py27-scipy and py26-scipy fail during "upgrade outdated" with "must set at least one Fortran variant"

[ebrignole@…]

Here's the screen dump and log file is attached

ed$ sudo port clean py27-scipy
Password:
--->  Cleaning py27-scipy

ed$ sudo port upgrade outdated
--->  Computing dependencies for py27-scipy
--->  Fetching archive for py27-scipy
--->  Attempting to fetch py27-scipy-0.17.0_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/py27-scipy
--->  Attempting to fetch py27-scipy-0.17.0_0.darwin_11.x86_64.tbz2 from http://sea.us.packages.macports.org/macports/packages/py27-scipy
--->  Attempting to fetch py27-scipy-0.17.0_0.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/py27-scipy
--->  Fetching distfiles for py27-scipy
Error: org.macports.fetch for port py27-scipy returned: must set at least one Fortran variant
Please see the log file for port py27-scipy for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_python_py-scipy/py27-scipy/main.log
Error: Unable to upgrade port: 1
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets

[ebrignole@…]

log file for port py27-scipy

[ryandesign (Ryan Carsten Schmidt)]

The message is correct. At least one Fortran variant must be selected. port variants py27-scipy will give you a list of available variants.

Please first run sudo port selfupdate and see if that resolves the issue. There was a problem where users who had previously selected the now-deleted gcc48 variant were not automatically upgraded to the gfortran variant. That was fixed last month in r145149.

[ebrignole@…]

I have found a solution to the issue that upgrades both py26-scipy and py27-scipy

 1) sudo port uninstall py26-scipy
 2) sudo port uninstall inactive
 3) sudo port uninstall leaves (repeat until no leaves remain)
 4) sudo port uninstall py27-scipy
 5) sudo port uninstall inactive
 6) sudo port uninstall leaves (repeat until no leaves remain)
 7) sudo port install py26-scipy (success!)
 8) sudo port install py27-scipy (fails)
 9) sudo port clean py27-scipy
10) sudo port uninstall inactive
11) sudo port uninstall leaves (repeat until no leaves remain)
12) sudo port install py27-scipy (success!!)

Does the fact that I must "uninstall leaves" after "install py26-scipy" to achieve a successful "install py27-scipy" indicate a conflict between dependencies for py26-scipy and py27-scipy? As far as I know I've been just using the default variants for years.

Below is the screen dump starting from step 2 above so you can see what programs might be the source of the conflict had to be uninstalled.

ed$ sudo port uninstall inactive
--->  Uninstalling eigen3 @3.2.7_1
--->  Cleaning eigen3
--->  Uninstalling gnuplot @5.0.2_0+aquaterm+luaterm+pangocairo+wxwidgets+x11
--->  Cleaning gnuplot
--->  Uninstalling graphite2 @1.2.4_0
--->  Cleaning graphite2
--->  Uninstalling ImageMagick @6.9.2-10_1+x11
--->  Cleaning ImageMagick
--->  Uninstalling libcaca @0.99.beta19_4+x11
--->  Cleaning libcaca
--->  Uninstalling python27 @2.7.11_0+universal
--->  Cleaning python27
--->  Uninstalling readline @6.3.003_1
--->  Cleaning readline
--->  Uninstalling tiff @4.0.6_0+universal
--->  Cleaning tiff

ed$ sudo port uninstall leaves
--->  Deactivating autoconf @2.69_5
--->  Cleaning autoconf
--->  Uninstalling autoconf @2.69_5
--->  Cleaning autoconf
--->  Deactivating automake @1.15_1
--->  Cleaning automake
--->  Uninstalling automake @1.15_1
--->  Cleaning automake
--->  Deactivating cmake @3.4.3_0
--->  Cleaning cmake
--->  Uninstalling cmake @3.4.3_0
--->  Cleaning cmake
--->  Deactivating py26-numpy @1.10.4_0+gfortran
--->  Cleaning py26-numpy
--->  Uninstalling py26-numpy @1.10.4_0+gfortran
--->  Cleaning py26-numpy

