Problems with upgrading to Yosemite OS

[spongda@…]

I recently upgraded my Mac operating system from OS 10.9 to OS 10.10.3 (Yosemite). I found that many of my MacPorts components were broken, mostly related to inability to connect to the display. I have now gone through all the steps given on your Migration page twice, but still get errors. These are listed on the attached log-file. What do I need to change to fix this?

[ryandesign (Ryan Carsten Schmidt)]

Ok, that's a very long transcript of restoring your ports, with many errors in it. You haven't shown us the main.log files from those errors so we don't know why they occurred. But what's evident is that your ports tree is at least two years out of date, and you should update it.

For example, your transcript shows that cctools-headers @836_0 was installed but cctools-headers was updated to @836_1 in r104907 in April 2013, so your ports tree is older than that. Your transcript shows cfitsio @3.310_0 was installed but cfitsio was updated to @3.340_0 in r105146 also in April 2013.

The transcript is full of "Error: Dependency 'clang-3.4' not found.", which is because MacPorts itself has evidently been updated the latest version—which knows about clang-3.4 and that it can be used to build some ports—but your ports tree is so old it doesn't contain clang-3.4. (It wasn't added until r107455 in June 2013.)

Usually, the ports tree is updated by running:

sudo port -v selfupdate

or

sudo port -v sync

I suggest running either with the -v flag so that if an error occurs you'll see what it was.

[spongda@…]

Thanks for the suggestions. I tried re-running sudo port -v selfupdate, but realized it had problems due to my being behind a firewall. So I set things up using subversion based on the directions at wiki:howto/SyncingWithSVN. I then ran sudo port -v sync and that completed successfully. I then returned to re-try sudo ./restore_ports.tcl myports.txt. It still had some errors (see attached screen dump port_restore.txt file and tarred-up main.log files). Not sure how to fix these, but I was able to at least manually install the Nedit editor, which I use a lot. But to get it to work, I had to define the DISPLAY:0.0 variable in my .profile file, which I don't recall having to do under previous versions.

Replying to ryandesign@…:

Ok, that's a very long transcript of restoring your ports, with many errors in it. You haven't shown us the main.log files from those errors so we don't know why they occurred. But what's evident is that your ports tree is at least two years out of date, and you should update it.

For example, your transcript shows that cctools-headers @836_0 was installed but cctools-headers was updated to @836_1 in r104907 in April 2013, so your ports tree is older than that. Your transcript shows cfitsio @3.310_0 was installed but cfitsio was updated to @3.340_0 in r105146 also in April 2013.

The transcript is full of "Error: Dependency 'clang-3.4' not found.", which is because MacPorts itself has evidently been updated the latest version—which knows about clang-3.4 and that it can be used to build some ports—but your ports tree is so old it doesn't contain clang-3.4. (It wasn't added until r107455 in June 2013.)

Usually, the ports tree is updated by running:

sudo port -v selfupdate

or

sudo port -v sync

I suggest running either with the -v flag so that if an error occurs you'll see what it was.

[ryandesign (Ryan Carsten Schmidt)]

Replying to spongda@…:

Thanks for the suggestions. I tried re-running sudo port -v selfupdate, but realized it had problems due to my being behind a firewall. So I set things up using subversion based on the directions at wiki:howto/SyncingWithSVN. I then ran sudo port -v sync and that completed successfully. I then returned to re-try sudo ./restore_ports.tcl myports.txt. It still had some errors (see attached screen dump port_restore.txt file and tarred-up main.log files). Not sure how to fix these, but I was able to at least manually install the Nedit editor, which I use a lot. But to get it to work, I had to define the DISPLAY:0.0 variable in my .profile file, which I don't recall having to do under previous versions.

The first few warnings are telling you that some of the ports you have installed no longer exist:

Warning: Skipping eggdbus (not in the ports tree)
Warning: Skipping gst-plugins-base (not in the ports tree)
Warning: Skipping gstreamer (not in the ports tree)
Warning: Skipping py27-distribute (not in the ports tree)
Warning: Skipping py27-gtk (not in the ports tree)

You should uninstall these ports.

The atlas error is self-explanitory:

Error: org.macports.configure for port atlas returned: Atlas could not detect any fortran compiler. If you really don’t need the fortran interface to be built, please use the +nofortran option, else install a fortran compiler (e.g. gcc4X) before building Atlas.

Most of the errors are attempts to install obsolete ports, for example:

Error: cctools-headers has been made obsolete by the port libmacho-headers. Please install libmacho-headers instead.

For each one, install the replacement port instead (or, if you don't specifically need them, don't install them).

The setuptools error occurs because you have distribute installed but distribute was replaced with setuptools:

Error: org.macports.activate for port py27-setuptools returned: Image error: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/easy_install is being used by the active py27-distribute port.  Please deactivate this port first, or use 'port -f activate py27-setuptools' to force the activation.

This will be fixed by uninstalling py27-distribute, as already mentioned above.

You shouldn't set DISPLAY in your environment manually; it should be set for you automatically if you have installed the xorg-server and xinit ports.

