[MacPorts] #50723: py27-scipy and py26-scipy fail during "upgrade outdated" with "must set at least one Fortran variant"

MacPorts noreply at macports.org
Mon Feb 29 09:40:05 PST 2016 

#50723: py27-scipy and py26-scipy fail during "upgrade outdated" with "must set at
least one Fortran variant"
--------------------------+--------------------
  Reporter:  ebrignole@…  |      Owner:  sean@…
      Type:  defect       |     Status:  new
  Priority:  Normal       |  Milestone:
 Component:  ports        |    Version:  2.3.4
Resolution:               |   Keywords:
      Port:  py-scipy     |
--------------------------+--------------------

Comment (by 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.
 }}}

-- 
Ticket URL: <https://trac.macports.org/ticket/50723#comment:2>
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