ed$ sudo port uninstall leaves
--->  Deactivating curl @7.47.1_0+ssl
--->  Cleaning curl
--->  Uninstalling curl @7.47.1_0+ssl
--->  Cleaning curl
--->  Deactivating libarchive @3.1.2_1
--->  Cleaning libarchive
--->  Uninstalling libarchive @3.1.2_1
--->  Cleaning libarchive
--->  Deactivating py26-cython @0.23.4_0
--->  Cleaning py26-cython
--->  Uninstalling py26-cython @0.23.4_0
--->  Cleaning py26-cython
--->  Deactivating py26-nose @1.3.7_0
--->  Cleaning py26-nose
--->  Uninstalling py26-nose @1.3.7_0
--->  Cleaning py26-nose

ed$ sudo port uninstall leaves
--->  Deactivating curl-ca-bundle @7.47.1_0
--->  Cleaning curl-ca-bundle
--->  Uninstalling curl-ca-bundle @7.47.1_0
--->  Cleaning curl-ca-bundle
--->  Deactivating lzo2 @2.09_0
--->  Cleaning lzo2
--->  Uninstalling lzo2 @2.09_0
--->  Cleaning lzo2
--->  Deactivating py26-setuptools @19.2_0
--->  Cleaning py26-setuptools
--->  Uninstalling py26-setuptools @19.2_0
--->  Cleaning py26-setuptools

ed$ sudo port uninstall leaves
Error: No ports matched the given expression

ed$ sudo port uninstall py27-scipy
--->  Deactivating py27-scipy @0.16.1_0+gcc47
--->  Cleaning py27-scipy
--->  Uninstalling py27-scipy @0.16.1_0+gcc47
--->  Cleaning py27-scipy

ed$ sudo port uninstall inactive
Error: No ports matched the given expression

ed$ sudo port uninstall leaves
--->  Deactivating swig-python @3.0.8_0
--->  Cleaning swig-python
--->  Uninstalling swig-python @3.0.8_0
--->  Cleaning swig-python

ed$ sudo port uninstall leaves
--->  Deactivating swig @3.0.8_0
--->  Cleaning swig
--->  Uninstalling swig @3.0.8_0
--->  Cleaning swig

ed$ sudo port uninstall leaves
Error: No ports matched the given expression

ed$ sudo port selfupdate
Password:
--->  Updating MacPorts base sources using rsync
MacPorts base version 2.3.4 installed,
MacPorts base version 2.3.4 downloaded.
--->  Updating the ports tree
--->  MacPorts base is already the latest version
The ports tree has been updated. To upgrade your installed ports, you should run
  port upgrade outdated

ed$ sudo port upgrade outdated
Nothing to upgrade.