[spongda@…]

Replying to ryandesign@…:

I followed your suggestions and was able to manually re-install everything I need for now. Haven't gotten the atlas install working yet; this was part of octave. Not sure why it doesn't think I have a Fortran compiler present, as I have several installed. I'll continue to look into this. Thanks much for your help

Replying to spongda@…:

Thanks for the suggestions. I tried re-running sudo port -v selfupdate, but realized it had problems due to my being behind a firewall. So I set things up using subversion based on the directions at wiki:howto/SyncingWithSVN. I then ran sudo port -v sync and that completed successfully. I then returned to re-try sudo ./restore_ports.tcl myports.txt. It still had some errors (see attached screen dump port_restore.txt file and tarred-up main.log files). Not sure how to fix these, but I was able to at least manually install the Nedit editor, which I use a lot. But to get it to work, I had to define the DISPLAY:0.0 variable in my .profile file, which I don't recall having to do under previous versions.

The first few warnings are telling you that some of the ports you have installed no longer exist:

Warning: Skipping eggdbus (not in the ports tree)
Warning: Skipping gst-plugins-base (not in the ports tree)
Warning: Skipping gstreamer (not in the ports tree)
Warning: Skipping py27-distribute (not in the ports tree)
Warning: Skipping py27-gtk (not in the ports tree)

You should uninstall these ports.

The atlas error is self-explanitory:

Error: org.macports.configure for port atlas returned: Atlas could not detect any fortran compiler. If you really don’t need the fortran interface to be built, please use the +nofortran option, else install a fortran compiler (e.g. gcc4X) before building Atlas.

Most of the errors are attempts to install obsolete ports, for example:

Error: cctools-headers has been made obsolete by the port libmacho-headers. Please install libmacho-headers instead.

For each one, install the replacement port instead (or, if you don't specifically need them, don't install them).

The setuptools error occurs because you have distribute installed but distribute was replaced with setuptools:

Error: org.macports.activate for port py27-setuptools returned: Image error: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/easy_install is being used by the active py27-distribute port.  Please deactivate this port first, or use 'port -f activate py27-setuptools' to force the activation.

This will be fixed by uninstalling py27-distribute, as already mentioned above.

You shouldn't set DISPLAY in your environment manually; it should be set for you automatically if you have installed the xorg-server and xinit ports.

[ryandesign (Ryan Carsten Schmidt)]

Replying to spongda@…:

Haven't gotten the atlas install working yet; this was part of octave. Not sure why it doesn't think I have a Fortran compiler present, as I have several installed.

Which ones do you have installed? Judging by this output...

$ port variants atlas
atlas has the variants:
[+]clang: use XCode clang and gfortran
     * conflicts with gcc47 gcc48 gcc49 mpclang34
   gcc47: build using macports-gcc-4.7
     * conflicts with clang gcc48 gcc49 mpclang34 perf
   gcc48: build using macports-gcc-4.8
     * conflicts with clang gcc47 gcc49 mpclang34 perf
   gcc49: build using macports-gcc-4.9
     * conflicts with clang gcc47 gcc48 mpclang34 perf
   mpclang34: use mp-clang-3.4 and gfortran
     * conflicts with clang gcc47 gcc48 gcc49 perf
   nofortran: Forgo use of fortran compiler
   perf: Uses clang-mp-3.4 for C and dragonegg-3.4 for Fortran
     * conflicts with clang gcc47 gcc48 gcc49 mpclang34
   universal: Build for multiple architectures

...atlas only supports the fortran compilers in the dragonegg-3.4, gcc47, gcc48, gcc49, and gfortran ports.

[spongda@…]

Log for unsucessful octave port

[spongda@…]

Replying to ryandesign@…:

I have the Intel ifort and the gfortran compilers installed, but these were done outside Macports. I just did the port install of gcc49 and now the atlas port seems to have successfully completed. Thanks.

Replying to spongda@…:

Haven't gotten the atlas install working yet; this was part of octave. Not sure why it doesn't think I have a Fortran compiler present, as I have several installed.

Which ones do you have installed? Judging by this output...

$ port variants atlas
atlas has the variants:
[+]clang: use XCode clang and gfortran
     * conflicts with gcc47 gcc48 gcc49 mpclang34
   gcc47: build using macports-gcc-4.7
     * conflicts with clang gcc48 gcc49 mpclang34 perf
   gcc48: build using macports-gcc-4.8
     * conflicts with clang gcc47 gcc49 mpclang34 perf
   gcc49: build using macports-gcc-4.9
     * conflicts with clang gcc47 gcc48 mpclang34 perf
   mpclang34: use mp-clang-3.4 and gfortran
     * conflicts with clang gcc47 gcc48 gcc49 perf
   nofortran: Forgo use of fortran compiler
   perf: Uses clang-mp-3.4 for C and dragonegg-3.4 for Fortran
     * conflicts with clang gcc47 gcc48 gcc49 mpclang34
   universal: Build for multiple architectures

...atlas only supports the fortran compilers in the dragonegg-3.4, gcc47, gcc48, gcc49, and gfortran ports.

[ryandesign (Ryan Carsten Schmidt)]

Right, MacPorts doesn't know about things you do outside of MacPorts. Glad you got it working.