It is no longer relevant.