ed$ sudo port install py26-scipy
--->  Computing dependencies for py26-scipy
--->  Dependencies to be installed: gcc5 py26-nose py26-setuptools py26-numpy py26-cython swig-python bison bison-runtime m4 gsed swig
--->  Fetching archive for gcc5
--->  Attempting to fetch gcc5-5.3.0_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/gcc5
--->  Attempting to fetch gcc5-5.3.0_0.darwin_11.x86_64.tbz2 from http://sea.us.packages.macports.org/macports/packages/gcc5
--->  Attempting to fetch gcc5-5.3.0_0.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/gcc5
--->  Fetching distfiles for gcc5
--->  Verifying checksums for gcc5
--->  Extracting gcc5
--->  Applying patches to gcc5
--->  Configuring gcc5
--->  Building gcc5
--->  Staging gcc5 into destroot
--->  Installing gcc5 @5.3.0_0
--->  Activating gcc5 @5.3.0_0
--->  Cleaning gcc5
--->  Fetching archive for py26-setuptools
--->  Attempting to fetch py26-setuptools-19.2_0.darwin_11.noarch.tbz2 from http://packages.macports.org/py26-setuptools
--->  Attempting to fetch py26-setuptools-19.2_0.darwin_11.noarch.tbz2 from http://sea.us.packages.macports.org/macports/packages/py26-setuptools
--->  Attempting to fetch py26-setuptools-19.2_0.darwin_11.noarch.tbz2 from http://lil.fr.packages.macports.org/py26-setuptools
--->  Fetching distfiles for py26-setuptools
--->  Verifying checksums for py26-setuptools
--->  Extracting py26-setuptools
--->  Configuring py26-setuptools
--->  Building py26-setuptools
--->  Staging py26-setuptools into destroot
--->  Installing py26-setuptools @19.2_0
--->  Activating py26-setuptools @19.2_0
--->  Cleaning py26-setuptools
--->  Fetching archive for py26-nose
--->  Attempting to fetch py26-nose-1.3.7_0.darwin_11.noarch.tbz2 from http://packages.macports.org/py26-nose
--->  Attempting to fetch py26-nose-1.3.7_0.darwin_11.noarch.tbz2 from http://sea.us.packages.macports.org/macports/packages/py26-nose
--->  Attempting to fetch py26-nose-1.3.7_0.darwin_11.noarch.tbz2 from http://lil.fr.packages.macports.org/py26-nose
--->  Fetching distfiles for py26-nose
--->  Verifying checksums for py26-nose
--->  Extracting py26-nose
--->  Configuring py26-nose
--->  Building py26-nose
--->  Staging py26-nose into destroot
--->  Installing py26-nose @1.3.7_0
--->  Activating py26-nose @1.3.7_0
--->  Cleaning py26-nose
--->  Fetching archive for py26-cython
--->  Attempting to fetch py26-cython-0.23.4_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/py26-cython
--->  Attempting to fetch py26-cython-0.23.4_0.darwin_11.x86_64.tbz2 from http://sea.us.packages.macports.org/macports/packages/py26-cython
--->  Attempting to fetch py26-cython-0.23.4_0.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/py26-cython
--->  Fetching distfiles for py26-cython
--->  Verifying checksums for py26-cython
--->  Extracting py26-cython
--->  Configuring py26-cython
--->  Building py26-cython
--->  Staging py26-cython into destroot
--->  Installing py26-cython @0.23.4_0
--->  Activating py26-cython @0.23.4_0

To make the Python 2.6 version of Cython the one that is run when you execute the commands without a version suffix, e.g. 'cython', run:

