New Ticket     Tickets     Wiki     Browse Source     Timeline     Roadmap     Ticket Reports     Search

Ticket #21468 (closed submission: fixed)

Opened 6 years ago

Last modified 5 years ago

apbs-1.1.0-1

Reported by: howarth@… Owned by: macports-tickets@…
Priority: Normal Milestone:
Component: ports Version: 1.8.0
Keywords: science Cc: Jeremy.Lavergne@…, macsforever2000@…
Port: apbs

Description

MacPort packaging for apbs-1.1.0-1 with python support enabled.

Attachments

Portfile.2 (3.2 KB) - added by macsforever2000@… 5 years ago.
Revised portfile
Portfile (3.1 KB) - added by howarth@… 5 years ago.
depends_lib on currently missing py26-zsi package
apbs.2.diff (2.3 KB) - added by howarth@… 5 years ago.
reduced patch
apbs.diff (2.3 KB) - added by howarth@… 5 years ago.
reduced patch
Portfile.diff (677 bytes) - added by howarth@… 5 years ago.
corrected reduced Portfile diff

Change History

comment:1 Changed 6 years ago by howarth@…

To test apbs in pymol, execute the following steps after install the apbs package...

cp /opt/local/lib/pymol/data/tut/1hpv.pdb . pymol Select the File->Open menu item and select the copy of 1hpv.pdb. Select the Plugins->APBS Tools... menu item Click on the "Set grid" button in the Pymol APBS Tools window. Click on the "Run APBS" button in the Pymol APBS Tools window. Wait for the apbs run to complete at which point the buttons in the APBS Tools window will work again. Select the VIsualization tab in the Pymol APBS Tools window and click the Update button. Click the Show button under the Molecular Surface section of the Visualization panel.

comment:2 Changed 6 years ago by snc@…

  • Cc Jeremy.Lavergne@… added

Have you considered using the python26 port group?

You can then use variables from within it in your patch (e.g. ${python.bin}-config). It might also handle some of the build/destroot functionality you've coded.

${prefix}/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/group/python26-1.0.tcl

Changed 5 years ago by macsforever2000@…

Revised portfile

comment:3 Changed 5 years ago by macsforever2000@…

I made some fixes to the portfile, but I see the following error:

--->  Building apbs
Error: Target org.macports.build returned: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_svn.macports.org_trunk_dports_science_apbs/work/apbs-1.1.0-source" && make all " returned error 2
Command output: make: *** No rule to make target `all'.  Stop.

Error: Status 1 encountered during processing.

comment:4 Changed 5 years ago by macsforever2000@…

  • Cc macsforever2000@… added

Cc Me!

comment:5 Changed 5 years ago by howarth@…

You removed...

use_configure yes

comment:6 Changed 5 years ago by macsforever2000@…

Heh, some fix eh? I added it back but now I see this error (also with the original portfile).

--->  Staging apbs into destroot
Error: Target org.macports.destroot returned: shell command "cd /opt/local/var/macports/build/_opt_mports_trunk_dports_science_apbs/work/apbs-1.1.0-source; make install DESTDIR=/opt/local/var/macports/build/_opt_mports_trunk_dports_science_apbs/work/destroot INSTALL='install -p' CPPROG='cp -p'" returned error 2
Command output: Making install in opal
Making install in ZSI
Making install in .
make[5]: Nothing to be done for `install-exec-am'.
mkdir -p @INSTALL_DIR@/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages
/opt/local/Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6 setup.py install --prefix=@INSTALL_DIR@/opt/local
running install
Checking .pth file support in @INSTALL_DIR@/opt/local/lib/python2.6/site-packages/
error: can't create or remove files in install directory

The following error occurred while trying to add or remove files in the
installation directory:

    [Errno 2] No such file or directory: '@INSTALL_DIR@/opt/local/lib/python2.6/site-packages/test-easy-install-43824.pth'

The installation directory you specified (via --install-dir, --prefix, or
the distutils default setting) was:

    @INSTALL_DIR@/opt/local/lib/python2.6/site-packages/

This directory does not currently exist.  Please create it and try again, or
choose a different installation directory (using the -d or --install-dir
option).

make[5]: *** [install-data-local] Error 1
make[4]: *** [install-am] Error 2
make[3]: *** [install-recursive] Error 1
make[2]: *** [install-recursive] Error 1
make[1]: *** [install-recursive] Error 1
make: *** [install-recursive] Error 1

Error: Status 1 encountered during processing.

Changed 5 years ago by howarth@…

depends_lib on currently missing py26-zsi package

Changed 5 years ago by howarth@…

reduced patch

Changed 5 years ago by howarth@…

reduced patch

comment:7 Changed 5 years ago by howarth@…

Try the updated Portfile and apbs.diff.
You will need to create a local copy of a py26-zsi package
from the existing py25-zsi package (renaming and editing for the 26 release).

comment:8 Changed 5 years ago by macsforever2000@…

py26-zsi added in r59805.

comment:9 Changed 5 years ago by macsforever2000@…

  • Status changed from new to closed
  • Resolution set to fixed

apbs added in r59806. Thanks! I incorporated my changes to the portfile.

comment:10 Changed 5 years ago by howarth@…

Actually we can reduce the python build a bit more since only ApbsClient.py is provided by apbs. The remaining files were from contrib's ZSI.

comment:11 Changed 5 years ago by howarth@…

Oh, it looks like we do need the wsdl files. However we should be correcting ApbsClient.py.in.

Changed 5 years ago by howarth@…

corrected reduced Portfile diff

comment:12 Changed 5 years ago by macsforever2000@…

I committed your changes in r61626.

Note: See TracTickets for help on using tickets.