port select --set cython cython26

--->  Cleaning py26-cython
--->  Fetching archive for py26-numpy
--->  Attempting to fetch py26-numpy-1.10.4_0+gfortran.darwin_11.x86_64.tbz2 from http://packages.macports.org/py26-numpy
--->  Attempting to fetch py26-numpy-1.10.4_0+gfortran.darwin_11.x86_64.tbz2 from http://sea.us.packages.macports.org/macports/packages/py26-numpy
--->  Attempting to fetch py26-numpy-1.10.4_0+gfortran.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/py26-numpy
--->  Fetching distfiles for py26-numpy
--->  Verifying checksums for py26-numpy
--->  Extracting py26-numpy
--->  Applying patches to py26-numpy
--->  Configuring py26-numpy
--->  Building py26-numpy
--->  Staging py26-numpy into destroot
--->  Installing py26-numpy @1.10.4_0+gfortran
--->  Activating py26-numpy @1.10.4_0+gfortran
--->  Cleaning py26-numpy
--->  Fetching archive for bison-runtime
--->  Attempting to fetch bison-runtime-3.0.4_0.darwin_11.noarch.tbz2 from http://packages.macports.org/bison-runtime
--->  Attempting to fetch bison-runtime-3.0.4_0.darwin_11.noarch.tbz2.rmd160 from http://packages.macports.org/bison-runtime
--->  Installing bison-runtime @3.0.4_0
--->  Activating bison-runtime @3.0.4_0
--->  Cleaning bison-runtime
--->  Fetching archive for m4
--->  Attempting to fetch m4-1.4.17_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/m4
--->  Attempting to fetch m4-1.4.17_0.darwin_11.x86_64.tbz2.rmd160 from http://packages.macports.org/m4
--->  Installing m4 @1.4.17_0
--->  Activating m4 @1.4.17_0
--->  Cleaning m4
--->  Fetching archive for bison
--->  Attempting to fetch bison-3.0.4_1.darwin_11.x86_64.tbz2 from http://packages.macports.org/bison
--->  Attempting to fetch bison-3.0.4_1.darwin_11.x86_64.tbz2.rmd160 from http://packages.macports.org/bison
--->  Installing bison @3.0.4_1
--->  Activating bison @3.0.4_1
--->  Cleaning bison
--->  Fetching archive for gsed
--->  Attempting to fetch gsed-4.2.2_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/gsed
--->  Attempting to fetch gsed-4.2.2_0.darwin_11.x86_64.tbz2 from http://sea.us.packages.macports.org/macports/packages/gsed
--->  Attempting to fetch gsed-4.2.2_0.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/gsed
--->  Fetching distfiles for gsed
--->  Verifying checksums for gsed
--->  Extracting gsed
--->  Configuring gsed
--->  Building gsed
--->  Staging gsed into destroot
--->  Installing gsed @4.2.2_0
--->  Activating gsed @4.2.2_0
--->  Cleaning gsed
--->  Fetching archive for swig
--->  Attempting to fetch swig-3.0.8_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/swig
--->  Attempting to fetch swig-3.0.8_0.darwin_11.x86_64.tbz2 from http://sea.us.packages.macports.org/macports/packages/swig
--->  Attempting to fetch swig-3.0.8_0.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/swig
--->  Fetching distfiles for swig
--->  Verifying checksums for swig
--->  Extracting swig
--->  Configuring swig
--->  Building swig
--->  Staging swig into destroot
--->  Installing swig @3.0.8_0
--->  Activating swig @3.0.8_0
--->  Cleaning swig
--->  Fetching archive for swig-python
--->  Attempting to fetch swig-python-3.0.8_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/swig-python
--->  Attempting to fetch swig-python-3.0.8_0.darwin_11.x86_64.tbz2 from http://sea.us.packages.macports.org/macports/packages/swig-python
--->  Attempting to fetch swig-python-3.0.8_0.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/swig-python
--->  Fetching distfiles for swig-python
--->  Verifying checksums for swig-python
--->  Extracting swig-python
--->  Configuring swig-python
--->  Building swig-python
--->  Staging swig-python into destroot
--->  Installing swig-python @3.0.8_0
--->  Activating swig-python @3.0.8_0
--->  Cleaning swig-python
--->  Fetching archive for py26-scipy
--->  Attempting to fetch py26-scipy-0.17.0_0+gfortran.darwin_11.x86_64.tbz2 from http://packages.macports.org/py26-scipy
--->  Attempting to fetch py26-scipy-0.17.0_0+gfortran.darwin_11.x86_64.tbz2 from http://sea.us.packages.macports.org/macports/packages/py26-scipy
--->  Attempting to fetch py26-scipy-0.17.0_0+gfortran.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/py26-scipy
--->  Fetching distfiles for py26-scipy
--->  Attempting to fetch scipy-0.17.0.tar.gz from http://distfiles.macports.org/py-scipy
--->  Verifying checksums for py26-scipy                                             
--->  Extracting py26-scipy
--->  Configuring py26-scipy
--->  Building py26-scipy
--->  Staging py26-scipy into destroot
--->  Installing py26-scipy @0.17.0_0+gfortran
--->  Activating py26-scipy @0.17.0_0+gfortran
--->  Cleaning py26-scipy
--->  Updating database of binaries
--->  Scanning binaries for linking errors               
--->  No broken files found.                             

ed$ sudo port install py27-scipy
Password:
Error: Requested variants "+gfortran" do not match those the build was started with: "".
Error: Please use the same variants again, or run 'port clean py27-scipy' first to remove the existing partially completed build.
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port py27-scipy failed

ed$ sudo port clean py27-scipy
--->  Cleaning py27-scipy

ed$ sudo port uninstall inactive
Error: No ports matched the given expression

ed$ sudo port uninstall leaves
--->  Deactivating bison @3.0.4_1
--->  Cleaning bison
--->  Uninstalling bison @3.0.4_1
--->  Cleaning bison
--->  Deactivating gcc5 @5.3.0_0
--->  Cleaning gcc5
--->  Uninstalling gcc5 @5.3.0_0
--->  Cleaning gcc5
--->  Deactivating gsed @4.2.2_0
--->  Cleaning gsed
--->  Uninstalling gsed @4.2.2_0
--->  Cleaning gsed

ed$ sudo port uninstall leaves
--->  Deactivating bison-runtime @3.0.4_0
--->  Cleaning bison-runtime
--->  Uninstalling bison-runtime @3.0.4_0
--->  Cleaning bison-runtime
--->  Deactivating m4 @1.4.17_0
--->  Cleaning m4
--->  Uninstalling m4 @1.4.17_0
--->  Cleaning m4

ed$ sudo port uninstall leaves
Error: No ports matched the given expression

ed$ sudo port install py27-scipy
--->  Computing dependencies for py27-scipy
--->  Dependencies to be installed: gcc5
--->  Fetching archive for gcc5
--->  Attempting to fetch gcc5-5.3.0_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/gcc5
--->  Attempting to fetch gcc5-5.3.0_0.darwin_11.x86_64.tbz2 from http://sea.us.packages.macports.org/macports/packages/gcc5
--->  Attempting to fetch gcc5-5.3.0_0.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/gcc5
--->  Fetching distfiles for gcc5
--->  Verifying checksums for gcc5
--->  Extracting gcc5
--->  Applying patches to gcc5
--->  Configuring gcc5
--->  Building gcc5
--->  Staging gcc5 into destroot
--->  Installing gcc5 @5.3.0_0
--->  Activating gcc5 @5.3.0_0
--->  Cleaning gcc5
--->  Fetching archive for py27-scipy
--->  Attempting to fetch py27-scipy-0.17.0_0+gfortran.darwin_11.x86_64.tbz2 from http://packages.macports.org/py27-scipy
--->  Attempting to fetch py27-scipy-0.17.0_0+gfortran.darwin_11.x86_64.tbz2 from http://sea.us.packages.macports.org/macports/packages/py27-scipy
--->  Attempting to fetch py27-scipy-0.17.0_0+gfortran.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/py27-scipy
--->  Fetching distfiles for py27-scipy
--->  Verifying checksums for py27-scipy
--->  Extracting py27-scipy
--->  Configuring py27-scipy
--->  Building py27-scipy
--->  Staging py27-scipy into destroot
--->  Installing py27-scipy @0.17.0_0+gfortran
--->  Activating py27-scipy @0.17.0_0+gfortran
--->  Cleaning py27-scipy
--->  Updating database of binaries
--->  Scanning binaries for linking errors               
--->  No broken files found.                             

[EJFielding (Eric Fielding)]

I was getting the same error. I found that was because my py27-scipy was installed with the +gcc47 variant that no longer exists.

 fielding% sudo port variants py27-scipy
py27-scipy has the variants:
   atlas: Use MacPorts ATLAS libraries
     * conflicts with openblas
   clang37: Build using the MacPorts clang 3.7 compiler
     * conflicts with gcc49 gcc5 gcc6 llvm
   gcc48: Legacy compatibility variant
     * requires gfortran
   gcc49: Build using the MacPorts gcc 4.9 compiler
     * conflicts with clang37 gcc5 gcc6 gfortran llvm
   gcc5: Build using the MacPorts gcc 5 compiler
     * conflicts with clang37 gcc49 gcc6 gfortran llvm
   gcc6: Build using the MacPorts gcc 6 compiler
     * conflicts with clang37 gcc49 gcc5 gfortran llvm
[+]gfortran: Build using the MacPorts gcc 5 Fortran compiler
     * conflicts with gcc49 gcc5 gcc6
   llvm: Build using the Apple native llvm-gcc 4.2 compiler
     * conflicts with clang37 gcc49 gcc5 gcc6
   openblas: Use MacPorts OpenBLAS Libraries
     * conflicts with atlas

fielding% sudo port installed py27-scipy
The following ports are currently installed:
  py27-scipy @0.15.1_0+gcc47
  py27-scipy @0.16.0_0+gcc47
  py27-scipy @0.16.0_1+gcc47
  py27-scipy @0.16.1_0+gcc47 (active)

I just had to run a port clean and then install with a current variant.

 fielding% sudo port clean py27-scipy
--->  Cleaning py27-scipy
 fielding% sudo port install py27-scipy +gcc49

[mf2k (Frank Schima)]

It's not clear to me why this ticket is still open and what, if anything, needs to change.